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Journal articles on the topic 'TAXONOMIC SENSITIVITY'

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Author: Grafiati
Published: 11 September 2023

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1

Poe, Steven. "Sensitivity of Phylogeny Estimation to Taxonomic Sampling." Systematic Biology 47, no. 1 (March 1, 1998): 18–31. http://dx.doi.org/10.1080/106351598261003.

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2

Robinson, M., M. Gouy, C. Gautier, and D. Mouchiroud. "Sensitivity of the relative-rate test to taxonomic sampling." Molecular Biology and Evolution 15, no. 9 (September 1, 1998): 1091–98. http://dx.doi.org/10.1093/oxfordjournals.molbev.a026016.

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3

Rock, J., F. O. Costa, D. I. Walker, A. W. North, W. F. Hutchinson, and G. R. Carvalho. "DNA barcodes of fish of the Scotia Sea, Antarctica indicate priority groups for taxonomic and systematics focus." Antarctic Science 20, no. 3 (May 19, 2008): 253–62. http://dx.doi.org/10.1017/s0954102008001120.

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AbstractWe analysed cytochrome oxidase I (COI) barcodes for 35 putative fish species collected in the Scotia Sea, and compared the resultant molecular data with field-based morphological identifications, and additional sequence data obtained from GenBank and the Barcode of Life Data System (BOLD). There was high congruence between morphological and molecular classification, and COI provided effective species-level discrimination for nearly all putative species. No effect of geographic sampling was observed for COI sequence variation. For two families, including the Liparidae and Zoarcidae, for which morphological field identification was unable to resolve taxonomy, DNA barcoding revealed significant species-level divergence. However, the dataset lacked sufficient sensitivity for resolving species within theBathydracoandArtedidracogenera. Analysis of cytochromebfor these two genera also failed to resolve taxonomic identity. The data are discussed in relation to emergent priorities for additional taxonomic studies. We emphasize the utility of DNA barcoding in providing a valuable taxonomic framework for fundamental population studies through assigning life history stages or other morphologically ambiguous samples to parental species.
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4

Pacheco-Labrador, J., U. Weber, X. Ma, M. D. Mahecha, N. Carvalhais, C. Wirth, A. Huth, et al. "EVALUATING THE POTENTIAL OF DESIS TO INFER PLANT TAXONOMICAL AND FUNCTIONAL DIVERSITIES IN EUROPEAN FORESTS." International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences XLVI-1/W1-2021 (February 11, 2022): 49–55. http://dx.doi.org/10.5194/isprs-archives-xlvi-1-w1-2021-49-2022.

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Abstract. Tackling the accelerated human-induced biodiversity loss requires tools able to map biodiversity and its changes globally. Remote sensing (RS) offers unique capabilities of characterizing Earth surfaces; therefore, it could map plant biodiversity continuously and globally. This approach is supported by the Spectral Variation Hypothesis (SVH), which states that spectra and species (taxonomic and trait) diversities are linked through environmental heterogeneity. In this work, we evaluate the capability of the DESIS hyperspectral imager to capture plant diversity patterns as measured in dedicated plots of the network FunDivEUROPE. We computed functional and taxonomical diversity metrics from field taxonomic, structural, and foliar measurements in vegetation plots sampled in Spain and Romania. In addition, we also computed functional diversity metrics both from the DESIS reflectance factors and from vegetation parameters estimated via inversion of a radiative transfer model. Results showed that only metrics computed from spectral reflectance were able to capture taxonomic variability in the area. However, the lack of sensitivity was related to the insufficient plot size and the lack of spatial match between remote sensing and field data, but also the differences between the information contained in the field traits and remote sensing data, and the potential uncertainties in the remote estimates of vegetation parameters. Thus, while DESIS showed some sensitivity to plant diversity, further efforts are needed to deploy suitable biodiversity evaluation and validation plots and networks that support the development of biodiversity remote sensing products.
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5

Parra-Hernández, Ronald M., Jorge I. Posada-Quintero, Orlando Acevedo-Charry, and Hugo F. Posada-Quintero. "Uniform Manifold Approximation and Projection for Clustering Taxa through Vocalizations in a Neotropical Passerine (Rough-Legged Tyrannulet, Phyllomyias burmeisteri)." Animals 10, no. 8 (August 12, 2020): 1406. http://dx.doi.org/10.3390/ani10081406.

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Vocalizations from birds are a fruitful source of information for the classification of species. However, currently used analyses are ineffective to determine the taxonomic status of some groups. To provide a clearer grouping of taxa for such bird species from the analysis of vocalizations, more sensitive techniques are required. In this study, we have evaluated the sensitivity of the Uniform Manifold Approximation and Projection (UMAP) technique for grouping the vocalizations of individuals of the Rough-legged Tyrannulet Phyllomyias burmeisteri complex. Although the existence of two taxonomic groups has been suggested by some studies, the species has presented taxonomic difficulties in classification in previous studies. UMAP exhibited a clearer separation of groups than previously used dimensionality-reduction techniques (i.e., principal component analysis), as it was able to effectively identify the two taxa groups. The results achieved with UMAP in this study suggest that the technique can be useful in the analysis of species with complex in taxonomy through vocalizations data as a complementary tool including behavioral traits such as acoustic communication.
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6

Golubev, W. I. "Taxonomic specificity of the sensitivity to the Wickerhamomyces bovis fungistatic mycocin." Microbiology 85, no. 4 (July 2016): 444–48. http://dx.doi.org/10.1134/s0026261716040081.

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7

Weging, Silvio, Andreas Gogol-Döring, and Ivo Grosse. "Taxonomic analysis of metagenomic data with kASA." Nucleic Acids Research 49, no. 12 (March 30, 2021): e68-e68. http://dx.doi.org/10.1093/nar/gkab200.

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Abstract The taxonomic analysis of sequencing data has become important in many areas of life sciences. However, currently available tools for that purpose either consume large amounts of RAM or yield insufficient quality and robustness. Here, we present kASA, a k-mer based tool capable of identifying and profiling metagenomic DNA or protein sequences with high computational efficiency and a user-definable memory footprint. We ensure both high sensitivity and precision by using an amino acid-like encoding of k-mers together with a range of multiple k’s. Custom algorithms and data structures optimized for external memory storage enable a full-scale taxonomic analysis without compromise on laptop, desktop, and HPCC.
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8

Kyselková, M., J. Kopecký, M. Ságová-Marečková, G. L. Grundmann, and Y. Moënne-Loccoz. "Oligonucleotide microarray methodology for taxonomic and functional monitoringof microbial community composition." Plant, Soil and Environment 55, No. 9 (October 14, 2009): 379–88. http://dx.doi.org/10.17221/140/2009-pse.

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Microarray analysis is a cultivation-independent, high-throughput technology that can be used for direct and simultaneous identification of microorganisms in complex environmental samples. This review summarizes current methodologies for oligonucleotide microarrays used in microbial ecology. It deals with probe design, microarray manufacturing, sample preparation and labeling, and data handling, as well as with the key features of microarray analysis such as specificity, sensitivity and quantification potential. Microarray analysis has been validated as an effective approach to describe the composition and dynamics of taxonomic and functional microbial communities, in environments including soil, compost, sediment, air or humans. It is now part of the technical arsenal available to address key issues in microbial community ecology, ranging from biogeography to ecosystem functioning.
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9

Chessman, Bruce C. "New sensitivity grades for Australian river macroinvertebrates." Marine and Freshwater Research 54, no. 2 (2003): 95. http://dx.doi.org/10.1071/mf02114.

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The SIGNAL biotic index for river macroinvertebrates, originally developed and tested in eastern Australia, was revised for application to the entire continent. Macroinvertebrate survey data from the National River Health Program were used to set grade numbers between 1 and 10 to represent the water-quality sensitivities of 210 taxa. Grades were assigned at the taxonomic levels customarily used by government agencies (predominantly family level) and by community groups (mainly order). A new index version using these grades, SIGNAL2, was correlated with water temperature, turbidity, electrical conductivity, alkalinity, pH, dissolved oxygen, total nitrogen and total phosphorus. Because of natural spatial variation in water quality, index scores need to be interpreted in a local context or against site-specific predictions generated by the Australian River Assessment System (AUSRIVAS).
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10

Hutchison, Leonard J. "Studies on the systematics of ectomycorrhizal fungi in axenic culture. V. Linear growth response to standard extreme temperatures used as a taxonomic character." Canadian Journal of Botany 68, no. 10 (October 1, 1990): 2179–84. http://dx.doi.org/10.1139/b90-284.

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Ectomycorrhizal fungi showed characteristic differences in linear growth rate reduction when grown on modified Melin–Norkrans agar at 7 and 30 °C. The two standard temperature extremes differentiated ectomycorrhizal fungi into three growth response categories which reflected taxonomic affinity: sensitive, semitolerant, and tolerant. At 7 °C, species of Laccaria and Hebeloma generally exhibited tolerant or semitolerant growth, whereas at 30 °C growth tended to be restricted to species of Amanita, Laccaria, Suillus, and a few gasteromycetous fungi (e.g., Rhizopogon, Scleroderma, and Pisolithus). The results reveal the potential value of standard extreme temperatures as a taxonomic character for differentiating species or genera of ectomycorrhizal fungi in vitro. Tolerance or sensitivity to 30 °C by ectomycorrhizal fungi may reflect their association with specific host trees. Key words: ectomycorrhizal fungi, temperature, sensitivity, tolerance, cultures, identification.
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11

Artuso, Caterina, Paola Palladino, and Carmen Belacchi. "Sensitivity detection in memory recognition: interference control as index of taxonomic memory development?" Memory 28, no. 2 (December 23, 2019): 187–95. http://dx.doi.org/10.1080/09658211.2019.1705488.

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12

Laurion, Isabelle, and Warwick F. Vincent. "Cell size versus taxonomic composition as determinants of UV-sensitivity in natural phytoplankton communities." Limnology and Oceanography 43, no. 8 (December 1998): 1774–79. http://dx.doi.org/10.4319/lo.1998.43.8.1774.

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13

Bedano, José Camilo, and Andrea Ruf. "Sensitivity of different taxonomic levels of soil Gamasina to land use and anthropogenic disturbances." Agricultural and Forest Entomology 12, no. 2 (May 2010): 203–12. http://dx.doi.org/10.1111/j.1461-9563.2009.00470.x.

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14

Can, Mehmet, and Osman Gürsoy. "Clustering 16S rRNA for OTU prediction: A similarity based method." Heritage and Sustainable Development 1, no. 2 (December 30, 2019): 78–83. http://dx.doi.org/10.37868/hsd.v1i2.4.

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To study the phylogeny and taxonomy of samples from complex environments Next-generation sequencing (NGS)-based 16S rRNA sequencing , which has been successfully used jointly with the PCR amplification and NGS technology. First step for many downstream analyses is clustering 16S rRNA sequences into operational taxonomic units (OTUs). Heuristic clustering is one of the most widely employed approaches for generating OTUs in which one or more seed sequences to represent each cluster are selected. In this work we chose five random seeds for each cluster from a genes library, and we present a novel distance measure to cluster bacteria in the sample. Artificially created sets of 16S rRNA genes selected from databases are successfully clustered with more than %98 accuracy, sensitivity, and specificity.
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15

Ceballos-Escalera, Angelina, John Richards, Maria Belen Arias, Daegan J. G. Inward, and Alfried P. Vogler. "Metabarcoding of insect-associated fungal communities: a comparison of internal transcribed spacer (ITS) and large-subunit (LSU) rRNA markers." MycoKeys 88 (March 8, 2022): 1–33. http://dx.doi.org/10.3897/mycokeys.88.77106.

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Full taxonomic characterisation of fungal communities is necessary for establishing ecological associations and early detection of pathogens and invasive species. Complex communities of fungi are regularly characterised by metabarcoding using the Internal Transcribed Spacer (ITS) and the Large-Subunit (LSU) gene of the rRNA locus, but reliance on a single short sequence fragment limits the confidence of identification. Here we link metabarcoding from the ITS2 and LSU D1-D2 regions to characterise fungal communities associated with bark beetles (Scolytinae), the likely vectors of several tree pathogens. Both markers revealed similar patterns of overall species richness and response to key variables (beetle species, forest type), but identification against the respective reference databases using various taxonomic classifiers revealed poor resolution towards lower taxonomic levels, especially the species level. Thus, Operational Taxonomic Units (OTUs) could not be linked via taxonomic classifiers across ITS and LSU fragments. However, using phylogenetic trees (focused on the epidemiologically important Sordariomycetes) we placed OTUs obtained with either marker relative to reference sequences of the entire rRNA cistron that includes both loci and demonstrated the largely similar phylogenetic distribution of ITS and LSU-derived OTUs. Sensitivity analysis of congruence in both markers suggested the biologically most defensible threshold values for OTU delimitation in Sordariomycetes to be 98% for ITS2 and 99% for LSU D1-D2. Studies of fungal communities using the canonical ITS barcode require corroboration across additional loci. Phylogenetic analysis of OTU sequences aligned to the full rRNA cistron shows higher success rate and greater accuracy of species identification compared to probabilistic taxonomic classifiers.
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16

GOTO, Masao. "Sensitivity of plant pathogenic bacteria to 2,4-diamino-6,7-diisopropyl-pteridine and its taxonomic significance." Japanese Journal of Phytopathology 54, no. 1 (1988): 64–67. http://dx.doi.org/10.3186/jjphytopath.54.64.

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17

Fletcher, John S., Forrest L. Johnson, and James C. McFarlane. "Influence of greenhouse versus field testing and taxonomic differences on plant sensitivity to chemical treatment." Environmental Toxicology and Chemistry 9, no. 6 (June 1990): 769–76. http://dx.doi.org/10.1002/etc.5620090611.

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18

Di Lorenzo, Tiziana, Alessandro Murolo, Barbara Fiasca, Agostina Tabilio Di Camillo, Mattia Di Cicco, and Diana Maria Paola Galassi. "Potential of A Trait-Based Approach in the Characterization of An N-Contaminated Alluvial Aquifer." Water 11, no. 12 (December 3, 2019): 2553. http://dx.doi.org/10.3390/w11122553.

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Groundwater communities residing in contaminated aquifers have been investigated mainly through taxonomy-based approaches (i.e., analyzing taxonomic richness and abundances) while ecological traits have been rarely considered. The aim of this study was to assess whether a trait analysis adds value to the traditional taxonomy-based biomonitoring in N-contaminated aquifers. To this end, we monitored 40 bores in the Vomano alluvial aquifer (VO_GWB, Italy) for two years. The aquifer is a nitrate vulnerable zone according to the Water Framework Directive. The traditional taxonomy-based approach revealed an unexpectedly high biodiversity (38 taxa and 5725 individuals), dominated by crustaceans, comparable to that of other unpolluted alluvial aquifers worldwide. This result is in contrast with previous studies and calls into question the sensitivity of stygobiotic species to N-compounds. The trait analysis provided an added value to the study, unveiling signs of impairments of the groundwater community such as low juveniles-to-adults and males-to-females ratios and a crossover of biomasses and abundances curves suggestive of an intermediate alteration of the copepod assemblages.
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19

A. ZHIGILA, DANIEL, UMMULKHURSUM B. HUSSAINI, and NURU ADAMU GARKUWA. "TAXONOMY, DISTRIBUTION AND DIVERSITY OF PLANKTONIC ALGAE AT PINDIGA DAM, NIGERIA." BIMA JOURNAL OF SCIENCE AND TECHNOLOGY (2536-6041) 6, no. 03 (December 31, 2022): 64–72. http://dx.doi.org/10.56892/bima.v6i03.46.

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Taxonomic identification of algae at both generic and species levels is problematic owing to several reasons including cells’ fragility, sensitivity to chemical fixatives and inconspicuous morphological features. The planktonic algae in tropical African dams have been particularlyproblematic given the paucity of algal taxonomic experts in this region. In this study, we presentfor the first time the taxonomic and geographic appraisal of planktonic Algae at Pindiga Dam. Further, planktonic algal flora and its monthly variations at the Pindiga Dam were investigated. The study revealed a total of 35 genera. Species in the family Chlorophyceae were the most abundant (42%), followed by those in the families Bacillariophyceae (38%) and Charophyceae(25%). Other taxonomic groups present were Chryophyceae, Cryptophyceae, Cynophyceae and Euglenophyta (7%) each. Trachelomonas, Tetrahedrom and Pleurozester were the most abundant taxa. The Important Value Index (IVI) and species diversity of algae are dependent on the sampling month. For instance, Trachelomonas recorded the highest IVI (23.67) and thelowest was recorded by Cryptomonas (8.18) in April, but it was observed that in May; Tetrahedrom recorded the highest IVI (22.57) and the lowest was recorded by Zygnema (9.38). In June, another set of taxa recorded the highest and the Lowest IVI namely: Pleurogaster, Crucigenia (17.63) and Netrium, Oedogenium (8.93) each. The composition of planktonic algae families in Pindiga Dam could be said to be Chlorophyceae, Bacillariophyceae, and Cyanophyceae in order of the IVI. The Simpson’s index of diversity of planktonic algae at Pindiga Dam was 0.94542, 0.94708 and 0.95364 in April, May and June respectively. The species richness in April was 1.97, in May was 1.92 and in June was 2.10. The values were high indicating a more complex plankton community with a good measure of abundance and diversity. This study has provided baseline information on the taxonomy, distribution and diversity of planktonic algae in Pindiga Dam. This knowledge is useful to groups involved in water utilities; irrigation and drainage districts, industries, private pond owners, fish farmers and aqua culturist.
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20

Mello, Luiza Costa, and Denis M. S. Abessa. "Using the benthic macroinvertebrates as indicators of the water quality in the “Cachoeira do Paraíso” waterfall (Itinguçu State Park, Peruíbe, SP, Brazil) / Uso de macroinvertebrados bentônicos como indicadores de qualidade da água na Cachoeira do Paraíso (Parque Estadual do Itinguçu, Peruíbe, SP, Brasil)." Brazilian Journal of Animal and Environmental Research 4, no. 4 (October 14, 2021): 5121–40. http://dx.doi.org/10.34188/bjaerv4n4-020.

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Rivers protection is fundamental for the socioecological systems, and the benthic macroinvertebrates communities can be used to assess the quality of river waters. This study aimed to assess the water quality at the “Cachoeira do Paraíso” waterfall, Peruíbe, SP, based on the benthic macrofauna. Sampling took place at 3 sampling sites, under different levels of anthropic influence. Water physical-chemical and sedimentological parameters were evaluated, as well as macrobenthic organisms. Samplings were done by kick sampling technique. The organisms were identified at the lowest possible taxonomic level and points were attributed to each group according to their respective sensitivity and tolerance to pollutants. Then, a biological index was calculated to indicate the water quality. Ecological indices were calculated and compared using ANOVA. The water physical-chemical parameters showed to be within the legal standards. 13 taxonomic groups of benthic macroinvertebrates were identified, with the Shannon diversity indices indicating similar taxonomic diversity. The score given to each taxa generated biological indices for each sample, ranging from regular to excellent. Diptera (with head) I was the most representative taxon, and sensitive taxonomic groups, were found in all the sampling sites, suggesting a good quality of the water body during the period of study.
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21

Hume, Benjamin C. C., Maren Ziegler, Julie Poulain, Xavier Pochon, Sarah Romac, Emilie Boissin, Colomban de Vargas, Serge Planes, Patrick Wincker, and Christian R. Voolstra. "An improved primer set and amplification protocol with increased specificity and sensitivity targeting the Symbiodinium ITS2 region." PeerJ 6 (May 23, 2018): e4816. http://dx.doi.org/10.7717/peerj.4816.

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The Internal Transcribed Spacer 2 (ITS2) rRNA gene is a commonly targeted genetic marker to assess diversity of Symbiodinium, a dinoflagellate genus of algal endosymbionts that is pervasively associated with marine invertebrates, and notably reef-building corals. Here we tested three commonly used ITS2 primer pairs (SYM_VAR_5.8S2/SYM_VAR_REV, ITSintfor2/ITSReverse, and ITS-DINO/ITS2Rev2) with regard to amplification specificity and sensitivity towards Symbiodinium, as well as sub-genera taxonomic bias. We tested these primers over a range of sample types including three coral species, coral surrounding water, reef surface water, and open ocean water to assess their suitability for use in large-scale next generation sequencing projects and to develop a standardised PCR protocol. We found the SYM_VAR_5.8S2/SYM_VAR_REV primers to perform superior to the other tested ITS2 primers. We therefore used this primer pair to develop a standardised PCR protocol. To do this, we tested the effect of PCR-to-PCR variation, annealing temperature, cycle number, and different polymerase systems on the PCR efficacy. The Symbiodinium ITS2 PCR protocol developed here delivers improved specificity and sensitivity towards Symbiodinium with apparent minimal sub-genera taxonomic bias across all sample types. In particular, the protocol’s ability to amplify Symbiodinium from a range of environmental sources will facilitate the study of Symbiodinium populations across biomes.
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22

McLaughlin, Robert L., Louise Porto, David LG Noakes, Jeffrey R. Baylis, Leon M. Carl, Hope R. Dodd, Jon D. Goldstein, Daniel B. Hayes, and Robert G. Randall. "Effects of low-head barriers on stream fishes: taxonomic affiliations and morphological correlates of sensitive species." Canadian Journal of Fisheries and Aquatic Sciences 63, no. 4 (April 1, 2006): 766–79. http://dx.doi.org/10.1139/f05-256.

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Low-head barriers used in the control of parasitic sea lamprey (Petromyzon marinus) in the basin of the Laurentian Great Lakes can alter the richness and composition of nontarget fishes in tributary streams. Identification of taxa sensitive to these barriers is an important step toward mitigating these effects. Upstream–downstream distributions of fishes in 24 pairs of barrier and reference streams from throughout the basin were estimated using electrofishing surveys. For 48 common species from 34 genera and 12 taxonomic families, 8–19 species, 5–16 genera, and 2–7 families showed evidence of being sensitive to barriers, with the variation in number depending on the statistical measure applied. Barriers did not differentially affect species from certain genera or families, nor did they affect species of certain body form. Therefore, taxonomic affiliation and swimming morphology are not useful for predicting sensitivity to barriers for fishes that co-occurred with sea lampreys but were not sampled adequately by our survey. Our estimates of sensitivity will help fisheries managers make sound, defensible decisions regarding the construction, modification (for fish passage), and removal of small, in-stream barriers.
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23

Chu, Justin, Hamid Mohamadi, Emre Erhan, Jeffery Tse, Readman Chiu, Sarah Yeo, and Inanc Birol. "Mismatch-tolerant, alignment-free sequence classification using multiple spaced seeds and multiindex Bloom filters." Proceedings of the National Academy of Sciences 117, no. 29 (July 8, 2020): 16961–68. http://dx.doi.org/10.1073/pnas.1903436117.

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Alignment-free classification tools have enabled high-throughput processing of sequencing data in many bioinformatics analysis pipelines primarily due to their computational efficiency. Originallyk-mer based, such tools often lack sensitivity when faced with sequencing errors and polymorphisms. In response, some tools have been augmented with spaced seeds, which are capable of tolerating mismatches. However, spaced seeds have seen little practical use in classification because they bring increased computational and memory costs compared to methods that usek-mers. These limitations have also caused the design and length of practical spaced seeds to be constrained, since storing spaced seeds can be costly. To address these challenges, we have designed a probabilistic data structure called a multiindex Bloom Filter (miBF), which can store multiple spaced seed sequences with a low memory cost that remains static regardless of seed length or seed design. We formalize how to minimize the false-positive rate of miBFs when classifying sequences from multiple targets or references. Available within BioBloom Tools, we illustrate the utility of miBF in two use cases: read-binning for targeted assembly, and taxonomic read assignment. In our benchmarks, an analysis pipeline based on miBF shows higher sensitivity and specificity for read-binning than sequence alignment-based methods, also executing in less time. Similarly, for taxonomic classification, miBF enables higher sensitivity than a conventional spaced seed-based approach, while using half the memory and an order of magnitude less computational time.
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24

Onorati, Fulvio, Andrea Tornambé, Andrea Paina, Micol Bellucci, Gianluca Chiaretti, and Barbara Catalano. "Derivation of Sustainable Reference Chemical Levels for the Protection of Italian Freshwater Ecosystems." Water 15, no. 10 (May 10, 2023): 1811. http://dx.doi.org/10.3390/w15101811.

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The current environmental quality standards (EQSs) for freshwater ecosystems have been established in relation to the priority substances covered by Directive 2013/39/EU. The procedure for deriving EQSs that rely on the selection of the most sensitive toxicological data, with the application of arbitrary safety factors, is probably unrealistic for the Italian freshwater ecosystem. In this work, a procedure for the evaluation of specific sensitivity of 13 taxonomic groups from bacteria to amphibians and the derivation of protective chemical reference values specifically for the Italian aquatic communities was developed. Toxicological raw data of species belonging to the same taxonomic group spending at least one phase of their life cycle in Italian freshwater ecosystems were downloaded from EnviroTox and USEPA ECOTOX databases, aggregated, and then used as input for the model called Species Sensitivity Distribution in order to estimate the predicted no effect concentrations (PNECs). The comparison of relative sensitivity factors (RFSs) made it possible to identify the amphibians as the most sensitive group toward metals, trace elements, and pesticides, whereas crustacean were identified as the most sensitive group toward towards polycyclic aromatic hydrocarbons (PAHs). PNECs were estimated to cover 62 substances, of which 37 identified by Directive 2013/39/EU, and in most of the cases, the values were higher than EQSs. The PNECs reported in this work should be considered more realistic and tailored for Italian freshwater ecosystems, having significant repercussions in the classification of water bodies and the estimation of environmental impact assessment.
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25

Golubev, Wladyslav, and Takashi Nakase. "Mycocinogeny in the genus Bullera: taxonomic specificity of sensitivity to the mycocin produced by Bullera sinensis." FEMS Microbiology Letters 146, no. 1 (January 17, 2006): 59–64. http://dx.doi.org/10.1111/j.1574-6968.1997.tb10171.x.

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26

Freitag, Stefanie, and Albert S. Van Jaarsveld. "Sensitivity of selection procedures for priority conservation areas to survey extent, survey intensity and taxonomic knowledge." Proceedings of the Royal Society of London. Series B: Biological Sciences 265, no. 1405 (August 22, 1998): 1475–82. http://dx.doi.org/10.1098/rspb.1998.0460.

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27

Simmons, Nancy B., and Jonathan H. Geisler. "Sensitivity analysis of different methods of coding taxonomic polymorphism: an example from higher-level bat phylogeny." Cladistics 18, no. 6 (December 2002): 571–84. http://dx.doi.org/10.1111/j.1096-0031.2002.tb00293.x.

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28

Kammenga, J. E., C. A. M. Van Gestel, and J. Bakker. "Patterns of sensitivity to cadmium and pentachlorophenol among nematode species from different taxonomic and ecological groups." Archives of Environmental Contamination and Toxicology 27, no. 1 (July 1994): 88–94. http://dx.doi.org/10.1007/bf00203892.

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29

Sivolodskii, E. P. "Determination of the sensitivity of bacteria to barium ions, a taxonomic marker of the genus Pseudomonas." Microbiology 81, no. 1 (February 2012): 112–17. http://dx.doi.org/10.1134/s0026261711060208.

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30

O’Hara, Casey C., Melanie Frazier, and Benjamin S. Halpern. "At-risk marine biodiversity faces extensive, expanding, and intensifying human impacts." Science 372, no. 6537 (April 1, 2021): 84–87. http://dx.doi.org/10.1126/science.abe6731.

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Human activities and climate change threaten marine biodiversity worldwide, though sensitivity to these stressors varies considerably by species and taxonomic group. Mapping the spatial distribution of 14 anthropogenic stressors from 2003 to 2013 onto the ranges of 1271 at-risk marine species sensitive to them, we found that, on average, species faced potential impacts across 57% of their ranges, that this footprint expanded over time, and that the impacts intensified across 37% of their ranges. Although fishing activity dominated the footprint of impacts in national waters, climate stressors drove the expansion and intensification of impacts. Mitigating impacts on at-risk biodiversity is critical to supporting resilient marine ecosystems, and identifying the co-occurrence of impacts across multiple taxonomic groups highlights opportunities to amplify the benefits of conservation management.
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Zhuravleva, Anna S., Natal'ya M. Labutova, and Evgeniy E. Andronov. "Influence of oil pollution on the microbiocenosis of soils adjacent to the oil storage." Ecological genetics 15, no. 4 (December 25, 2017): 60–68. http://dx.doi.org/10.17816/ecogen15460-68.

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The aim of the work was an investigation of the effect of hydrocarbons on bacterial and fungal cenoses of sod-podzolic soils on the territory adjacent to the oil storage in the village Malye Kolpany, Leningrad Region. NGS methods were used to analyze the taxonomic composition and structure of the bacteriocenosis and the method of direct microscopy by Demkina-Mirchink to determine the length of the fungal mycelium and the number of spores. Taxonomic and structural changes in the bacterial community led to the dominance of genera containing numerous species-oil destructors. It is established that the main role in the decomposition of oil in the investigated territorybelongs to prokaryotes related to the genera Pseudoxanthomonas, Methylobacterium and Nocardioides. Mycocenosis showed high sensitivity and low adaptability to oil contamination.
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Freelance, Christopher B., Simon M. Tierney, Juanita Rodriguez, Devi M. Stuart-Fox, Bob B. M. Wong, and Mark A. Elgar. "The eyes have it: dim-light activity is associated with the morphology of eyes but not antennae across insect orders." Biological Journal of the Linnean Society 134, no. 2 (July 12, 2021): 303–15. http://dx.doi.org/10.1093/biolinnean/blab088.

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Abstract The perception of cues and signals in visual, olfactory and auditory modalities underpins all animal interactions and provides crucial fitness-related information. Sensory organ morphology is under strong selection to optimize detection of salient cues and signals in a given signalling environment, the most well-studied example being selection on eye design in different photic environments. Many dim-light active species have larger compound eyes relative to body size, but little is known about differences in non-visual sensory organ morphology between diurnal and dim-light active insects. Here, we compare the micromorphology of the compound eyes (visual receptors) and antennae (olfactory and mechanical receptors) in representative pairs of day active and dim-light active species spanning multiple taxonomic orders of insects. We find that dim-light activity is associated with larger compound eye ommatidia and larger overall eye surface area across taxonomic orders but find no evidence that morphological adaptations that enhance the sensitivity of the eye in dim-light active insects are accompanied by morphological traits of the antennae that may increase sensitivity to olfactory, chemical or physical stimuli. This suggests that the ecology and natural history of species is a stronger driver of sensory organ morphology than is selection for complementary investment between sensory modalities.
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Gonzalez, Darinka Costa, Reinaldo Lucas Cajaiba, Eduardo Périco, Wully Barreto da Silva, Antônio Domingos Brescovite, António Maria Luis Crespi, and Mário Santos. "Assessing Ecological Disturbance in Neotropical Forest Landscapes Using High-Level Diversity and High-Level Functionality: Surprising Outcomes from a Case Study with Spider Assemblages." Land 10, no. 7 (July 19, 2021): 758. http://dx.doi.org/10.3390/land10070758.

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Spiders have been increasingly used as environmental and ecological indicators in conservation and ecosystem management. In the Neotropics, there is a shortage of information regarding spiders’ taxonomies and ecological responses to anthropogenic disturbances. To unravel these hitches, we tested the possibility of using high-level diversity and high-level functionality indicators to evaluate spider assemblages’ sensitivity to landscape changes. This approach, if proven informative, might overcome the relevant limitations of taxonomic derived indexes, which are considered time-consuming, cost-demanding and dependent on the (few) expert taxonomists’ availability. Our results highlight the pertinence of both indicators’ responses to the structural changes induced by increasing anthropogenic disturbance, and are associated with reductions in ecosystem complexity, microclimates, and microhabitats. Overall, both indicators were sensitive to structural changes induced by anthropogenic disturbance and should be considered a useful resource for assessing the extent of ecosystems’ disruptions in the Neotropics, and also to guide managers in landscapes’ restoration.
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Barboza, Anthony Diego Muller, Victor Satler Pylro, Rodrigo Josemar Seminot Jacques, Paulo Ivonir Gubiani, Fernando Luiz Ferreira de Quadros, Júlio Kuhn da Trindade, Eric W. Triplett, and Luiz Roesch. "Seasonal dynamics alter taxonomical and functional microbial profiles in Pampa biome soils under natural grasslands." PeerJ 6 (June 13, 2018): e4991. http://dx.doi.org/10.7717/peerj.4991.

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Soil microbial communities’ assembly is strongly tied to changes in temperature and moisture. Although microbial functional redundancy seems to overcome taxonomical composition changes, the sensitivity and resilience of soil microbial communities from subtropical regions in response to seasonal variations are still poorly understood. Thus, the development of new strategies for biodiversity conservation and sustainable management require a complete understanding of the soil abiotic process involved in the selection of microbial taxa and functions. In this work, we used state of the art molecular methodologies (Next Generation Sequencing) to compare the taxonomic (metataxonomics) and functional (metatranscriptomics) profiles among soil samples from two subtropical natural grasslands located in the Pampa biome, Brazil, in response to short-term seasonal variations. Our data suggest that grasslands maintained a stable microbial community membership along the year with oscillation in abundance. Apparently soil microbial taxa are more susceptible to natural climatic disturbances while functions are more stable and change with less intensity along the year. Finally, our data allow us to conclude that the most abundant microbial groups and functions were shared between seasons and locations reflecting the existence of a stable taxonomical and functional core microbiota.
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Ivashchenko, Kristina V., Maria V. Korneykova, Olesya I. Sazonova, Anna A. Vetrova, Anastasia O. Ermakova, Pavel I. Konstantinov, Yulia L. Sotnikova, et al. "Phylloplane Biodiversity and Activity in the City at Different Distances from the Traffic Pollution Source." Plants 11, no. 3 (January 31, 2022): 402. http://dx.doi.org/10.3390/plants11030402.

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The phylloplane is an integrated part of green infrastructure which interacts with plant health. Taxonomic characterization of the phylloplane with the aim to link it to ecosystem functioning under anthropogenic pressure is not sufficient because only active microorganisms drive biochemical processes. Activity of the phylloplane remains largely overlooked. We aimed to study the interactions among the biological characteristics of the phylloplane: taxonomic diversity, functional diversity and activity, and the pollution grade. Leaves of Betula pendula were sampled in Moscow at increasing distances from the road. For determination of phylloplane activity and functional diversity, a MicroResp tool was utilized. Taxonomic diversity of the phylloplane was assessed with a combination of microorganism cultivation and molecular techniques. Increase of anthropogenic load resulted in higher microbial respiration and lower DNA amount, which could be viewed as relative inefficiency of phylloplane functioning in comparison to less contaminated areas. Taxonomic diversity declined with road vicinity, similar to the functional diversity pattern. The content of Zn in leaf dust better explained the variation in phylloplane activity and the amount of DNA. Functional diversity was linked to variation in nutrient content. The fraction of pathogenic fungi of the phylloplane was not correlated with any of the studied elements, while it was significantly high at the roadsides. The bacterial classes Gammaproteobacteria and Cytophagia, as well as the Dothideomycetes class of fungi, are exposed to the maximal effect of distance from the highway. This study demonstrated the sensitivity of the phylloplane to road vicinity, which combines the effects of contaminants (mainly Zn according to this study) and potential stressful air microclimatic conditions (e.g., low relative air humidity, high temperature, and UV level). Microbial activity and taxonomic diversity of the phylloplane could be considered as an additional tool for bioindication.
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María Galindo-Uribe, Diana, Julio Mario Hoyos-Hoyos, Paola Isaacs-Cubides, Nicolás Corral-Gómez, and Nicolás Urbina-Cardona. "Classification and sensitivity of taxonomic and functional diversity indices of anurans in the Andean coffee cultural landscape." Ecological Indicators 136 (March 2022): 108650. http://dx.doi.org/10.1016/j.ecolind.2022.108650.

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Hayashi, Takehiko I., and Nobuhisa Kashiwagi. "A Bayesian Method for Deriving Species-Sensitivity Distributions: Selecting the Best-Fit Tolerance Distributions of Taxonomic Groups." Human and Ecological Risk Assessment: An International Journal 16, no. 2 (April 7, 2010): 251–63. http://dx.doi.org/10.1080/10807031003670279.

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38

Jakobsson, Simon, Heather Wood, Johan Ekroos, and Regina Lindborg. "Contrasting multi-taxa functional diversity patterns along vegetation structure gradients of woody pastures." Biodiversity and Conservation 29, no. 13 (August 18, 2020): 3551–72. http://dx.doi.org/10.1007/s10531-020-02037-y.

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Abstract Woody pastures represent keystone habitats for biodiversity in agricultural landscapes, contributing to increased resource availability, landscape heterogeneity and structural variability. High taxonomic diversity is closely linked to vegetation structure in woody pastures, but examining functional characteristics of species assemblages can shed more light on the ecological mechanisms driving divergent responses to habitat characteristics and help guide good management practices. To this end, we use a multi-taxa approach to investigate how plant, bat and bird taxonomic and functional diversity are affected by pasture tree and shrub density, structural complexity and proximate forest cover in southern Sweden. In particular, we use a trait exclusion approach to estimate the sensitivity of diversity-environment relationships to specific traits. We found little congruence between corresponding diversity metrics across taxa. Bird species richness responded stronger to environmental variables than functional diversity metrics, whereas the functional response to the environment was stronger than the taxonomic response among plants and bats. While increasing tree densities increased the taxonomic diversity of all three taxa, a simultaneous functional response was only evident for plants. Contrasting measures of vegetation structure affected different aspects of functional diversity across taxa, driven by different traits. For plants and birds, traits linked to resource use contributed particularly to the functional response, whereas body mass had stronger influence on bat functional diversity metrics. Multi-taxa functional approaches are essential to understand the effects of woody pasture structural attributes on biodiversity, and ultimately inform management guidelines to preserve the biological values in woody pastures.
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39

Miossec, Matthieu J., Sandro L. Valenzuela, Marcos Pérez-Losada, W. Evan Johnson, Keith A. Crandall, and Eduardo Castro-Nallar. "Evaluation of computational methods for human microbiome analysis using simulated data." PeerJ 8 (August 11, 2020): e9688. http://dx.doi.org/10.7717/peerj.9688.

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Background Our understanding of the composition, function, and health implications of human microbiota has been advanced by high-throughput sequencing and the development of new genomic analyses. However, trade-offs among alternative strategies for the acquisition and analysis of sequence data remain understudied. Methods We assessed eight popular taxonomic profiling pipelines; MetaPhlAn2, metaMix, PathoScope 2.0, Sigma, Kraken, ConStrains, Centrifuge and Taxator-tk, against a battery of metagenomic datasets simulated from real data. The metagenomic datasets were modeled on 426 complete or permanent draft genomes stored in the Human Oral Microbiome Database and were designed to simulate various experimental conditions, both in the design of a putative experiment; read length (75–1,000 bp reads), sequence depth (100K–10M), and in metagenomic composition; number of species present (10, 100, 426), species distribution. The sensitivity and specificity of each of the pipelines under various scenarios were measured. We also estimated the relative root mean square error and average relative error to assess the abundance estimates produced by different methods. Additional datasets were generated for five of the pipelines to simulate the presence within a metagenome of an unreferenced species, closely related to other referenced species. Additional datasets were also generated in order to measure computational time on datasets of ever-increasing sequencing depth (up to 6 × 107). Results Testing of eight pipelines against 144 simulated metagenomic datasets initially produced 1,104 discrete results. Pipelines using a marker gene strategy; MetaPhlAn2 and ConStrains, were overall less sensitive, than other pipelines; with the notable exception of Taxator-tk. This difference in sensitivity was largely made up in terms of runtime, significantly lower than more sensitive pipelines that rely on whole-genome alignments such as PathoScope2.0. However, pipelines that used strategies to speed-up alignment between genomic references and metagenomic reads, such as kmerization, were able to combine both high sensitivity and low run time, as is the case with Kraken and Centrifuge. Absent species genomes in the database mostly led to assignment of reads to the most closely related species available in all pipelines. Our results therefore suggest that taxonomic profilers that use kmerization have largely superseded those that use gene markers, coupling low run times with high sensitivity and specificity. Taxonomic profilers using more time-consuming read reassignment, such as PathoScope 2.0, provided the most sensitive profiles under common metagenomic sequencing scenarios. All the results described and discussed in this paper can be visualized using the dedicated R Shiny application (https://github.com/microgenomics/HumanMicrobiomeAnalysis). All of our datasets, pipelines and results are made available through the GitHub repository for future benchmarking.
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LiPuma, John J., Betty Jo Dulaney, Jennifer D. McMenamin, Paul W. Whitby, Terrence L. Stull, Tom Coenye, and Peter Vandamme. "Development of rRNA-Based PCR Assays for Identification of Burkholderia cepacia Complex Isolates Recovered from Cystic Fibrosis Patients." Journal of Clinical Microbiology 37, no. 10 (1999): 3167–70. http://dx.doi.org/10.1128/jcm.37.10.3167-3170.1999.

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PCR assays targeting rRNA genes were developed to identify species (genomovars) within the Burkholderia cepacia complex. Each assay was tested with 177 bacterial isolates that also underwent taxonomic analysis by whole-cell protein profile. These isolates were from clinical and environmental sources and included 107 B. cepacia complex strains, 23 Burkholderia gladiolistrains, 20 Ralstonia pickettii strains, 10Pseudomonas aeruginosa strains, 8 Stenotrophomonas maltophilia strains, and 9 isolates belonging to nine other species. The sensitivity and specificity of the 16S rRNA-based assay for Burkholderia multivorans (genomovar II) were 100 and 99%, respectively; for Burkholderia vietnamiensis(genomovar V), sensitivity and specificity were 87 and 92%, respectively. An assay based on 16S and 23S rRNA gene analysis ofB. cepacia ATCC 25416 (genomovar I) was useful in identifying genomovars I, III, and IV as a group (sensitivity, 100%, and specificity, 99%). Another assay, designed to be specific at the genus level, identified all but one of the Burkholderia andRalstonia isolates tested (sensitivity, 99%, and specificity, 96%). The combined use of these assays offers a significant improvement over previously published PCR assays forB. cepacia.
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41

Pandey, Sanjit, Nagavardhini Avuthu, and Chittibabu Guda. "StrainIQ: A Novel n-Gram-Based Method for Taxonomic Profiling of Human Microbiota at the Strain Level." Genes 14, no. 8 (August 18, 2023): 1647. http://dx.doi.org/10.3390/genes14081647.

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The emergence of next-generation sequencing (NGS) technology has greatly influenced microbiome research and led to the development of novel bioinformatics tools to deeply analyze metagenomics datasets. Identifying strain-level variations in microbial communities is important to understanding the onset and progression of diseases, host–pathogen interrelationships, and drug resistance, in addition to designing new therapeutic regimens. In this study, we developed a novel tool called StrainIQ (strain identification and quantification) based on a new n-gram-based (series of n number of adjacent nucleotides in the DNA sequence) algorithm for predicting and quantifying strain-level taxa from whole-genome metagenomic sequencing data. We thoroughly evaluated our method using simulated and mock metagenomic datasets and compared its performance with existing methods. On average, it showed 85.8% sensitivity and 78.2% specificity on simulated datasets. It also showed higher specificity and sensitivity using n-gram models built from reduced reference genomes and on models with lower coverage sequencing data. It outperforms alternative approaches in genus- and strain-level prediction and strain abundance estimation. Overall, the results show that StrainIQ achieves high accuracy by implementing customized model-building and is an efficient tool for site-specific microbial community profiling.
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42

Chowdhury, Chumki, Natasha Majumder, Sanjay Kumar Mandal, Manab Kumar Dutta, Raghab Ray, and Tapan Kumar Jana. "Cell Size versus Taxonomic Composition as Determinants of As (III & V) Sensitivity in the Estuarine Diatom Communities." Journal of Water Resource and Protection 03, no. 06 (2011): 363–69. http://dx.doi.org/10.4236/jwarp.2011.36046.

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43

Brix, Kevin V., David K. DeForest, and William J. Adams. "Assessing acute and chronic copper risks to freshwater aquatic life using species sensitivity distributions for different taxonomic groups." Environmental Toxicology and Chemistry 20, no. 8 (August 2001): 1846–56. http://dx.doi.org/10.1002/etc.5620200831.

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44

Zhao, G. H., B. Hu, J. K. Song, Y. Q. Jia, H. M. Li, C. R. Wang, Q. Lin, Q. X. Xu, S. K. Yu, and Y. Deng. "Characterization of Oesophagostomum asperum and O. columbianum by internal transcribed spacers of nuclear ribosomal DNA." Journal of Helminthology 88, no. 1 (November 30, 2012): 74–81. http://dx.doi.org/10.1017/s0022149x12000764.

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AbstractIn the present study, the internal transcribed spacers (ITS) of ribosomal DNA (rDNA) of Oesophagostomum asperum and O. columbianum were amplified and sequenced. The ITS-1, 5.8S and ITS-2 rDNA sequences of O. asperum were 374 bp, 153 bp and 259 bp in length, respectively, and the corresponding sequences of O. columbianum were 259, 153 and 218 bp in length, respectively. Sequence differences in the ITS-1 and ITS-2 rDNA between the two Oesophagostomum species were 9.5–10.2% and 12.7–13.9%, respectively. Sequence differences in the ITS-1 and ITS-2 rDNA among members of the genus Oesophagostomum were 2.5–11.6% and 6.8–22.3%, respectively. Based on genetic markers in the ITS rDNA, an effective polymerase chain reaction (PCR) approach was developed to differentiate O. columbianum from O. asperum with a sensitivity of 0.2 ng/μl DNA. Since accurate characterization of parasites at different taxonomic levels is essential for population genetic studies and control of parasitosis, the present findings have important implications for studying epidemiology, taxonomy and population biology, as well as for the control of oesophagostomiasis.
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Olson, Nathan D., Justin M. Zook, Jayne B. Morrow, and Nancy J. Lin. "Challenging a bioinformatic tool’s ability to detect microbial contaminants usingin silicowhole genome sequencing data." PeerJ 5 (September 12, 2017): e3729. http://dx.doi.org/10.7717/peerj.3729.

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High sensitivity methods such as next generation sequencing and polymerase chain reaction (PCR) are adversely impacted by organismal and DNA contaminants. Current methods for detecting contaminants in microbial materials (genomic DNA and cultures) are not sensitive enough and require either a known or culturable contaminant. Whole genome sequencing (WGS) is a promising approach for detecting contaminants due to its sensitivity and lack of need fora prioriassumptions about the contaminant. Prior to applying WGS, we must first understand its limitations for detecting contaminants and potential for false positives. Herein we demonstrate and characterize a WGS-based approach to detect organismal contaminants using an existing metagenomic taxonomic classification algorithm. Simulated WGS datasets from ten genera as individuals and binary mixtures of eight organisms at varying ratios were analyzed to evaluate the role of contaminant concentration and taxonomy on detection. For the individual genomes the false positive contaminants reported depended on the genus, withStaphylococcus,Escherichia, andShigellahaving the highest proportion of false positives. For nearly all binary mixtures the contaminant was detected in thein-silicodatasets at the equivalent of 1 in 1,000 cells, thoughF. tularensiswas not detected in any of the simulated contaminant mixtures andY. pestiswas only detected at the equivalent of one in 10 cells. Once a WGS method for detecting contaminants is characterized, it can be applied to evaluate microbial material purity, in efforts to ensure that contaminants are characterized in microbial materials used to validate pathogen detection assays, generate genome assemblies for database submission, and benchmark sequencing methods.
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46

Laini, Alex, Simone Guareschi, Rossano Bolpagni, Gemma Burgazzi, Daniel Bruno, Cayetano Gutiérrez-Cánovas, Rafael Miranda, Cédric Mondy, Gábor Várbíró, and Tommaso Cancellario. "biomonitoR: an R package for managing ecological data and calculating biomonitoring indices." PeerJ 10 (October 14, 2022): e14183. http://dx.doi.org/10.7717/peerj.14183.

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The monitoring of biological indicators is required to assess the impacts of environmental policies, compare ecosystems and guide management and conservation actions. However, the growing availability of ecological data has not been accompanied by concomitant processing tools able to facilitate data handling and analysis. Multiple common challenges limit the usefulness of biomonitoring information across ecosystems and biological groups. Biomonitoring data analysis is currently constrained by time-consuming steps for data preparation and a data processing environment with limited integration in terms of software, biological groups, and protocols. We introduce biomonitoR, a package for the R programming language that addresses technical challenges for the management of ecological data and metrics calculation. biomonitoR implements most of the biological indices currently used or proposed in different fields of ecology and water resource management. Its combination of customizable functions aims to support a transferable and comprehensive biomonitoring workflow in a user-friendly environment. biomonitoR represents a versatile toolbox with five main assets: (i) it checks taxonomic information against reference datasets allowing for customization of trait and sensitivity scores; (ii) it supports heterogeneous taxonomic resolution allowing computations at multiple taxonomic levels; (iii) it calculates multiple biological indices, including metrics for both broad and stressor-specific ecological assessments; (iv) it enables user-friendly data visualization, helping both decision-making processes and data interpretation; and (v) it allows working with an interactive web application straight from R. Overall, biomonitoR can benefit the wide biomonitoring community, including environmental private consultants, ecologists and natural resource managers.
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47

Ritchie, Andrew M., and Simon Y. W. Ho. "Influence of the tree prior and sampling scale on Bayesian phylogenetic estimates of the origin times of language families." Journal of Language Evolution 4, no. 2 (July 1, 2019): 108–23. http://dx.doi.org/10.1093/jole/lzz005.

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Abstract Bayesian phylogenetic methods derived from evolutionary biology can be used to reconstruct the history of human languages using databases of cognate words. These analyses have produced exciting results regarding the origins and dispersal of linguistic and cultural groups through prehistory. Bayesian lexical dating requires the specification of priors on all model parameters. This includes the use of a prior on divergence times, often combined with a prior on tree topology and referred to as a tree prior. Violation of the underlying assumptions of the tree prior can lead to an erroneous estimate of the timescale of language evolution. To investigate these impacts, we tested the sensitivity of Bayesian dating to the tree prior in analyses of four lexical data sets. Our results show that estimates of the origin times of language families are robust to the choice of tree prior for lexical data, though less so than when Bayesian phylogenetic methods are used to analyse genetic data sets. We also used the relative fit of speciation and coalescent tree priors to determine the ability of speciation models to describe language diversification at four different taxonomic levels. We found that speciation priors were preferred over a constant-size coalescent prior regardless of taxonomic scale. However, data sets with narrower taxonomic and geographic sampling exhibited a poorer fit to ideal birth–death model expectations. Our results encourage further investigation into the nature of language diversification at different sampling scales.
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48

Belair, Marie, Flora Pensec, Jean-Luc Jany, Gaétan Le Floch, and Adeline Picot. "Profiling Walnut Fungal Pathobiome Associated with Walnut Dieback Using Community-Targeted DNA Metabarcoding." Plants 12, no. 12 (June 20, 2023): 2383. http://dx.doi.org/10.3390/plants12122383.

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Walnut dieback can be caused by several fungal pathogenic species, which are associated with symptoms ranging from branch dieback to fruit necrosis and blight, challenging the one pathogen–one disease concept. Therefore, an accurate and extensive description of the walnut fungal pathobiome is crucial. To this end, DNA metabarcoding represents a powerful approach provided that bioinformatic pipelines are evaluated to avoid misinterpretation. In this context, this study aimed to determine (i) the performance of five primer pairs targeting the ITS region in amplifying genera of interest and estimating their relative abundance based on mock communities and (ii) the degree of taxonomic resolution using phylogenetic trees. Furthermore, our pipelines were also applied to DNA sequences from symptomatic walnut husks and twigs. Overall, our results showed that the ITS2 region was a better barcode than ITS1 and ITS, resulting in significantly higher sensitivity and/or similarity of composition values. The ITS3/ITS4_KYO1 primer set allowed to cover a wider range of fungal diversity, compared to the other primer sets also targeting the ITS2 region, namely, GTAA and GTAAm. Adding an extraction step to the ITS2 sequence influenced both positively and negatively the taxonomic resolution at the genus and species level, depending on the primer pair considered. Taken together, these results suggested that Kyo set without ITS2 extraction was the best pipeline to assess the broadest fungal diversity, with a more accurate taxonomic assignment, in walnut organs with dieback symptoms.
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Bellino, Alessandro, Daniela Baldantoni, Vittoria Milano, Lucia Santorufo, Jérôme Cortet, and Giulia Maisto. "Spatial Patterns and Scales of Collembola Taxonomic and Functional Diversity in Urban Parks." Sustainability 13, no. 23 (November 25, 2021): 13029. http://dx.doi.org/10.3390/su132313029.

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Anthropogenic pressures can affect the distribution of species and elicit the appearance of spatial patterns that provide insights into the species’ responses to environmental filtering, mediated by their functional traits. Due to the functional redundancy in ecological communities, the spatial variations of species and functional traits can occur at different scales, but little is known on this topic, especially for soil arthropods with limited dispersion capabilities and highly dependent on environmental characteristics. The present research aims at shedding light on the spatial ecology of both the taxonomic and functional biodiversity of collembolan communities colonizing urban parks, adopted as model taxa for their functional traits, diversity and sensitivity to environmental drivers. To this end, the spatial patterns and scales of collembolan communities from 8 parks in Naples (Italy) and 14 in Montpellier (France) were investigated through an approach based on Moran eigenvector maps, modified to allow for evaluating the community spatial connectivity and the scales underpinning the spatial variation of each species and functional trait. The obtained findings demonstrate a limited spatial connectivity of collembolan communities in terms of both taxonomic and functional diversity, with mostly species-specific micro-scale variations that may be shaped by environmental constraints.
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Yugueros, Javier, Alejandro Temprano, Beatriz Berzal, Marı́a Sánchez, Carmen Hernanz, José Marı́a Luengo, and Germán Naharro. "Glyceraldehyde-3-Phosphate Dehydrogenase-Encoding Gene as a Useful Taxonomic Tool for Staphylococcusspp." Journal of Clinical Microbiology 38, no. 12 (2000): 4351–55. http://dx.doi.org/10.1128/jcm.38.12.4351-4355.2000.

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The gap gene of Staphylococcus aureus, encoding glyceraldehyde-3-phosphate dehydrogenase, was used as a target to amplify a 933-bp DNA fragment by PCR with a pair of primers 26 and 25 nucleotides in length. PCR products, detected by agarose gel electrophoresis, were also amplified from 12 Staphylococcusspp. analyzed previously. Hybridization with an internal 279-bp DNA fragment probe was positive in all PCR-positive samples. No PCR products were amplified when other gram-positive and gram-negative bacterial genera were analyzed using the same pair of primers.AluI digestion of PCR-generated products gave 12 different restriction fragment length polymorphism (RFLP) patterns, one for each species analyzed. However, we could detect two intraspecies RFLP patterns in Staphylococcus epidermidis,Staphylococcus hominis, and Staphylococcus simulans which were different from the other species. An identical RFLP pattern was observed for 112 S. aureusisolates from humans, cows, and sheep. The sensitivity of the PCR assays was very high, with a detection limit for S. aureuscells of 20 CFU when cells were suspended in saline. PCR amplification of the gap gene has the potential for rapid identification of at least 12 species belonging to the genusStaphylococcus, as it is highly specific.
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