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353 results for “Molecular markers”
FIG. 2 in Phylogeny of the genus Pinnixa White, 1846 (Crustacea, Brachyura, Pinnotheridae) and allies inferred from mitochondrial and nuclear molecular markers, with generic reassignment of twenty-one species
FIG. 2. — Morphological characters of the type species of Pinnixa White, 1846 s.s., P. cylindrica (Say, 1818), along with those for five molecularly segregated genera formerly treated in Pinnixa s.l.: A-D, Pinnixa cylindrica: A, male dorsal view; B, male cheliped; C, third maxilliped (adapted from Rathbun 1918:160 fig. 99a); D, male pleon; E-G: Glassella costaricana (Wicksten, 1982): E, female holotype dorsal view; F, female cheliped; G, third maxilliped (adapted from Campos & Wicksten 1997: fig. 1, fig. 2c, a, with permission from Allen Press); H, I, Glassella faxoni (Rathbun, 1918) n. comb.: H, third maxilliped; I, male pleon (adapted from Rathbun 1918:133 fig. 77b, a); J-M: Rathbunixa sayana (Stimpson, 1960) n. comb.: J, male dorsal view; K, male cheliped; L, third maxilliped; M, male pleon (L, M adapted from Rathbun 1918:158 fig. 98a, b); N-Q: Sayixa monodactyla (Say, 1818) n. comb., male (ULLZ 8713, Fort Pierce, FL, USA); N, dorsal view; O, cheliped; P, third maxilliped; Q, pleon; R, T, U, Scleroplax granulata Rathbun, 1893; R, female carapace and pereopods 2-5; T, third maxilliped; U, male pleon (R, T adapted from Campos 2006:fig. 1a-c, with permission from Magnolia Press; U, adapted from Rathbun 1918:171 fig. 109a); S, Scleroplax littoralis (Holmes, 1894) n. comb., female and male chelipeds (adapted from Rathbun 1918:146 fig. 89a, b); V-Y, Tubicolixa chaetopterana (Stimpson, 1860) n. comb.: V, male dorsal view; W, female and male chelipeds; X, third maxilliped; Y, male pleon (X, Y, adapted from Rathbun 1918:152 fig. 94a, b).
Data from: Phylogeny of Tetillidae (Porifera, Demospongiae, Spirophorida) based on three molecular markers
Tetillidae are spherical to elliptical cosmopolitan demosponges. The family comprises eight genera: namely, Acanthotetilla Burton, 1959, Amphitethya Lendenfeld, 1907, Cinachyra Sollas, 1886, Cinachyrella Wilson, 1925, Craniella Schmidt, 1870, Fangophilina Schmidt, 1880, Paratetilla Dendy, 1905, and Tetilla Schmidt, 1868. These genera are characterized by few conflicting morphological characters, resulting in an ambiguity of phylogenetic relationships. The phylogeny of tetillid genera was investigated using the cox1, 18S rRNA and 28S rRNA (C1-D2 domains) genes in 88 specimens (8 genera, 28 species). Five clades were identified: (i) Cinachyrella, Paratetilla and Amphitethya species, (ii) Cinachyrella levantinensis, (iii) Tetilla, (iv) Craniella, Cinachyra and Fangophilina and (v) Acanthotetilla. Consequently, the phylogenetic analysis supports the monophyly of Tetilla, a genus lacking any known morphological synapomorphy. Acanthotetilla is also recovered. In contrast, within the first clade, species of the genera Paratetilla and Amphitethya were nested within Cinachyrella. Similarly, within the fourth clade, species of the genera Cinachyra and Fangophilina were nested within Craniella. As previously postulated by taxonomists, the loss of ectodermal specialization (i.e., a cortex) has occurred several times independently. Nevertheless, the presence or absence of a cortex and its features carry a phylogenetic signal. Surprisingly, the common view that assumes close relationships among sponges with porocalices (i.e., surface depressions) is refuted.
Data from: Characterizing genic and non-genic molecular markers: comparison of microsatellites and SNPs
The implications of transitioning to single nucleotide polymorphism (SNPs) from microsatellite markers (MSs) have been investigated in a number of population genetics studies, but the effect of genomic location on the amount of information each type of marker reveals has not been explored in detail. We developed novel SNP markers flanking 1 kb regions of 13 genic (within gene or <1 kb away from gene) and 13 nongenic (>10 kb from annotated gene) MSs in the threespine stickleback genome to obtain comparable data for both types of markers. We analysed patterns of genetic diversity and divergence on various geographic scales after converting the SNP loci within each genomic region into haplotypes. Marker type (SNP haplotype or MS) and location (genic or nongenic) significantly affected most estimates of population diversity and divergence. Between-lineage divergence was significantly higher in SNP haplotypes (genic and nongenic), however, within-lineage divergence was similar between marker types. Most divergence and diversity measures were uncorrelated between markers, except for population differentiation which was correlated between MSs and SNP haplotypes (both genic and nongenic). Broad-scale population structure and assignment were similarly resolved by both marker types, however, only the MSs were able to delimit fine-scale population structuring, particularly when genic and nongenic markers were combined. These results demonstrate that estimates of genetic variability and differentiation among populations can be strongly influenced by marker type, their genomic location in relation to genes and by the interaction of these two factors. This highlights the importance of having an awareness of the inherent strengths and limitations associated with different molecular tools to select the most appropriate methods for accurately addressing various ecological and evolutionary questions.
Data from: Are molecular markers useful predictors of adaptive potential?
Estimates of molecular genetic variation are often used as a cheap and simple surrogate for a population's adaptive potential, yet empirical evidence suggests they are unlikely to be a valid proxy. However, this evidence is based on molecular genetic variation poorly predicting estimates of adaptive potential rather than how well it predicts true values. As a consequence, the relationship has been systematically underestimated and the precision with which it could be measured severely overstated. By collating a large database, and using suitable statistical methods, we obtain a 95% upper bound of 0.26 for the proportion of variance in quantitative genetic variation explained by molecular diversity. The relationship is probably too weak to be useful, but this conclusion must be taken as provisional: less noisy estimates of quantitative genetic variation are required. In contrast, and perhaps surprisingly, current sampling strategies appear sufficient for characterising a population's molecular genetic variation at comparable markers.
Data from: Delimiting species-poor datasets using single molecular markers: a study of barcode gaps, haplowebs and GMYC
Most single-locus molecular approaches to species delimitation available to date have been designed and tested on data sets comprising at least tens of species, whereas the opposite case (species-poor data sets for which the hypothesis that all individuals are conspecific cannot by rejected beforehand) has rarely been the focus of such attempts. Here we compare the performance of barcode gap detection, haplowebs and generalized mixed Yule–coalescent (GMYC) models to delineate chimpanzees and bonobos using nuclear sequence markers, then apply these single-locus species delimitation methods to data sets of one, three, or six species simulated under a wide range of population sizes, speciation rates, mutation rates and sampling efforts. Our results show that barcode gap detection and GMYC models are unable to delineate species properly in data sets composed of one or two species, two situations in which haplowebs outperform them. For data sets composed of three or six species, bGMYC and haplowebs outperform the single-threshold and multiple-threshold versions of GMYC, whereas a clear barcode gap is only observed when population sizes and speciation rates are both small. The latter conditions represent a "sweet spot" for molecular taxonomy where all the single-locus approaches tested work well; however, the performance of these methods decreases strongly when population sizes and speciation rates are high, suggesting that multilocus approaches may be necessary to tackle such cases.
Data from: Coral feeding on microalgae assessed with molecular trophic markers
Herbivory in corals, especially for symbiotic species, remains controversial. To investigate the capacity of scleractinian and soft corals to capture microalgae, we conducted controlled laboratory experiments offering five algal species: the cryptophyte Rhodomonas marina, the haptophytes Isochrysis galbana and Phaeocystis globosa, and the diatoms Conticribra weissflogii and Thalassiosira pseudonana. Coral species included the symbiotic soft corals Heteroxenia fuscescens and Sinularia flexibilis, the asymbiotic scleractinian coral Tubastrea coccinea, and the symbiotic scleractinian corals Stylophora pistillata, Pavona cactus and Oculina arbuscula. Herbivory was assessed by end-point PCR amplification of algae-specific 18S rRNA gene fragments purified from coral tissue genomic DNA extracts. The ability to capture microalgae varied with coral and algal species and could not be explained by prey size or taxonomy. Herbivory was not detected in S. flexibilis and S. pistillata. P. globosa was the only algal prey that was never captured by any coral. Although predation defence mechanisms have been shown for Phaeocystis spp. against many potential predators, this study is the first to suggest this for corals. This study provides new insights on herbivory in symbiotic corals and suggests that corals may be selective herbivorous feeders.
Data from: Is telomere length a molecular marker of individual quality? insights from a long-lived bird
1. In wild vertebrates, some individuals survive and reproduce better than others and this has led to the concept of individual quality. Despite its importance when studying ecological processes and life-history trade-offs, measuring individual quality is complex because individuals must be followed during a large part of their life. 2. Recently, telomere biology has been successfully brought into ecology and telomere length has been suggested to be a promising molecular tool to evaluate individual quality in wild vertebrates ('the telomere – individual quality hypothesis'). 3. In this study, we tested this hypothesis in a long-lived species, the Black-browed albatross (Thalassarche melanophrys) by simultaneously measuring telomere length and several potential complementary phenotypic proxies of individual quality in a single year. In addition, we followed the return rate and the reproductive performance of these same albatrosses for a decade. 4. We found that long telomeres were associated with several markers of high individual quality (foraging behaviour, body size, and stress hormone levels). Furthermore, we found that a single measure of telomere length could predict future offspring productivity, for at least several years following telomere measurement (better productivity being associated with longer telomeres). 5. Altogether, these results support the 'telomere – individual quality hypothesis' and suggest that telomere length can be useful to estimate individual quality in long-lived seabirds.
Supplementary material 1 from: Konvičková H, John V, Konvička M, Rindoš M, Hrček J (2024) High hymenopteran parasitoid infestation rates in Czech populations of the Euphydryas aurinia butterfly inferred using a new molecular marker. Journal of Hymenoptera Research 97: 29-42. https://doi.org/10.3897/jhr.97.113231
List of sampled colonies of E. aurinia
Figure 1 from: Konvičková H, John V, Konvička M, Rindoš M, Hrček J (2024) High hymenopteran parasitoid infestation rates in Czech populations of the Euphydryas aurinia butterfly inferred using a new molecular marker. Journal of Hymenoptera Research 97: 29-42. https://doi.org/10.3897/jhr.97.113231
Figure 1 The distribution of Euphydryas aurinia in the Czech Republic, historic records included, based on Beneš et al. (2002), with actualisations. The inset in upper right corner shows the position of the country in Europe.
Figure 3 from: Konvičková H, John V, Konvička M, Rindoš M, Hrček J (2024) High hymenopteran parasitoid infestation rates in Czech populations of the Euphydryas aurinia butterfly inferred using a new molecular marker. Journal of Hymenoptera Research 97: 29-42. https://doi.org/10.3897/jhr.97.113231
Figure 3 Per-site hymenopteran parasitoids infestation rates in colonies of the butterfly Euphydryas aurinia in two consecutive years (2019–20), with information of caterpillar web counts in the respective colonies in 2018–2021 (above), and illustration of the relationship between hymenopteran parasitoids infestation rates and E. aurinia caterpillar web counts in the previous year (below).
Figure 2 from: Konvičková H, John V, Konvička M, Rindoš M, Hrček J (2024) High hymenopteran parasitoid infestation rates in Czech populations of the Euphydryas aurinia butterfly inferred using a new molecular marker. Journal of Hymenoptera Research 97: 29-42. https://doi.org/10.3897/jhr.97.113231
Figure 2 Electrophoresis gels used to assess whether the primers used can discriminate lepidopteran hosts and hymenopteran parasitoids a various adult hymenopteran parasitoids (PCRs are positive) and positive (P) and negative (N) samples of E. auriniab four species of adult butterflies; PCRs are negative. The adult specimens of Hymenoptera and Lepidoptera were identified by M. Rindoš, M. Konvička, and Z. Faltýnek Fric.
Genetic dataset of Systematic Identification of Needlefish (Belonidae) Species using Molecular Genetic and Morphological Markers in the Mediterranean and Black Seas
<p>The sequences used in the study from NCBI and BOLD databases.</p>
Supplementary material 1 from: Leite BR, Vieira PE, Troncoso JS, Costa FO (2021) Comparing species detection success between molecular markers in DNA metabarcoding of coastal macroinvertebrates. Metabarcoding and Metagenomics 5: e70063. https://doi.org/10.3897/mbmg.5.70063
Table S1, Figures S1–S5
Supplementary material 2 from: Leite BR, Vieira PE, Troncoso JS, Costa FO (2021) Comparing species detection success between molecular markers in DNA metabarcoding of coastal macroinvertebrates. Metabarcoding and Metagenomics 5: e70063. https://doi.org/10.3897/mbmg.5.70063
Tables S2, S3
FIGURE 1 in Assessment of SCoT and ISSR molecular markers in genetic diversity of rigid ryegrass (Lolium rigidum Gaud.) in Iran
FIGURE 1. Geographical distribution of the studied Lolium rigidum populations.
FIGURE 1 in Comparative study and genetic diversity of Salicornia persica (Chenopodiaceae) using SCOT molecular markers
FIGURE 1. Distribution map of the studied populations.
FIGURE 3. UPGMA dendrogram 33 in Analysis of genetic diversity among five closely related species used as 'Xihuangcao' herbs using ISSR and SCoT molecular markers
FIGURE 3. UPGMA dendrogram 33 populations of 'Xihuangcao' based on SCoT.
FIGURE 4 in Analysis of genetic diversity among five closely related species used as 'Xihuangcao' herbs using ISSR and SCoT molecular markers
FIGURE 4. Principal coordinate analysis of 33 populations of 'Xihuangcao' based on SCoT.
FIGURE 2 in Analysis of genetic diversity among five closely related species used as 'Xihuangcao' herbs using ISSR and SCoT molecular markers
FIGURE 2. Principal coordinate analysis of 33 populations of 'Xihuangcao' based on ISSR.
FIGURE 127 in Revision of the Genus Leptogomphus Selys in Borneo, including gene trees and a two marker molecular phylogeny (Odonata: Anisoptera: Gomphidae)
FIGURE 127. Distribution of L. pasia (white circle) and L. sii (black square).
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.