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515 results for “species selection”
Figure 2 in The neotropical species of Mesocyclops (Copepoda, Cyclopoida): an upgraded identification key and comments on selected taxa
Figure 2. (A) Abdomen ventral (female from Taxisco, Guatemala, MNHN Cp 697, labelled as Mesocyclops varius); (B) Mesocyclops brasilianus, female from Itacoatiara, Brazil (INPA-1396), abdomen, ventral; (C) abdomen, ventral (female from Mare à Camaguan and Caracas, Venezuela, MNHN-Cp1882, labelled as Mesocyclops venezolanus); (D) caudal rami, ventral (MNHN Cp 697); (E) M. brasilianus (INPA-1396), anal somite, and caudal rami, ventral; (F) anal somite and caudal rami, view (MNHN-Cp1880).
Figure 1 in The neotropical species of Mesocyclops (Copepoda, Cyclopoida): an upgraded identification key and comments on selected taxa
Figure 1. (A) First leg, coxa, basis, and first endopodal segment, frontal (female from Taxisco, Guatemala, MNHN Cp 697, labelled as Mesocyclops varius); (B) Mesocyclops brasilianus, female from Itacoatiara, Brazil (INPA- 1396), first leg, coxa, basis, and first endopodal segment, caudal; (C) first leg, coxa, basis, and first endopodal segment, caudal (female from Mare à Camaguan and Caracas, Venezuela, MNHN-Cp1882, labelled as Mesocyclops venezolanus); (D) fourth leg, coxa, and basis, frontal (MNHN Cp 697); (E) M. brasilianus (INPA- 1396), fourth leg, coxa, and basis, caudal; (F) fourth leg, coxa, and basis, caudal (MNHN-Cp1882); (G) fifth pediger and genital somite, ventral (MNHN Cp 697); (H) M. brasilianus (INPA-1396), fifth pediger and genital somite, ventral; (I) fifth pediger and genital somite, ventral (MNHN-Cp1882).
Figure 3 in The neotropical species of Mesocyclops (Copepoda, Cyclopoida): an upgraded identification key and comments on selected taxa
Figure 3. Frequencies of the length ratio of dorsal/lateral caudal setae in the populations of Mesocyclops brasilianus populations examined. Lines refer to the ratio range of each population.
Figure 5 in The neotropical species of Mesocyclops (Copepoda, Cyclopoida): an upgraded identification key and comments on selected taxa
Figure 5. (A) Mesocyclops ogunnus, female, maxillular palp (from van de Velde 1984); (B) M. thermocyclopoides, female (ECOCH-Z-01214), maxillular palp; (C) caudal rami, ventral; (D) antennal basis, caudal; (E) M. thermocyclopoides, male (ECOCH-Z-01215), antennal basis, caudal; (F) M. aspericornis, female (ECOCH-Z- 01234), caudal rami, ventral; (G) antennal basis, caudal; (H) M. reidae, male (ECOCH-Z-01255), fourth leg, intercoxal sclerite, coxa, and basis, caudal; (I) M. brasilianus, female (ECOCH-Z-01195), fourth leg, intercoxal sclerite, coxa, and basis, caudal.
Figure 8 in The neotropical species of Mesocyclops (Copepoda, Cyclopoida): an upgraded identification key and comments on selected taxa
Figure 8. (A) Mesocyclops ellipticus, female (ECOCH-Z-01252), fifth pediger, genital somite, ventral; (B) anal somite, dorsal; (C) M. intermedius, female (ZMA Co 102-731), fifth pediger, genital somite, ventral; (D) anal somite, dorsal; (E) anal somite, caudal rami, ventral; (F) M. paranaensis, female (MNHN Cp 1883), anal somite, caudal rami, ventral; (G) M. brasilianus, female (ECOCH-Z-01196), fifth pediger, genital somite, ventral; (H) M. meridianus, female (ECOCH-Z-01202).
Figure 7 in The neotropical species of Mesocyclops (Copepoda, Cyclopoida): an upgraded identification key and comments on selected taxa
Figure 7. (A) Mesocyclops annulatus, female (MNHN Cp 864), fourth leg, intercoxal sclerite; (B) M. ellipticus, male (ECOCH-Z-01250); (C) M. annulatus, female (MNHN Cp 864), fifth pediger, genital somite, ventral; (D) M. longisetus s.str., female (ECOCH-Z-01236), fifth pediger, genital somite, ventral; (E) 16th antennular segment, inner; (F) M. longisetus curvatus, female (ECOCH-Z-01240), fifth pediger, genital somite, ventral; (G) M. longisetus curvatus, male, 16th antennular segment, inner (from Suárez-Morales et al. 1996, copyright waiver); (H) M. longisetus curvatus, female, fourth leg, third endopodal segment (modified from Reid and Reed 1994, copyright waiver); (I) M. longisetus curvatus, female (ECOCH-Z-01240), caudal rami, ventral; (J) M. longisetus araucanus, female, fourth leg, third endopodal segment (from Löffler 1961); (K) M. longisetus araucanus, female, caudal ramii, ventral (from Löffler 1961).
Figs. 8–12. Strongylogaster Dahlbom, 1835 in Taxonomy, distribution and biology of selected European Dinax, Strongylogaster and Taxonus species (Hymenoptera: Symphyta)
Figs. 8–12. Strongylogaster Dahlbom, 1835, larvae: 8 – S. xanthocera (Stephens, 1835): a – immature instar (dorsal view); b – last instar (lateral view); c – last instar (laterodorsal view). 9 – S. multifasciata (Geoffroy, 1785): a – last instar (laterodorsal view); b – last instar (dorsal view). 10 – S. macula (Klug, 1817): last instar (laterodorsal view). 11 – S. baikalensis Naito, 1990: last instar (laterodorsal view). 12 – S. mixta (Klug, 1817): a – immature instar (laterodorsal view); b – last instar (lateral view); c – last instar (lateral view). Scale for last instar larva: 10 mm.
Figs. 18–20 in Taxonomy, distribution and biology of selected European Dinax, Strongylogaster and Taxonus species (Hymenoptera: Symphyta)
Figs. 18–20, Taxonus Hartig, 1837, last instar larvae: 18 – Taxonus agrorum Fallén, 1808: a – bare larva (lateral view); b – bare larva (dorsal view); c – pruinose larva (lateral view). 19 – T. sticticus (Klug, 1817): a – laterodorsal view; b – dorsal view. 20 – T. alboscutellatus Niezabitowski, 1899: a – dorsal view (plain form); b – laterodorsal view (plain form); c – dorsal view (patterned form). Scale: 10 mm.
Figs. 2–7. Strongylogaster Dahlbom, 1835 in Taxonomy, distribution and biology of selected European Dinax, Strongylogaster and Taxonus species (Hymenoptera: Symphyta)
Figs. 2–7. Strongylogaster Dahlbom, 1835, adults: 2 – S. macula (Klug, 1817); 3 – S. baikalensis Naito, 1990; 4 – S. mixta (Klug, 1817); 5 – S. filicis (Klug, 1817); 6 – S. multifasciata (Geoffroy, 1785); 7 – S. xanthocera (Stephens, 1835). Scale: 10 mm.
Fig. 1 in Taxonomy, distribution and biology of selected European Dinax, Strongylogaster and Taxonus species (Hymenoptera: Symphyta)
Fig. 1. Dinax ermak (Zhelochovtsev, 1968): a – female (dorsal view); b – male (dorsal view); c – female (lateral view); d – last instar larva (dorsal view); e – last instar larva (laterodorsal view); f – eonymph (dorsal view); g – eonymph (laterodorsal view). Scale: 5 mm.
Figs.15–17. Taxonus Hartig, 1837 in Taxonomy, distribution and biology of selected European Dinax, Strongylogaster and Taxonus species (Hymenoptera: Symphyta)
Figs.15–17. Taxonus Hartig, 1837, adults: 15 – T. agrorum Fallén, 1808; 16 – T. sticticus (Klug, 1817); 17 – T. alboscutellatus Niezabitowski, 1899. Scale: 10 mm.
Figs. 13–14. Strongylogaster Dahlbom, 1835 in Taxonomy, distribution and biology of selected European Dinax, Strongylogaster and Taxonus species (Hymenoptera: Symphyta)
Figs. 13–14. Strongylogaster Dahlbom, 1835, penis valve, lateral view: 13 – S. baikalensis Naito, 1990; 14 – S. macula (Klug, 1817). Scale: 0.5 mm.
Fig. 1 in Home range size and microhabitat selection by a tropical partridge species in moist evergreen forest
Fig. 1. Analysis of green-legged partridges' group range based on radio locations using the characteristic hull polygon (CHP) and minimum convex polygon (MCP; 100%, 95% and 50%) methods. F refers to females, and M refers to males.
Fig. 3. Protective mimicry between select reef fish species and the genus Haemulon. A in Mixed-species schooling behavior and protective mimicry involving coral reef fish from the genus Haemulon (Haemulidae)
Fig. 3. Protective mimicry between select reef fish species and the genus Haemulon. A) Mulloidichthys martinicus with a school of adult H. aurolineatum; B) Sparisoma axillare with H. parra juveniles; C) Harengula clupeola with a school of juvenile H. aurolineatum. Circles highlight non-Haemulon species. Photos: P. H. C. Pereira
Gene and repeat annotation for snowy owl (Bubo scandiacus) and selected species
<p>Here we provide the gene and repeat annotation for snowy owl (<em>Bubo scandiacus</em>), in addition to gene and repeat annotation done for some species this was compared to. It is unfortunately currently not possible to upload repeat annotation tracks to an international nucleotide sequence database such as ENA. While uploading the gene annotation is possible, some of the cross references to different databases in the functional annotation are removed. Further, the names of the entries in the publicly available genome assemblies on ENA have different names than what is found in the annotation tracks here, so we also provide the FASTA files for the snowy owl assemblies (bBubSca1.1.hap1.fasta.gz and bBubSca1.1.hap2.fasta.gz). Ideally, all this should have been available via ENA.</p> <p>We annotated the snowy owl genome assemblies, in addition to downy woodpecker (<em>Dryobates pubescens</em>; <a href="https://www.ncbi.nlm.nih.gov/assembly/GCA_014839835.1">GCA_014839835.1</a>), Northern Carmine bee-eater (<em>Merops nubicus</em>; <a href="https://www.ncbi.nlm.nih.gov/assembly/GCA_009819595.1">GCA_009819595.1</a>), Northern goshawk (<em>Accipiter gentilis</em>; <a href="https://www.ncbi.nlm.nih.gov/assembly/GCA_929443795.2">GCA_929443795.2</a>) and barn owl (<em>Tyto alba</em>; <a href="https://www.ncbi.nlm.nih.gov/assembly/GCF_018691265.1#/st">GCF_018691265.1</a>), since no genome annotation was publicly available for these species. We used a pre-release version of the EBP-Nor genome annotation pipeline (<a href="https://github.com/ebp-nor/GenomeAnnotation">https://github.com/ebp-nor/GenomeAnnotation</a>). First, AGAT (https://zenodo.org/record/7255559) agat_sp_keep_longest_isoform.pl and agat_sp_extract_sequences.pl were used on the GRCg7b (GCA_016699485.1) chicken genome assembly and annotation to generate one protein (the longest isoform) per gene. Miniprot (Li, 2023) was used to align the proteins to the curated assemblies. UniProtKB/Swiss-Prot (Consortium et al., 2022) release 2022_03 in addition to the vertebrata part of OrthoDB v11 (Kuznetsov et al., 2022) were also aligned separately to the assemblies. Red (Girgis, 2015) was run via redmask (<a href="https://github.com/nextgenusfs/redmask">https://github.com/nextgenusfs/redmask</a>) on the snowy owl assemblies to mask repetitive areas (we used the soft-masked genome assemblies available at NCBI for the other species). GALBA (Brůna et al., 2023; Buchfink et al., 2015; Hoff and Stanke, 2018; Li, 2023; Stanke et al., 2006) was run with the chicken proteins using the miniprot mode on the masked assemblies. The funannotate-runEVM.py script from Funannotate was used to run EvidenceModeler (Haas et al., 2008) on the alignments of chicken proteins, UniProtKB/Swiss-Prot proteins, vertebrata proteins and the predicted genes from GALBA. The resulting predicted proteins were compared to the protein repeats that Funannotate distributes using DIAMOND blastp and the predicted genes were filtered based on this comparison using AGAT. The filtered proteins were compared to the UniProtKB/Swiss-Prot release 2022_03 using DIAMOND (Buchfink et al., 2015) blastp to find gene names and InterProScan was used to discover functional domains. AGATs agat_sp_manage_functional_annotation.pl was used to attach the gene names and functional annotations to the predicted genes. EMBLmyGFF3 (Norling et al., 2018) was used to combine the fasta files and GFF3 files into a EMBL format for submission to ENA. These files end in gff.gz (the ones ending in fa.out.gff.gz are repeat annotations), proteins.fa.gz and mrna.fa.gz. </p> <p>All species in this study downy woodpecker (<em>Dryobates pubescens</em>; <a href="https://www.ncbi.nlm.nih.gov/assembly/GCA_014839835.1">GCA_014839835.1</a>), Northern Carmine bee-eater (<em>Merops nubicus</em>; <a href="https://www.ncbi.nlm.nih.gov/assembly/GCA_009819595.1">GCA_009819595.1</a>), Northern goshawk (<em>Accipiter gentilis</em>; <a href="https://www.ncbi.nlm.nih.gov/assembly/GCA_929443795.2">GCA_929443795.2</a>), barn owl (T<em>yto alba</em>; <a href="https://www.ncbi.nlm.nih.gov/assembly/GCF_018691265.1#/st">GCF_018691265.1</a>), chicken (<em>Gallus gallus</em>; <a href="https://www.ncbi.nlm.nih.gov/assembly/GCF_016699485.2/">GCF_016699485.2</a>), zebra finch (<em>Taeniopygia guttat</em>a; <a href="https://www.ncbi.nlm.nih.gov/assembly/GCA_003957565.4">GCA_003957565.4</a>) and California condor (<em>Gymnogyps californianus</em>; <a href="https://www.ncbi.nlm.nih.gov/assembly/GCF_018139145.2">GCF_018139145.2</a>) in addition to hap1 of snowy owl was repeat masked with a bird-specific library from <a href="https://www.pnas.org/doi/abs/10.1073/pnas.1616702114">https://www.pnas.org/doi/abs/10.1073/pnas.1616702114</a>, provided by Alexander Suh. These files are named such as MerNubi.fa.out.gff.gz, MerNubi.fa.masked.gz and MerNubi.fna.cat.gz. </p> <p>We have also included the species specific repeat library as generated by RepeatModeler running on hap1 of snowy owl. This is called bBubSca1.1.hap1.repeatlibrary.fa.gz, with the files bBubSca1.1.hap1.fasta.masked.gz, bBubSca1.1.hap1.fasta.out.gff.gz, <span>bBubSca1.1.hap1.divsum.gz </span>and bBubSca1.1.hap1.fasta.cat.gz resulting from running RepeatMasker one hap1 using that library.</p> <p>From the Genespace analyses we have included all files including OrthoFinder results. This is found in the file genespace.tgz.</p>
Meta-analysis of major histocompatibility complex (MHC) class IIA reveals polymorphism and positive selection in many vertebrate species
<p>Pathogen-mediated selection and sexual selection are important drivers of evolution. Both processes are known to target genes of the major histocompatibility complex (MHC), a gene family encoding cell-surface proteins that display pathogen peptides to the immune system. The MHC is also a model for understanding processes such as gene duplication and trans-species allele sharing. The class II MHC protein is a heterodimer whose peptide-binding groove is encoded by an MHC-IIA gene and an MHC-IIB gene. However, our literature review found that class II MHC papers on infectious disease or sexual selection included IIA data only 18% and 9% of the time, respectively. To assess whether greater emphasis on MHC-IIA is warranted, we analyzed MHC-IIA sequence data from 50 species of vertebrates (fish, amphibians, birds, mammals) to test for polymorphism and positive selection. We found that the number of MHC-IIA alleles within a species was often high, and covaried with sample size and number of MHC-IIA genes assayed. While MHC-IIA variability tended to be lower than that of MHC-IIB, the difference was only ~25%, with ~3 fewer IIA alleles than IIB. Furthermore, the unexpectedly high MHC-IIA variability showed clear signatures of positive selection in most species, and positive selection on MHC-IIA was stronger in fish than in other surveyed vertebrate groups. Our findings underscore that MHC-IIA can be an important target of selection. Future work should therefore expand the characterization of MHC-IIA at both allelic and genomic scales, and incorporate MHC-IIA into models of fitness consequences of MHC variation.</p>
Contrasting genome-wide signatures of selection in two closely related Epichloe plant pathogen species
<p>Deposited here composite plots for each species, each pairwise population combination and each of the seven chromosomes as shown and referred to in the manuscript.</p> <p>The filename contains [species abbrevation]_[chromosome number]_[population 1]_[population 2]. Chromosome-wide SNP data and sweeps identified for the population pair are shown. The top panel shows pairwise FST values, averaged across 5kb windows. Shaded rectangles represent the locations of AT-rich regions. The second panel shows the absolute values of the integrated haplotype score (iHS) calculated at each SNP locus for which the ancestral allele state was known. Scores for pop1 are shown at the top and scores for pop2 are negatively transformed and showed at the bottom. Horizontal dashed lines indicate the 99.9% percentile threshold which was used as a cutoff to identify outlier SNPs and inferred iHS sweeps are shown as shaded rectangles. The third panel shows the cross-population extended haplotype homozygosity (XP-EHH) scores calculated between the two populations. Dashed lines indicate 99.9% percentile threshold which was used as a cutoff to identify outlier SNPs and inferred divergent sweeps are shown as shaded rectangles. Positive and negative XP-EHH values refer to the direction of selection: positive values indicate selection in pop1 negative values indicate selection in pop2. In the bottom panel, composite likelihood ratio (CLR) scores are plotted for pop1 (black) and pop2 (blue), colored dashed lines indicate respective 99.9% threshold and colored rectangles highlight inferred CLR-sweeps.</p>
Spatially and temporally varying selection influence species boundaries in two sympatric Mimulus
<p><span>Spatially and temporally varying selection can maintain genetic variation within and between populations, but it is less known how these forces influence divergence between closely related species. We identify the interaction of temporal and spatial variation in selection and their role in either reinforcing or eroding divergence between two closely related <em>Mimulus</em> species. Using repeated reciprocal transplant experiments with advanced generation hybrids we compare the strength of selection on quantitative traits involved in adaptation and reproductive isolation in <em>Mimulus</em> <em>guttatus</em> and <em>Mimulus</em> <em>laciniatus</em> between two years with dramatically different water availability. We found strong divergent habitat-mediated selection on traits in the direction of species differences during a drought in 2013, suggesting that spatially varying selection maintains species divergence. However, a relaxation in divergent selection on most traits in an unusually wet year (2019), including flowering time which is involved in pre-zygotic isolation, suggests that temporal variation in selection may weaken species differences. Therefore, we find evidence that temporally and spatially varying selection may have opposing roles in mediating species boundaries. Given our changing climate, future growing seasons are expected to be more similar to the dry year, suggesting that in this system climate change may actually increase species divergence. </span></p>
Nutrient-based species selection is a prevalent driver of community assembly and functional trait space in tropical forests
<p><span>1. Soil nutrient availability and functional traits interact in complex ways during the assembly of tree communities hindering our understanding of the implications that this may have for their phylogenetic and functional diversity. </span></p> <p><span>2. We combined abundance, taxonomic, phylogenetic and functional trait data of 222 tree species distributed along nutrient concentration gradients at twenty-four plots in two tropical forest study sites. We analysed micro and macronutrient concentration in organic and topsoil horizons and tested for: (1) nutrient-based species sorting due to contrasting trait-environment relationships; (2) whether nutrient filtering has consequences for phylogenetic and functional diversity, and functional space size and occupancy; and (3) we mapped trait distributions across the phylogeny of tree species to track the evolutionary signature of nutrient availability.</span></p> <p><span>3. We found that total nitrogen (N), available phosphorus and total potassium in soil accounted for 68% of the variation in tropical tree species community composition, with strong associations with nutrient concentration for 89% of the tree species included in the analysis. This nutrient-based species selection was mediated by interactions between the three soil nutrient concentrations with leaf nitrogen, leaf thickness and wood density. Soil N concentration was positively associated with the functional space at the site level. At a plot level soil N concentration positively correlated with functional evenness and it was negatively associated with the functional space not occupied by any species in the tree community. Despite the phylogenetic conservatism of leaf N across tree lineages even when not considering legumes, many sister-species pairs show contrasting values which match with their habitat preferences thus indicating the evolutionary lability of this trait, particularly within recently diversified clades. </span></p> <p><span>4. Synthesis. Our results demonstrate that soil nutrient-based species selection is a prevalent driver of community assembly in tropical forests, a process mediated by key functional traits within the leaf and wood economics spectrum. Functional space size and its filling increase with soil nutrient concentration, whereas niche vacancy decreases. This selection process has likely influenced tropical tree species diversification patterns via habitat specialization.</span></p>
Dataset for "Single-Step Selective Oxidation of Methane by Iron-Oxo Species in the Metal-Organic Framework MFU-4l"
<p>Dataset belonging to publication "Single-Step Selective Oxidation of Methane by Iron-Oxo Species in the Metal-Organic Framework MFU-4l"</p>
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