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165 results for “specific diversity”
The pan-genome of Aspergillus fumigatus provides a high-resolution view of its population structure revealing high-levels of lineage-specific diversity driven by recombination
<p><em>Aspergillus fumigatus </em>is a deadly agent of human fungal disease, where virulence heterogeneity is thought to be at least partially structured by genetic variation between strains. While population genomic analyses based on reference genome alignments offer valuable insights into how gene variants are distributed across populations, these approaches fail to capture intraspecific variation in genes absent from the reference genome. Pan-genomic analyses based on <em>de novo</em> assemblies offer a promising alternative to reference-based genomics, with the potential to address the full genetic repertoire of a species. Here, we use a combination of population genomics, phylogenomics, and pan-genomics to assess population structure and recombination frequency, phylogenetically structured gene presence-absence variation, evidence for metabolic specificity, and the distribution of putative antifungal resistance genes in <em>A. fumigatus</em>. We provide evidence for three distinct populations of <em>A. fumigatus</em>, structured by both gene variation (SNPs and indels) and distinct gene presence-absence variation with unique suites of accessory genes present exclusively in each clade. Accessory genes displayed functional enrichment for nitrogen and carbohydrate metabolism, hinting that populations may be stratified by environmental niche specialization. Similarly, the distribution of antifungal resistance genes and resistance alleles were often structured by phylogeny. Despite low levels of outcrossing, <em>A. fumigatus</em> demonstrated a large pan-genome including many genes unrepresented in the Af293 reference genome. These results highlight the inadequacy of relying on a single-reference based approach for evaluating intraspecific variation, and the power of combined genomic approaches to elucidate population structure, genetic diversity, and the putative ecological drivers of clinically relevant fungi.</p> <p>Accompanying manuscript is available as preprint at <a href="https://dx.doi.org/10.1101/2021.12.12.472145">https://dx.doi.org/10.1101/2021.12.12.472145</a> </p> <p>Lotus A. Lofgren, Brandon S. Ross, Robert A. Cramer, Jason E. Stajich. Combined Pan-, Population-, and Phylo-Genomic Analysis of <em>Aspergillus fumigatus</em> Reveals Population Structure and Lineage-Specific Diversity bioRxiv 2021.12.12.472145; doi: https://doi.org/10.1101/2021.12.12.472145</p>
Data and Code for "Cell Type-specific Genome Scans of DNA Methylation Diversity Indicate an Important Role for Transposable Elements"
<p>This is a release of the gitlab repository "meta-methylome" (https://gitlab.com/okartal/meta-methylome.git) that, in addition to the code, also contains the resulting genomic data.</p> <p>Extract the directory on the command line using</p> <pre><code class="language-bash">$ tar -xhzvf meta-methylome.tar.gz</code></pre> <p>to preserve the symbolic links.</p>
Fig. 4 in Silk Spinning Behavior Varies from Species-Specific to Individualistic in Embioptera: Do Environmental Correlates Account for this Diversity?
Fig. 4. Computation of similarity between two sequences. For two individuals of Aposthonia borneensis (Hagen) (Oligotomidae), the first 500 steps of their spin sequences are shown (A and B).The red bar underlining a short sequence indicates one 15-step subsequence that is highly similar between these two individuals. For all possible pairs of 15 step subsequences, the heatmap displays the sequence similarity (C), with red areas indicating regions of the spin sequence that are highly similar.The profiles on the margins of the heat map indicate the marginal maxima—that is, for each 15-step subsequence, what is the similarity to the most similar subsequence in the other individual. Portions of the sequence with similarities about 12 were deemed sufficiently similar to the other sequence (vertical or horizontal lines), amounting to about 5% of individual 1's sequence and 10% of individual 2's sequence.
Fig. 3 in Silk Spinning Behavior Varies from Species-Specific to Individualistic in Embioptera: Do Environmental Correlates Account for this Diversity?
Fig. 3. Kinematic diagrams displaying relative proportion of spin-steps in each position as relative size of the circles. Saturated black color of the body represents dorsal spinning; dark gray represents kinematics when the embiopteran faces the framework silk and spins with her ventral surface facing the camera and the emerging silk structure. Spinning was recorded during hour-long filming sessions in the laboratory in an apparatus as shown in Supp Fig. 1 [online only]. (A) Notoligotoma hardyi average spin dynamics, (B) Haploembia tarsalis average spin dynamics, (C) Diagram shows the positions of the different possible spinsteps whereby the words are placed in the position of the front foot as the embiopteran steps around her body to release silk with each foot fall.The same steps are taken on the left as well during spinning. See Supp Video 2 [online only] for examples of spinning behavior exhibited by individual females.
Fig. 5 in Silk Spinning Behavior Varies from Species-Specific to Individualistic in Embioptera: Do Environmental Correlates Account for this Diversity?
Fig. 5. Phylogenetic relationships and sequence similarities (n = 15) for all individuals in this study. (A) Sequence similarities are depicted as a heat map, with the diagonal representing self-similarities.The small outlined boxes along the diagonal indicate all intraspecific comparisons, and the mean intraspecific similarity for each species is depicted above the heat map. For comparison, the inset graph, (B) shows the similarity among pairs of species for a trait that is evolving according to the Ornstein-Uhlenbeck model.The large clade constituting the top 19 species shows high similarity among species (mostly dark colors in the upper left), but low similarity to the two outgroups to this clade (bottom six species, shows as lighter gray colors).The phylogenetic tree is based on Miller et al. 2012.
Fig. 7 in Silk Spinning Behavior Varies from Species-Specific to Individualistic in Embioptera: Do Environmental Correlates Account for this Diversity?
Fig. 7. Predictors of intraspecific similarity scores. The three panels show the partial residual plots for the three variables selected in the final model for a subsequence length of 15. Intraspecific similarity as a function of: (A) mean annual temperature, (B) temperature seasonality, and (C) silk gallery structure. Two-letter codes indicate the species as in Fig. 6.
Energy input, habitat heterogeneity, and host specificity on avian haemosporidian diversity at continental scales
<p>The correct identification of biotic and abiotic drivers affecting parasite diversity and assemblage composition at different spatial scales is crucial for understanding how pathogen distribution responds to anthropogenic disturbance and climate change. Here, we used a database of avian haemosporidian parasites to identify such drivers and their effect on the taxonomic and phylogenetic diversity of genera Plasmodium, Haemoproteus, and Leucocytozoon from three zoogeographic regions. We explored how parasite diversity is related to energy input (i.e., temperature, precipitation, and potential evapotranspiration [PET]), to habitat heterogeneity (i.e., climatic seasonality, vegetation density, ecosystem heterogeneity, human disturbance, and host richness), and to a novel assemblage-level metric related to parasite niche overlap (degree of generalism). We found that the relative importance of the predictors differed between the three studied parasite genera and across diversity metrics. Among the most consistent predictors, host richness was positively related to the taxonomic diversity of the three genera. Energy input and human footprint explained the phylogenetic diversity of Haemoproteus. Finally, the degree of generalism explained the diversity of Plasmodium and Leucocytozoon. Our results suggest that different dimensions of haemosporidian diversity are shaped by energy input, host heterogeneity, and assembly processes related to parasite resource use within local parasite assemblages.</p>
Fig. 6 in SPECIFIC AND TROPHIC DIVERSITY OF SOIL NEMATODES IN FOREST ECOSYSTEMS FROM THE ZARAND MOUNTAINS
Fig. 6. - Relative abundance of the nematode FEeding groups in podzolic brown soil of the dmmast oak FOrest FRom BIIrzava (b).
Fig. 5 in SPECIFIC AND TROPHIC DIVERSITY OF SOIL NEMATODES IN FOREST ECOSYSTEMS FROM THE ZARAND MOUNTAINS
Fig. 5. - Relative abundance of the nematode feeding groups in brown earth soil of the durmast oak forest from Corbe�ti.
Fig. 4 in SPECIFIC AND TROPHIC DIVERSITY OF SOIL NEMATODES IN FOREST ECOSYSTEMS FROM THE ZARAND MOUNTAINS
Fig. 4. - Relative abundance of the nematode feeding groups in brown earth soil of the hoRNbeam-beech FOrest from Cladova (b).
Fig. 2 in SPECIFIC AND TROPHIC DIVERSITY OF SOIL NEMATODES IN FOREST ECOSYSTEMS FROM THE ZARAND MOUNTAINS
Fig. 2. - Relative abundance of the nematode FEeding groups in brown acid soil of the beech forest fRom Miidrige�ti a.
Fig. 3 in SPECIFIC AND TROPHIC DIVERSITY OF SOIL NEMATODES IN FOREST ECOSYSTEMS FROM THE ZARAND MOUNTAINS
Fig. 3. - Relative abundance of the nematode feeding groups in brown acid soil of the hornbeambeech forest from Miidrige�ti (b).
Fig. 1 in SPECIFIC AND TROPHIC DIVERSITY OF SOIL NEMATODES IN FOREST ECOSYSTEMS FROM THE ZARAND MOUNTAINS
Fig. 1. - Dendrogram of cluster analysis FOR nematode communities, based on specific affinity, in the deciduous FOrests from the ZaRand Mountains.
suggests that northern specimens of R. barnardi should be reexamined to confirm their specific identity. MAP 154. Distribution of Rhoptropus sp. in Angola. in Diversity and Distribution of the Amphibians and Terrestrial Reptiles of Angola Atlas of Historical and Bibliographic Records (1840-2017)
suggests that northern specimens of R. barnardi should be reexamined to confirm their specific identity. MAP 154. Distribution of Rhoptropus sp. in Angola.
Fig. 1 in Ecology of bat flies in Singapore: A study on the diversity, infestation bias and host specificity (Diptera: Nycteribiidae)
Fig. 1. Pteropodid fruit bats in Singapore with their ectoparasitic Nycteribiidae bat flies. Cynopterus brachyotis (a) and Leptocyclopodia ferrarii (b); Eonycteris spelaea (c) and Eucampsipoda sundaica (d); Penthetor lucasi (e), Eucampsipoda penthetoris (f), and Archinycteribia octophthalma (g).
Fig. 2 in Ecology of bat flies in Singapore: A study on the diversity, infestation bias and host specificity (Diptera: Nycteribiidae)
Fig. 2. Posterior mean intensity of the three species of bats and 89% HDPI (High Density Posterior Interval).
Figure 1 in Cryptic genetic diversity and host specificity of Bothriocephalus acheilognathi Yamaguti, 1934 (Eucestoda: Bothriocephalidea)
Figure 1. Sample localities of Bothriocephalus acheilognathi studied in China. The code number is corresponding to the locality in Table 1.
Figiure 3 in Cryptic genetic diversity and host specificity of Bothriocephalus acheilognathi Yamaguti, 1934 (Eucestoda: Bothriocephalidea)
Figiure 3. Phylogenetic relationships of Bothriocephalus based on the ribosoml internal transcribed spacer sequences (ITS1+ITS2) using maximum likelihood (ML) method. Numbers near branch node are the bootstrap support value for ML, maximum parsimoy (MP), and posterior probability for Bayesian inference (BI).
High functional diversity in deep-sea fish communities and increasing intra-specific trait variation with increasing latitude
<p>Variation in both inter- and intra-specific traits affect community dynamics, yet we know little regarding the relative importance of external environmental filters vs internal biotic interactions that shape the functional space of communities along broad-scale environmental gradients, such as latitude, elevation or depth. We examined changes in several key aspects of functional alpha-diversity for marine fishes along depth and latitude gradients by quantifying intra- and inter-specific richness, dispersion and regularity in functional trait space. We derived eight functional traits related to food acquisition and locomotion, and calculated seven complementary indices of functional diversity for 144 species of marine ray-finned fishes along large-scale depth (50 m – 1200 m) and latitudinal gradients (29° – 51° S) in New Zealand waters. Traits were derived from morphological measurements taken directly from footage obtained using Baited Remote Underwater Stereo-Video systems and museum specimens. We partitioned functional variation into intra- and inter-specific components for the first time using a PERMANOVA approach. We also implemented two tree-based diversity metrics in a functional distance-based context for the first time: namely, the variance in pairwise functional distance, and the variance in nearest-neighbour distance. Functional alpha diversity increased with increasing depth, and decreased with increasing latitude. More specifically, the dispersion and mean nearest-neighbour distances among species in trait space, and intra-specific trait variability all increased with depth, whereas functional hypervolume (richness) was stable across depth. In contrast, functional hypervolume, dispersion and regularity indices all decreased with increasing latitude; however, intra-specific trait variation increased with latitude, suggesting that intra-specific trait variability becomes increasingly important at higher latitudes. These results suggest that competition within and among species are key processes shaping functional multi-dimensional space for fishes in the deep sea. Increasing morphological dissimilarity with increasing depth may facilitate niche partitioning to promote coexistence, whereas abiotic filtering may be the dominant process structuring communities with increasing latitude.</p>
Host specificity of herbivorous insects promotes negative species–genetic diversity relationship
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