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opencc-by-4.0Nov 2020View details →

Analysis of fungal genomes reveals commonalities of intron gain or loss and functions in intron-poor species

Datasets for DOI: <a href="https://doi.org/10.1101/2020.08.11.247098">10.1101/2020.08.11.247098</a>. Jupyter notebooks to reproduce the analysis of this study is available at <a href="https://github.com/Brookesloci/fungi_intron_paper_2020">GitHub</a> <ul> <li>annotations.total.txt.gz - gene annotation file of 350 fungi species and outgroups Homo sapiens and Fonticula alba</li> <li>site_histories_41490_51_2L_1G.txt.gz - intron site histories of 263 fungi species and outgroups Homo sapiens and Fonticula alba.</li> </ul>

opencc-zeroDec 2015View details →

Data from: De novo transcriptome analysis of the common New Zealand stick insect Clitarchus hookeri (Phasmatodea) reveals genes involved in olfaction, digestion and sexual reproduction

Phasmatodea, more commonly known as stick insects, have been poorly studied at the molecular level for several key traits, such as components of the sensory system and regulators of reproduction and development, impeding a deeper understanding of their functional biology. Here, we employ de novo transcriptome analysis to identify genes with primary functions related to female odour reception, digestion, and male sexual traits in the New Zealand common stick insect Clitarchus hookeri (White). The female olfactory gene repertoire revealed ten odorant binding proteins with three recently duplicated, 12 chemosensory proteins, 16 odorant receptors, and 17 ionotropic receptors. The majority of these olfactory genes were over-expressed in female antennae and have the inferred function of odorant reception. Others that were predominantly expressed in male terminalia (n = 3) and female midgut (n = 1) suggest they have a role in sexual reproduction and digestion, respectively. Over-represented transcripts in the midgut were enriched with digestive enzyme gene families. Clitarchus hookeri is likely to harbour nine members of an endogenous cellulase family (glycoside hydrolase family 9), two of which appear to be specific to the C. hookeri lineage. All of these cellulase sequences fall into four main phasmid clades and show gene duplication events occurred early in the diversification of Phasmatodea. In addition, C. hookeri genome is likely to express γ-proteobacteria pectinase transcripts that have recently been shown to be the result of horizontal transfer. We also predicted 711 male terminalia-enriched transcripts that are candidate accessory gland proteins, 28 of which were annotated to have molecular functions of peptidase activity and peptidase inhibitor activity, two groups being widely reported to regulate female reproduction through proteolytic cascades. Our study has yielded new insights into the genetic basis of odour detection, nutrient digestion, and male sexual traits in stick insects. The C. hookeri reference transcriptome, together with identified gene families, provides a comprehensive resource for studying the evolution of sensory perception, digestive systems, and reproductive success in phasmids.

opencc-zeroDec 2019View details →

Data from: A critical analysis of the potential for EU Common Agricultural Policy measures to support wild pollinators on farmland

1. Agricultural intensification and associated loss of high-quality habitats are key drivers of insect pollinator declines. With the aim of decreasing the environmental impact of agriculture, the 2014 EU Common Agricultural Policy (CAP) defined a set of habitat and landscape features (Ecological Focus Areas: EFAs) farmers could select from as a requirement to receive basic farm payments. To inform the post-2020 CAP, we performed a European-scale evaluation to determine how different EFA options vary in their potential to support insect pollinators under standard and pollinator-friendly management, as well as the extent of farmer uptake. 2. A structured Delphi elicitation process engaged 22 experts from 18 European countries to evaluate EFAs options. By considering life cycle requirements of key pollinating taxa (i.e. bumble bees, solitary bees and hoverflies), each option was evaluated for its potential to provide forage, bee nesting sites and hoverfly larval resources. 3. EFA options varied substantially in the resources they were perceived to provide and their effectiveness varied geographically and temporally. For example, field margins provide relatively good forage throughout the season in Southern and Eastern Europe but lacked early-season forage in Northern and Western Europe. Under standard management, no single EFA option achieved high scores across resource categories and a scarcity of late season forage was perceived. 4. Experts identified substantial opportunities to improve habitat quality by adopting pollinator-friendly management. Improving management alone was, however, unlikely to ensure that all pollinator resource requirements were met. Our analyses suggest that a combination of poor management, differences in the inherent pollinator habitat quality and uptake bias towards catch crops and nitrogen-fixing crops severely limit the potential of EFAs to support pollinators in European agricultural landscapes. 5. Policy Implications. To conserve pollinators and help protect pollination services, our study highlights the need to create a variety of interconnected, well-managed habitats that complement each other in the resources they offer. To achieve this the CAP post-2020 should take a holistic view to implementation that integrates the different delivery vehicles aimed at protecting biodiversity (e.g. enhanced conditionality, eco-schemes and Agri-Environment and Climate Measures). To improve habitat quality we recommend an effective monitoring framework with target-orientated indicators and to facilitate the spatial targeting of options collaboration between land managers should be incentivised.

opencc-zeroDec 2016View details →

Data from: The relationship between blood parasites and ornamentation depends on the level of analysis in the common yellowthroat

The Hamilton–Zuk hypothesis predicts that ornament expression is a signal of the ability of individuals to resist parasite infection. Thus, across a population (i.e. between-individuals) more ornamented individuals should have lower levels of parasitism. Numerous studies have tested this prediction and the results are mixed. One reason for these conflicting results may be that many studies have examined this relationship at the between-individual level, which may be affected by confounding factors such as selective mortality. Using within-subject centering we examined the relationship between male ornamentation and avian blood parasites at both the between- and within-individual levels. These relationships focus on differences in genetically-based resistance to parasites and the trade-off in resource allocation between parasite resistance and ornament expression within an individual, respectively. We studied male common yellowthroats Geothlypis trichas, which have two plumage ornaments, a yellow, carotenoid-based bib (throat and chest) and a black, melanin-based facial mask. Surprisingly, within-individuals, an increase in parasitism between years was associated with an increase in mask size and, potentially, greater concentration of carotenoids in the yellow feathers. This suggests that males may be able to tolerate an increase in parasitism and still increase ornament expression. In contrast, ornamentation was not related to parasitism at the between-individual level. Thus, our study revealed relationships between ornaments and parasitism at the within-individual level that were not present at the between-individual level. Our results highlight the importance of examining both within- and between-individual relationships as correlations between variables, such as ornaments and parasites, may depend on the level of analysis (i.e. within- or between-individuals).

opencc-zeroDec 2015View details →

Data from: Genotypic diversity mitigates negative effects of density on plant performance: a field experiment and life-cycle analysis of common evening primrose Oenothera biennis

1.Genotypic diversity in plant populations is known to enhance plant performance and ecosystem function. Nonetheless, the effect of genotypic diversity has rarely been examined across a population's lifecycle despite the expectation that changing conditions, such as population density, will alter the benefits of diversity. 2.We simultaneously manipulated a component of genotypic diversity (richness, the number of genotypes) and density of common evening primrose Oenothera biennis to address the consequences for herbivory and lifetime fitness in a two-year field experiment that spanned seed germination to life-time fruit production. We genotyped >1100 seedlings with microsatellite DNA markers to determine realized diversity and density in plots sown with O.biennis seeds. Our design achieved quantitative variation in plant density and diversity, with one to 44 individuals established in field plots and two to eight genotypes per polyculture plot (based on microsatellite analysis of reproductive plants). 3.We found a strong interaction between seed density and genetic diversity, with germination and establishment being 24% higher in genetic polycultures than monocultures, but only at low seed density. At high seed density, the opposite pattern emerged, with polycultures having 12% fewer individuals established than monocultures. Initial effects of emergence on plot density persisted through to the fruiting stage. 4.Higher plant densities result in increased mortality, decreased probability of reproduction, decreased plant height, and lower levels of life-time fruit production per plant. Increasing genotypic diversity increased the probability of reproduction overall, and showed a significant interaction with plant density mitigating the negative effects of high density on individual height and lifetime fruit production. 5.Synthesis. Plant density and genotypic diversity interacted from the very earliest stages of seed germination and establishment of O. biennis. This effect persisted over the two-year life-cycle of plants, and genotypic diversity buffered against the negative fitness consequences of high plant density. These results imply a dynamic interplay between the long-held paradigm of density effects in plant ecology and the genetic structure of populations.

opencc-zeroDec 2017View details →

Data from: Population genetic analysis of Chadian Guinea worms reveals that human and non-human hosts share common parasite populations

Following almost 10 years of no reported cases, Guinea worm disease (GWD or dracunculiasis) reemerged in Chad in 2010 with peculiar epidemiological patterns and unprecedented prevalence of infection among non-human hosts, particularly domestic dogs. Since 2014, animal infections with Guinea worms have also been observed in the other three countries with endemic transmission (Ethiopia, Mali, and South Sudan), causing concern and generating interest in the parasites' true taxonomic identity and population genetics. We present the first extensive population genetic data for Guinea worm, investigating mitochondrial and microsatellite variation in adult female worms from both human and non-human hosts in the four endemic countries to elucidate the origins of Chad's current outbreak and possible host-specific differences between parasites. Genetic diversity of Chadian Guinea worms was considerably higher than that of the other three countries, even after controlling for sample size through rarefaction, and demographic analyses are consistent with a large, stable parasite population. Genealogical analyses eliminate the other three countries as possible sources of parasite reintroduction into Chad, and sequence divergence and distribution of genetic variation provide no evidence that parasites in human and non-human hosts are separate species or maintain isolated transmission cycles. Both among and within countries, geographic origin appears to have more influence on parasite population structure than host species. Guinea worm infection in non-human hosts has been occasionally reported throughout the history of the disease, particularly when elimination programs appear to be reaching their end goals. However, no previous reports have evaluated molecular support of the parasite species identity. Our data confirm that Guinea worms collected from non-human hosts in the remaining endemic countries of Africa are Dracunculus medinensis and that the same population of worms infects both humans and dogs in Chad. Our genetic data and the epidemiological evidence suggest that transmission in the Chadian context is currently being maintained by canine hosts.

opencc-by-4.0Jan 2024View details →

A comparative analysis of somatic mutations occurring at "common" loci and other loci with the TCGA somatic mutation dataset.

A comparative analysis of somatic mutations occurring at "common" loci and other loci with the TCGA somatic mutation dataset.

opencc-by-4.0Nov 2015View details →

Supplementary material 1 from: Colihueque N, Gantz A, Rau JR, Parraguez M (2015) Genetic divergence analysis of the Common Barn Owl Tyto alba (Scopoli, 1769) and the Short-eared Owl Asio flammeus (Pontoppidan, 1763) from southern Chile using COI sequence. ZooKeys 534: 135-146. https://doi.org/10.3897/zookeys.534.5953

Pictures of external morphology of specimens of Tyto alba and Asio flammeus collected in southern Chile: Explanation note: Pictures of ventral and dorsal views of specimens showing plumage color and overall appearance. Data on body mass of these specimens are also provided.

opennotspecifiedApr 2021View details →

Fig. 1 Pattern representing a in Genetic analysis of dicyemid infrapopulations suggests sexual reproduction and host colonization by multiple individuals is common

Fig. 1 Pattern representing a distribution of microsatellite alleles in individual dicyemids. Dicyemids in each host individual did not share identical patterns of microsatellite alleles. Each row represents a single dicyemid individual. Microsatellite alleles are colour coded according to

opennotspecifiedApr 2021View details →

Fig. 3 in Genetic analysis of dicyemid infrapopulations suggests sexual reproduction and host colonization by multiple individuals is common

Fig. 3 Percentage of variance present in the samples (based on the four-level AMOVA computed in Arlequin using Rst metrics). Groups set as two localities from Tyrrhenian (Italy, Naples) and Adriatic seas (Pula, Croatia). Hierarchical levels showing significant variation (p <0.05) are marked by an asterisk

FIGURE 4 in Taxonomic reassessment of Gracilaria cearensis (Rhodophyta, Gracilariales), a poorly defined yet common flattened species based on morphological and molecular analysis including topotype collections

FIGURE 4. Neighbor-joining tree based on UPA sequence data and K2P corrected distances showing the G. cearensis clade and related species. Bootstrap values (2000 replicates) are indicated at the nodes. Only bootstrap values ≥ 50 are shown on the tree. Sequences generated in the present study are indicated in bold. Scale bar represents estimated number of substitutions per site.

FIGURE 3 in Taxonomic reassessment of Gracilaria cearensis (Rhodophyta, Gracilariales), a poorly defined yet common flattened species based on morphological and molecular analysis including topotype collections

FIGURE 3. Maximum likelihood phylogenetic tree of selected Gracilariaceae taxa estimated using rbcL DNA sequence data. Note phylogenetic position of G. cearensis in relation to other taxa. Numbers at the nodes indicate bootstrap values (≥ 50) for ML (1000 replicates), MP (2000 replicates) and Bayesian posterior probabilities (≥ 0.5), respectively;—indicates lack of support. Branches with 100% support in all analyses are indicated by thicker lines. Arrows indicate the position of support values when they do not fit on the branches. The sequences generated in the present study are indicated in bold. Scale bar represents estimated number of substitutions per site.

FIGURE 2. Gracilaria cearensis. A in Taxonomic reassessment of Gracilaria cearensis (Rhodophyta, Gracilariales), a poorly defined yet common flattened species based on morphological and molecular analysis including topotype collections

FIGURE 2. Gracilaria cearensis. A. Transverse section close to base of main axis, showing various layers of cortical cells and medullary cells with thickened walls. B. Transverse section close to apex, showing abrupt transition between cortex and medulla. C. Transverse section showing gradual transition between cortex and medulla. Note medulla composed of thick-walled cells. D. Detail of cortical region, composed of 1–2 cortical cell layers. Note the gradual transition between cortex and medulla. E. Surface view of tetrasporic blade. F. Transverse section of tetrasporophyte cortex, showing cruciate tetrasporangia. G. Surface view of a male thallus with scattered spermatangia. H. Transverse section of spermatangial thallus, showing shallow textorii-type conceptacles. I. Longitudinal section of a cystocarp. J. Longitudinal section of cystocarp, showing tubular nutritive cells (arrows). K. Detail showing the central fusion cell (f). L. Tubular nutritive cells connecting gonimoblasts to pericarp (arrows). Note small cortical cells in cystocarp floor (arrowhead). Scale bars: A–C, I, J = 100 μm, D–H, K, L = 25 μm.

FIGURE 1. Gracilaria cearensis. A in Taxonomic reassessment of Gracilaria cearensis (Rhodophyta, Gracilariales), a poorly defined yet common flattened species based on morphological and molecular analysis including topotype collections

FIGURE 1. Gracilaria cearensis. A. Holotype (SPF 2321). B–E. Phenotypic variation of the habit. Note typical dichotomous branching in all specimens and the absence of stipe in specimen C. F. Detail showing characteristic proliferations along the margins. G. Detail of branches' basal constrictions. Scale bars = 1 cm.