A genomic database of all Earth's eukaryotic species could contribute to many scientific discoveries; however, only a tiny fraction of species have genomic information available. In 2018, scientists across the world united under the Earth BioGenome Project (EBP), aiming to produce a database of high-quality reference genomes containing all ~1.5 million recognized eukaryotic species. As the European node of the EBP, the European Reference Genome Atlas (ERGA) sought to implement a new decentralised, equitable and inclusive model for producing reference genomes. For this, ERGA launched a Pilot Project establishing the first distributed reference genome production infrastructure and testing it on 98 eukaryotic species from 33 European countries. Here we outline the infrastructure and explore its effectiveness for scaling high-quality reference genome production, whilst considering equity and inclusion. The outcomes and lessons learned provide a solid foundation for ERGA while offering key learnings to other transnational, national genomic resource projects and the EBP.
- Publikační typ
- časopisecké články MeSH
Long-read sequencing is driving rapid progress in genome assembly across all major groups of life, including species of the family Drosophilidae, a longtime model system for genetics, genomics, and evolution. We previously developed a cost-effective hybrid Oxford Nanopore (ONT) long-read and Illumina short-read sequencing approach and used it to assemble 101 drosophilid genomes from laboratory cultures, greatly increasing the number of genome assemblies for this taxonomic group. The next major challenge is to address the laboratory culture bias in taxon sampling by sequencing genomes of species that cannot easily be reared in the lab. Here, we build upon our previous methods to perform amplification-free ONT sequencing of single wild flies obtained either directly from the field or from ethanol-preserved specimens in museum collections, greatly improving the representation of lesser studied drosophilid taxa in whole-genome data. Using Illumina Novaseq X Plus and ONT P2 sequencers with R10.4.1 chemistry, we set a new benchmark for inexpensive hybrid genome assembly at US $150 per genome while assembling genomes from as little as 35 ng of genomic DNA from a single fly. We present 183 new genome assemblies for 179 species as a resource for drosophilid systematics, phylogenetics, and comparative genomics. Of these genomes, 62 are from pooled lab strains and 121 from single adult flies. Despite the sample limitations of working with small insects, most single-fly diploid assemblies are comparable in contiguity (>1 Mb contig N50), completeness (>98% complete dipteran BUSCOs), and accuracy (>QV40 genome-wide with ONT R10.4.1) to assemblies from inbred lines. We present a well-resolved multi-locus phylogeny for 360 drosophilid and 4 outgroup species encompassing all publicly available (as of August 2023) genomes for this group. Finally, we present a Progressive Cactus whole-genome, reference-free alignment built from a subset of 298 suitably high-quality drosophilid genomes. The new assemblies and alignment, along with updated laboratory protocols and computational pipelines, are released as an open resource and as a tool for studying evolution at the scale of an entire insect family.
Environmental DNA (eDNA) metabarcoding has gained growing attention as a strategy for monitoring biodiversity in ecology. However, taxa identifications produced through metabarcoding require sophisticated processing of high-throughput sequencing data from taxonomically informative DNA barcodes. Various sets of universal and taxon-specific primers have been developed, extending the usability of metabarcoding across archaea, bacteria and eukaryotes. Accordingly, a multitude of metabarcoding data analysis tools and pipelines have also been developed. Often, several developed workflows are designed to process the same amplicon sequencing data, making it somewhat puzzling to choose one among the plethora of existing pipelines. However, each pipeline has its own specific philosophy, strengths and limitations, which should be considered depending on the aims of any specific study, as well as the bioinformatics expertise of the user. In this review, we outline the input data requirements, supported operating systems and particular attributes of thirty-two amplicon processing pipelines with the goal of helping users to select a pipeline for their metabarcoding projects.
- Klíčová slova
- amplicon data analysis, bioinformatics, environmental DNA, metabarcoding, pipeline, review,
- MeSH
- analýza dat MeSH
- Archaea genetika klasifikace MeSH
- Bacteria genetika klasifikace MeSH
- environmentální DNA genetika MeSH
- Eukaryota genetika klasifikace MeSH
- metagenomika metody MeSH
- software * MeSH
- taxonomické DNA čárové kódování * metody MeSH
- výpočetní biologie * metody MeSH
- vysoce účinné nukleotidové sekvenování metody MeSH
- Publikační typ
- časopisecké články MeSH
- přehledy MeSH
- Názvy látek
- environmentální DNA MeSH
Functional trait approaches are common in ecology, but a lack of clear hypotheses on how traits relate to environmental gradients (i.e., trait-niche relationships) often makes uncovering mechanisms difficult. Furthermore, measures of community functional structure differ in their implications, yet inferences are seldom compared among metrics. Community-weighted mean trait values (CWMs), a common measure, are largely driven by the most common species and thus do not reflect community-wide trait-niche relationships per se. Alternatively, trait-niche relationships can be estimated across a larger group of species using hierarchical joint species distribution models (JSDMs), quantified by a parameter Γ. We investigated how inferences about trait-niche relationships are affected by the choice of metric. Using deadwood-dependent (saproxylic) beetles in fragmented Finnish forests, we followed a protocol for investigating trait-niche relationships by (1) identifying environmental filters (climate, forest age, and deadwood volume), (2) relating these to an ecological function (dispersal ability), and (3) identifying traits related to this function (wing morphology). We tested 18 hypothesized dispersal relationships using both CWM and Γ estimates across these environmental gradients. CWMs were more likely than Γ to show support for trait-niche relationships. Up to 13% of species' realized niches were explained by dispersal traits, but the directions of effects were consistent with fewer than 11%-39% of our 18 trait-niche hypotheses (depending on the metric used). This highlights the difficulty in connecting morphological traits and ecological functions in insects, despite the clear conceptual link between landscape connectivity and flight-related traits. Caution is thus warranted in hypothesis development, particularly where apparent trait-function links are less clear. Inferences differ when CWMs versus Γ estimates are used, necessitating the choice of a metric that reflects study questions. CWMs help explain the effects of environmental gradients on community trait composition, whereas the effects of traits on species' niches are better estimated using hierarchical JSDMs.
- Klíčová slova
- Bayesian joint species distribution model, community‐weighted mean trait values, deadwood, dispersal capacity, morphological traits, phylogeny, response trait, wing length,
- Publikační typ
- časopisecké články MeSH
Despite host-fungal symbiotic interactions being ubiquitous in all ecosystems, understanding how symbiosis has shaped the ecology and evolution of fungal spores that are involved in dispersal and colonization of their hosts has been ignored in life-history studies. We assembled a spore morphology database covering over 26,000 species of free-living to symbiotic fungi of plants, insects and humans and found more than eight orders of variation in spore size. Evolutionary transitions in symbiotic status correlated with shifts in spore size, but the strength of this effect varied widely among phyla. Symbiotic status explained more variation than climatic variables in the current distribution of spore sizes of plant-associated fungi at a global scale while the dispersal potential of their spores is more restricted compared to free-living fungi. Our work advances life-history theory by highlighting how the interaction between symbiosis and offspring morphology shapes the reproductive and dispersal strategies among living forms.
Climate, topography and the 3D structure of forests are major drivers affecting local species communities. However, little is known about how the specific functional traits of saproxylic (wood-living) beetles, involved in the recycling of wood, might be affected by those environmental characteristics.Here, we combine ecological and morphological traits available for saproxylic beetles and airborne laser scanning (ALS) data in Bayesian trait-based joint species distribution models to study how traits drive the distributions of more than 230 species in temperate forests of Europe.We found that elevation (as a proxy for temperature and precipitation) and the proportion of conifers played important roles in species occurrences while variables related to habitat heterogeneity and forest complexity were less relevant. Furthermore, we showed that local communities were shaped by environmental variation primarily through their ecological traits whereas morphological traits were involved only marginally. As predicted, ecological traits influenced species' responses to forest structure, and to other environmental variation, with canopy niche, wood decay niche and host preference as the most important ecological traits. Conversely, no links between morphological traits and environmental characteristics were observed. Both models, however, revealed strong phylogenetic signal in species' response to environmental characteristics.These findings imply that alterations of climate and tree species composition have the potential to alter saproxylic beetle communities in temperate forests. Additionally, ecological traits help explain species' responses to environmental characteristics and thus should prove useful in predicting their responses to future change. It remains challenging, however, to link simple morphological traits to species' complex ecological niches. Read the free Plain Language Summary for this article on the Journal blog.
- Klíčová slova
- Bayesian modelling, Coleoptera, HMSC, LiDAR, airborne laser scanning, environmental gradient, functional traits, phylogeny,
- Publikační typ
- časopisecké články MeSH
Snow ecosystems are an important component of polar and mountainous regions, influencing water regime, biogeochemical cycles and supporting snow specific taxa. Although snow is considered to be one of the most unique, and at the same time a disappearing habitat, knowledge of its taxonomic diversity is still limited. It is true especially for micrometazoans appearing in snow algae blooming areas. In this study, we used morphological and molecular approaches to identify two tardigrade species found in green snow patches of Mt. Gassan in Japan. By morphology, light (PCM) and scanning electron microscopy (SEM), and morphometry we described Hypsibius nivalis sp. nov. which differs from other similar species by granular, polygonal sculpture on the dorsal cuticle and by the presence of cuticular bars next to the internal claws. Additionally, phylogenetic multilocus (COI, 18S rRNA, 28S rRNA) analysis of the second taxon, Hypsibius sp. identified by morphology as convergens-pallidus group, showed its affinity to the Hypsibiidae family and it is placed as a sister clade to all species in the Hypsibiinae subfamily. Our study shows that microinvertebrates associated with snow are poorly known and the assumption that snow might be inhabited by snow-requiring tardigrade taxa cannot be ruled out. Furthermore, our study contributes to the understanding subfamily Hypsibiinae showing that on its own the morphology of specimens belonging to convergens-pallidus group is insufficient in establishing a true systematic position of specimens.
- MeSH
- ekosystém MeSH
- fylogeneze MeSH
- RNA ribozomální 28S MeSH
- Tardigrada * genetika MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Japonsko MeSH
- Názvy látek
- RNA ribozomální 28S MeSH
AIM: Understanding the variation in community composition and species abundances (i.e., β-diversity) is at the heart of community ecology. A common approach to examine β-diversity is to evaluate directional variation in community composition by measuring the decay in the similarity among pairs of communities along spatial or environmental distance. We provide the first global synthesis of taxonomic and functional distance decay along spatial and environmental distance by analysing 148 datasets comprising different types of organisms and environments. LOCATION: Global. TIME PERIOD: 1990 to present. MAJOR TAXA STUDIED: From diatoms to mammals. METHOD: We measured the strength of the decay using ranked Mantel tests (Mantel r) and the rate of distance decay as the slope of an exponential fit using generalized linear models. We used null models to test whether functional similarity decays faster or slower than expected given the taxonomic decay along the spatial and environmental distance. We also unveiled the factors driving the rate of decay across the datasets, including latitude, spatial extent, realm and organismal features. RESULTS: Taxonomic distance decay was stronger than functional distance decay along both spatial and environmental distance. Functional distance decay was random given the taxonomic distance decay. The rate of taxonomic and functional spatial distance decay was fastest in the datasets from mid-latitudes. Overall, datasets covering larger spatial extents showed a lower rate of decay along spatial distance but a higher rate of decay along environmental distance. Marine ecosystems had the slowest rate of decay along environmental distances. MAIN CONCLUSIONS: In general, taxonomic distance decay is a useful tool for biogeographical research because it reflects dispersal-related factors in addition to species responses to climatic and environmental variables. Moreover, functional distance decay might be a cost-effective option for investigating community changes in heterogeneous environments.
- Klíčová slova
- biogeography, environmental gradient, spatial distance, trait, β‐diversity,
- Publikační typ
- časopisecké články MeSH
Programmed cell death ligand (PD-L1)/PD-1 expression has been studied in a variety of cancers and blockage of PD-L1/PD-1 pathway is a cornerstone of immunotherapy. We studied PD-L1/PD-1 immunohistochemical expression in 47 thyroid gland specimens in groups of (1) Hashimoto thyroiditis (HT) only; (2) HT and follicular epithelial dysplasia (FED); and (3) HT, FED, and papillary thyroid carcinoma (PTC). PD-1 positivity was found in immune cells, namely in lymphocytes, macrophages, and plasma cells with mean values for lymphocytes and macrophages 9% in HT group, 4% in FED group, and 4% in PTC group. PD-L1 positivity was identified in both immune cells and in the normal epithelial cells. In the HT group, mean PD-L1 staining on immune cells was 6%, in FED group 5%, and in PTC group 7%. The mean PD-L1 staining on the epithelial cells in the inflammatory parenchyma was 11.7% in HT, 13.4% in FED, and 8.3% in PTC group. The mean PD-L1 staining of FED foci was 47.2% in FED group and 33.6% in PTC group. The mean tumor proportion score (TPS) was 10.4%, and the mean combined positive score (CPS) was 15.5. At the moment, PTC is not a target of immunotherapy. However, understanding the complex issue of concurrent inflammation and autoimmunity can importantly influence the cancer treatment in future.
- Klíčová slova
- Hashimoto thyroiditis, PD-1, PD-L1, follicular epithelial dysplasia, papillary thyroid carcinoma, thyroid gland,
- MeSH
- antigeny CD274 metabolismus MeSH
- antigeny CD279 MeSH
- Hashimotova nemoc * MeSH
- lidé MeSH
- nádory štítné žlázy * patologie MeSH
- papilární karcinom štítné žlázy metabolismus patologie MeSH
- papilární karcinom * metabolismus patologie MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- antigeny CD274 MeSH
- antigeny CD279 MeSH
- CD274 protein, human MeSH Prohlížeč
- PDCD1 protein, human MeSH Prohlížeč
