Diversity, multifaceted evolution, and facultative saprotrophism in the European Batrachochytrium salamandrivorans epidemic

AbstractWhile emerging fungi threaten global biodiversity, the paucity of fungal genome assemblies impedes thoroughly characterizing epidemics and developing effective mitigation strategies. Here, we generate de novo genomic assemblies for six outbreaks of the emerging pathogen Batrachochytrium salamandrivorans (Bsal). We reveal the European epidemic currently damaging amphibian populations to comprise multiple, highly divergent lineages demonstrating isolate-specific adaptations and metabolic capacities. In particular, we show extensive gene family expansions and acquisitions, through a variety of evolutionary mechanisms, and an isolate-specific saprotrophic lifecycle. This finding both explains the chytrid’s ability to divorce transmission from host density, producing Bsal’s enigmatic host population declines, and is a key consideration in developing successful mitigation measures.

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Dynamics of host populations affected by the emerging fungal pathogen Batrachochytrium salamandrivorans

Royal Society Open Science ◽

10.1098/rsos.160801 ◽

2017 ◽

Vol 4 (3) ◽

pp. 160801 ◽

Cited By ~ 16

Author(s):

Benedikt R. Schmidt ◽

Claudio Bozzuto ◽

Stefan Lötters ◽

Sebastian Steinfartz

Keyword(s):

Emerging Infectious Diseases ◽

Disease Outbreaks ◽

Host Population ◽

Mitigation Measures ◽

Disease Emergence ◽

Batrachochytrium Salamandrivorans ◽

In The Wild ◽

Successful Control ◽

Using Data ◽

Local Extirpation

Emerging infectious diseases cause extirpation of wildlife populations. We use an epidemiological model to explore the effects of a recently emerged disease caused by the salamander-killing chytrid fungus Batrachochytrium salamandrivorans ( Bsal ) on host populations, and to evaluate which mitigation measures are most likely to succeed. As individuals do not recover from Bsal , we used a model with the states susceptible, latent and infectious, and parametrized the model using data on host and pathogen taken from the literature and expert opinion. The model suggested that disease outbreaks can occur at very low host densities (one female per hectare). This density is far lower than host densities in the wild. Therefore, all naturally occurring populations are at risk. Bsal can lead to the local extirpation of the host population within a few months. Disease outbreaks are likely to fade out quickly. A spatial variant of the model showed that the pathogen could potentially spread rapidly. As disease mitigation during outbreaks is unlikely to be successful, control efforts should focus on preventing disease emergence and transmission between populations. Thus, this emerging wildlife disease is best controlled through prevention rather than subsequent actions.

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Modeling Epidemic Spread among a Commuting Population Using Transport Schemes

Mathematics ◽

10.3390/math9161861 ◽

2021 ◽

Vol 9 (16) ◽

pp. 1861

Author(s):

Daniela Calvetti ◽

Alexander P. Hoover ◽

Johnie Rose ◽

Erkki Somersalo

Keyword(s):

Network Model ◽

Transport Theory ◽

Optimal Transport ◽

State Level ◽

Compartment Model ◽

Census Bureau ◽

Mitigation Strategies ◽

Mitigation Measures ◽

Metapopulation Model ◽

Infection Dynamics

Understanding the dynamics of the spread of COVID-19 between connected communities is fundamental in planning appropriate mitigation measures. To that end, we propose and analyze a novel metapopulation network model, particularly suitable for modeling commuter traffic patterns, that takes into account the connectivity between a heterogeneous set of communities, each with its own infection dynamics. In the novel metapopulation model that we propose here, transport schemes developed in optimal transport theory provide an efficient and easily implementable way of describing the temporary population redistribution due to traffic, such as the daily commuter traffic between work and residence. Locally, infection dynamics in individual communities are described in terms of a susceptible-exposed-infected-recovered (SEIR) compartment model, modified to account for the specific features of COVID-19, most notably its spread by asymptomatic and presymptomatic infected individuals. The mathematical foundation of our metapopulation network model is akin to a transport scheme between two population distributions, namely the residential distribution and the workplace distribution, whose interface can be inferred from commuter mobility data made available by the US Census Bureau. We use the proposed metapopulation model to test the dynamics of the spread of COVID-19 on two networks, a smaller one comprising 7 counties in the Greater Cleveland area in Ohio, and a larger one consisting of 74 counties in the Pittsburgh–Cleveland–Detroit corridor following the Lake Erie’s American coastline. The model simulations indicate that densely populated regions effectively act as amplifiers of the infection for the surrounding, less densely populated areas, in agreement with the pattern of infections observed in the course of the COVID-19 pandemic. Computed examples show that the model can be used also to test different mitigation strategies, including one based on state-level travel restrictions, another on county level triggered social distancing, as well as a combination of the two.

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Design of COVID-19 staged alert systems to ensure healthcare capacity with minimal closures

Nature Communications ◽

10.1038/s41467-021-23989-x ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Haoxiang Yang ◽

Özge Sürer ◽

Daniel Duque ◽

David P. Morton ◽

Bismark Singh ◽

...

Keyword(s):

Hospital Admissions ◽

Optimal Strategies ◽

Mitigation Strategies ◽

Mitigation Measures ◽

Public Confidence ◽

Proof Of Concept ◽

Alert System ◽

System Safety ◽

Reducing Costs ◽

Restrictive Measures

AbstractCommunity mitigation strategies to combat COVID-19, ranging from healthy hygiene to shelter-in-place orders, exact substantial socioeconomic costs. Judicious implementation and relaxation of restrictions amplify their public health benefits while reducing costs. We derive optimal strategies for toggling between mitigation stages using daily COVID-19 hospital admissions. With public compliance, the policy triggers ensure adequate intensive care unit capacity with high probability while minimizing the duration of strict mitigation measures. In comparison, we show that other sensible COVID-19 staging policies, including France’s ICU-based thresholds and a widely adopted indicator for reopening schools and businesses, require overly restrictive measures or trigger strict stages too late to avert catastrophic surges. As proof-of-concept, we describe the optimization and maintenance of the staged alert system that has guided COVID-19 policy in a large US city (Austin, Texas) since May 2020. As cities worldwide face future pandemic waves, our findings provide a robust strategy for tracking COVID-19 hospital admissions as an early indicator of hospital surges and enacting staged measures to ensure integrity of the health system, safety of the health workforce, and public confidence.

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Extended haplotype-phasing of long-read de novo genome assemblies using Hi-C

Nature Communications ◽

10.1038/s41467-020-20536-y ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Zev N. Kronenberg ◽

Arang Rhie ◽

Sergey Koren ◽

Gregory T. Concepcion ◽

Paul Peluso ◽

...

Keyword(s):

Zebra Finch ◽

Cultured Cells ◽

De Novo ◽

Single Cells ◽

Variant Calling ◽

Chromatin Interaction ◽

Extended Haplotype ◽

Benchmark Datasets ◽

And Performance ◽

Genome Assemblies

AbstractHaplotype-resolved genome assemblies are important for understanding how combinations of variants impact phenotypes. To date, these assemblies have been best created with complex protocols, such as cultured cells that contain a single-haplotype (haploid) genome, single cells where haplotypes are separated, or co-sequencing of parental genomes in a trio-based approach. These approaches are impractical in most situations. To address this issue, we present FALCON-Phase, a phasing tool that uses ultra-long-range Hi-C chromatin interaction data to extend phase blocks of partially-phased diploid assembles to chromosome or scaffold scale. FALCON-Phase uses the inherent phasing information in Hi-C reads, skipping variant calling, and reduces the computational complexity of phasing. Our method is validated on three benchmark datasets generated as part of the Vertebrate Genomes Project (VGP), including human, cow, and zebra finch, for which high-quality, fully haplotype-resolved assemblies are available using the trio-based approach. FALCON-Phase is accurate without having parental data and performance is better in samples with higher heterozygosity. For cow and zebra finch the accuracy is 97% compared to 80–91% for human. FALCON-Phase is applicable to any draft assembly that contains long primary contigs and phased associate contigs.

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Assessing Soil Loss by Water Erosion in a Typical Mediterranean Ecosystem of Northern Greece under Current and Future Rainfall Erosivity

Water ◽

10.3390/w13152002 ◽

2021 ◽

Vol 13 (15) ◽

pp. 2002

Author(s):

Stefanos Stefanidis ◽

Vasileios Alexandridis ◽

Chrysoula Chatzichristaki ◽

Panagiotis Stefanidis

Keyword(s):

Open Source ◽

Soil Loss ◽

Renewable Resource ◽

Mitigation Strategies ◽

Mitigation Measures ◽

Mediterranean Ecosystem ◽

Rainfall Erosivity ◽

Negative Consequences ◽

Northern Greece ◽

Erosion Risk

Soil is a non-renewable resource essential for life existence. During the last decades it has been threatened by accelerating erosion with negative consequences for the environment and the economy. The aim of the current study was to assess soil loss changes in a typical Mediterranean ecosystem of Northern Greece, under climate change. To this end, freely available geospatial data was collected and processed using open-source software package. The widespread RUSLE empirical erosion model was applied to estimate soil loss. Current and future rainfall erosivity were derived from a national scale study considering average weather conditions and RCMs outputs for the medium Representative Concentration Pathway scenario (RCP4.5). Results showed that average rainfall erosivity (R-Factor) was 508.85 MJ mm ha h−1 y−1 while the K-factor ranged from 0.0008 to 0.05 t ha h ha−1 MJ−1 mm−1 and LS-factor reached 60.51. Respectively, C-factor ranged from 0.01 to 0.91 and P-factor ranged from 0.42 to 1. The estimated potential soil loss rates will remain stable for the near future period (2021–2050), while an increase of approximately 9% is expected by the end of the 21th century (2071–2100). The results suggest that appropriate erosion mitigation strategies should be applied to reduce erosion risk. Subsequently, appropriate mitigation measures per Land Use/Land Cover (LULC) categories are proposed. It is worth noting that the proposed methodology has a high degree of transferability as it is based on open-source data.

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Parasite infection and host dynamics in a naturally fluctuating rodent population

Canadian Journal of Zoology ◽

10.1139/z2012-083 ◽

2012 ◽

Vol 90 (9) ◽

pp. 1149-1160 ◽

Cited By ~ 17

Author(s):

J.C. Winternitz ◽

M.J. Yabsley ◽

S.M. Altizer

Keyword(s):

Population Density ◽

Experimental Studies ◽

Host Density ◽

Positive Association ◽

Population Cycles ◽

Host Population ◽

Reproductive Status ◽

Vole Cycles ◽

Host Infection ◽

The Impact

Parasites can both influence and be affected by host population dynamics, and a growing number of case studies support a role for parasites in causing or amplifying host population cycles. In this study, we examined individual and population predictors of gastrointestinal parasitism on wild cyclic montane voles ( Microtus montanus (Peale, 1848)) to determine if evidence was consistent with theory implicating parasites in population cycles. We sampled three sites in central Colorado for the duration of a multiannual cycle and recorded the prevalence and intensity of directly transmitted Eimeria Schneider, 1875 and indirectly transmitted cestodes from a total of 267 voles. We found significant associations between host infection status, individual traits (sex, age, and reproductive status) and population variables (site, trapping period, and population density), including a positive association between host density and cestode prevalence, and a negative association between host density and Eimeria prevalence. Both cestode and Eimeria intensity correlated positively with host age, reproductive status, and population density, but neither parasite was associated with poorer host condition. Our findings suggest that parasites are common in this natural host, but determining their potential to influence montane vole cycles requires future experimental studies and long-term monitoring to determine the fitness consequences of infection and the impact of parasite removal on host dynamics.

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Emerging mitigation measures and strategies are needed for riverine ecology to ensure sustainable hydropeaking production in Norway

10.5194/egusphere-egu21-16429 ◽

2021 ◽

Author(s):

Jo Halvard Halleraker ◽

Mahmoud S. R. Kenawi ◽

Jan Henning L’Abée - Lund ◽

Anders G. Finstad ◽

Knut Alfredsen

Keyword(s):

Biological Indicators ◽

Ecological Impacts ◽

Mitigation Strategies ◽

Mitigation Measures ◽

National Database ◽

Political Agenda ◽

Regulated Rivers ◽

Hydropower Production ◽

Multiple Pressures ◽

Environmental Requirements

Riverine biodiversity is threatened with severe degradation from multiple pressures worldwide. One of the key pressures in European rivers are hydromorphological alterations. Rehabilitation of river habitats is accordingly high on the political agenda at the start of UN decade of ecological restoration (2021-2030).Water storage for hydropower production (HP) has severe impacts on aquatic ecology in Norway, with more than 3000 water bodies designated as heavily modified due to hydropower. Norway is the largest hydropower producer in Europe with a huge amount of high head storage schemes. Ca 86 TWh of this is&#160;storage hydropower, which constitutes more than 50% of the total in Europe. This makes Norway a potentially significant supplier of hydropeaking services. Flexible hydropower operations are crucial for EUs Green Deal in balancing electricity from renewable intermittent power generation such as wind and solar.&#160;Many Norwegian HP licenses were issued before modern environmental requirements evolved. Few are re-licensed with emerging strategies to mitigate hydropeaking. Still, there seems to be a common understanding of relevant mitigation strategies emerging between many large hydropower producers. For example, flow ramping from hydropower tailrace water with direct outlet into fjords or other lake reservoirs may be less environmentally harmful than outlet into riverine habitat.In this study, we have assessed the Norwegian hydropower portfolio of more than 1600 HP facilities constructing a national database focusing on the knowledge base for assessing potential downstream hydropower ecological impacts. The ecological severity of such flow ramping and the restoration/mitigation potential, may depend on;&#160;About 51 % of the HPs (ca 80TWh) have tailrace into shorter rivers (<1 km) or directly into fjords or lake/reservoirs. Many of the largest HPs are in this category (e.g 50 HP> 500 MW). Close to 800 HP might have downstream impacts on rivers (> 0.5 km; about 49 % of all HP, in total of ca 56 TWh). Probably > 3 000 km of regulated rivers in Norway therefor might need more ecosystem-based mode of HP operation.&#160;Flow ramping analysis: &#160;Ecosystem-based HP operational rules are established in a selection of sustainably managed Norwegian rivers, still with significant baseload production (0.35-0.76 - TWh annual prod). However, eco-friendly mode of operation seems to be rare as our analysis indicate that flow ramping with potential ecological degradation seems widespread in many rivers. Surprisingly, even in many with operational ramping restriction as required mitigation.Our database may be further improved and updated (with e.g. more flow ramping data and biological indicators) and serve as a basis for a national hydropeaking strategy, and hence make more of the Norwegian hydropower portfolio in line with the EUs sustainability taxonomy.

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Donkey genome and insight into the imprinting of fast karyotype evolution

Scientific Reports ◽

10.1038/srep14106 ◽

2015 ◽

Vol 5 (1) ◽

Cited By ~ 12

Author(s):

Jinlong Huang ◽

Yiping Zhao ◽

Dongyi Bai ◽

Wunierfu Shiraigol ◽

Bei Li ◽

...

Keyword(s):

Target Genes ◽

Karyotype Evolution ◽

De Novo ◽

Cycle Phase ◽

Satellite Sequences ◽

Chromatid Segregation ◽

Karyotypic Instability ◽

Wild Ass ◽

Genome Assemblies ◽

Insight Into

Abstract The donkey, like the horse, is a promising model for exploring karyotypic instability. We report the de novo whole-genome assemblies of the donkey and the Asiatic wild ass. Our results reflect the distinct characteristics of donkeys, including more effective energy metabolism and better immunity than horses. The donkey shows a steady demographic trajectory. We detected abundant satellite sequences in some inactive centromere regions but not in neocentromere regions, while ribosomal RNAs frequently emerged in neocentromere regions but not in the obsolete centromere regions. Expanded miRNA families and five newly discovered miRNA target genes involved in meiosis may be associated with fast karyotype evolution. APC/C, controlling sister chromatid segregation, cytokinesis and the establishment of the G1 cell cycle phase were identified by analysis of miRNA targets and rapidly evolving genes.

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Contiguity: Contig adjacency graph construction and visualisation

10.7287/peerj.preprints.1037v1 ◽

2015 ◽

Cited By ~ 8

Author(s):

Mitchell J Sullivan ◽

Nouri L Ben Zakour ◽

Brian M Forde ◽

Mitchell Stanton-Cook ◽

Scott A Beatson

Keyword(s):

De Novo ◽

Reference Sequence ◽

De Bruijn Graph ◽

Interactive Software ◽

Graph Exploration ◽

Adjacency Graph ◽

Highly Sensitive ◽

Long Read ◽

Genome Assemblies ◽

Adjacency Graphs

Contiguity is an interactive software for the visualization and manipulation of de novo genome assemblies. Contiguity creates and displays information on contig adjacency which is contextualized by the simultaneous display of a comparison between assembled contigs and reference sequence. Where scaffolders allow unambiguous connections between contigs to be resolved into a single scaffold, Contiguity allows the user to create all potential scaffolds in ambiguous regions of the genome. This enables the resolution of novel sequence or structural variants from the assembly. In addition, Contiguity provides a sequencing and assembly agnostic approach for the creation of contig adjacency graphs. To maximize the number of contig adjacencies determined, Contiguity combines information from read pair mappings, sequence overlap and De Bruijn graph exploration. We demonstrate how highly sensitive graphs can be achieved using this method. Contig adjacency graphs allow the user to visualize potential arrangements of contigs in unresolvable areas of the genome. By combining adjacency information with comparative genomics, Contiguity provides an intuitive approach for exploring and improving sequence assemblies. It is also useful in guiding manual closure of long read sequence assemblies. Contiguity is an open source application, implemented using Python and the Tkinter GUI package that can run on any Unix, OSX and Windows operating system. It has been designed and optimized for bacterial assemblies. Contiguity is available at http://mjsull.github.io/Contiguity .

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Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird-of-paradise

10.1101/2019.12.19.882399 ◽

2019 ◽

Cited By ~ 5

Author(s):

Valentina Peona ◽

Mozes P.K. Blom ◽

Luohao Xu ◽

Reto Burri ◽

Shawn Sullivan ◽

...

Keyword(s):

Dark Matter ◽

Genome Assembly ◽

Sex Chromosome ◽

De Novo ◽

Model Organism ◽

Technology Choice ◽

High Quality ◽

Sequencing Technologies ◽

Downstream Analysis ◽

Genome Assemblies

AbstractGenome assemblies are currently being produced at an impressive rate by consortia and individual laboratories. The low costs and increasing efficiency of sequencing technologies have opened up a whole new world of genomic biodiversity. Although these technologies generate high-quality genome assemblies, there are still genomic regions difficult to assemble, like repetitive elements and GC-rich regions (genomic “dark matter”). In this study, we compare the efficiency of currently used sequencing technologies (short/linked/long reads and proximity ligation maps) and combinations thereof in assembling genomic dark matter starting from the same sample. By adopting different de-novo assembly strategies, we were able to compare each individual draft assembly to a curated multiplatform one and identify the nature of the previously missing dark matter with a particular focus on transposable elements, multi-copy MHC genes, and GC-rich regions. Thanks to this multiplatform approach, we demonstrate the feasibility of producing a high-quality chromosome-level assembly for a non-model organism (paradise crow) for which only suboptimal samples are available. Our approach was able to reconstruct complex chromosomes like the repeat-rich W sex chromosome and several GC-rich microchromosomes. Telomere-to-telomere assemblies are not a reality yet for most organisms, but by leveraging technology choice it is possible to minimize genome assembly gaps for downstream analysis. We provide a roadmap to tailor sequencing projects around the completeness of both the coding and non-coding parts of the genomes.

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