Chapter 14 Distribution patterns of wood-decay basidiomycetes at the landscape to global scale

Author(s):  
Jacob Heilmann-Clausen ◽  
Lynne Boddy
2019 ◽  
Author(s):  
Ningbo Chen ◽  
Weiwei Fu ◽  
Jianbang Zhao ◽  
Jiafei Shen ◽  
Qiuming Chen ◽  
...  

AbstractNext-generation sequencing has yielded a vast amount of cattle genomic data for the global characterization of population genetic diversity and the identification of regions of the genome under natural and artificial selection. However, efficient storage, querying and visualization of such large datasets remain challenging. Here, we developed a comprehensive Bovine Genome Variation Database (BGVD, http://animal.nwsuaf.edu.cn/BosVar) that provides six main functionalities: Gene Search, Variation Search, Genomic Signature Search, Genome Browser, Alignment Search Tools and the Genome Coordinate Conversion Tool. The BGVD contains information on genomic variations comprising ∼60.44 M SNPs, ∼6.86 M indels, 76,634 CNV regions and signatures of selective sweeps in 432 samples from modern cattle worldwide. Users can quickly retrieve distribution patterns of these variations for 54 cattle breeds through an interactive source of breed origin map using a given gene symbol or genomic region for any of the three versions of the bovine reference genomes (ARS-UCD1.2, UMD3.1.1, and Btau 5.0.1). Signals of selection are displayed as Manhattan plots and Genome Browser tracks. To further investigate and visualize the relationships between variants and signatures of selection, the Genome Browser integrates all variations, selection data and resources from NCBI, the UCSC Genome Browser and AnimalQTLdb. Collectively, all these features make the BGVD a useful archive for in-depth data mining and analyses of cattle biology and cattle breeding on a global scale.


PLoS ONE ◽  
2021 ◽  
Vol 16 (11) ◽  
pp. e0259004
Author(s):  
Facheng Ye ◽  
G. R. Shi ◽  
Maria Aleksandra Bitner

The global distribution patterns of 14918 geo-referenced occurrences from 394 living brachiopod species were mapped in 5° grid cells, which enabled the visualization and delineation of distinct bioregions and biodiversity hotspots. Further investigation using cluster and network analyses allowed us to propose the first systematically and quantitatively recognized global bioregionalization framework for living brachiopods, consisting of five bioregions and thirteen bioprovinces. No single environmental or ecological variable is accountable for the newly proposed global bioregionalization patterns of living brachiopods. Instead, the combined effects of large-scale ocean gyres, climatic zonation as well as some geohistorical factors (e.g., formation of land bridges and geological recent closure of ancient seaways) are considered as the main drivers at the global scale. At the regional scale, however, the faunal composition, diversity and biogeographical differentiation appear to be mainly controlled by seawater temperature variation, regional ocean currents and coastal upwelling systems.


mSystems ◽  
2020 ◽  
Vol 5 (1) ◽  
Author(s):  
Flora Vincent ◽  
Chris Bowler

ABSTRACT Diatoms are a major component of phytoplankton, believed to be responsible for around 20% of the annual primary production on Earth. As abundant and ubiquitous organisms, they are known to establish biotic interactions with many other members of plankton. Through analyses of cooccurrence networks derived from the Tara Oceans expedition that take into account both biotic and abiotic factors in shaping the spatial distributions of species, we show that only 13% of diatom pairwise associations are driven by environmental conditions; the vast majority are independent of abiotic factors. In contrast to most other plankton groups, on a global scale, diatoms display a much higher proportion of negative correlations with other organisms, particularly toward potential predators and parasites, suggesting that their biogeography is constrained by top-down pressure. Genus-level analyses indicate that abundant diatoms are not necessarily the most connected and that species-specific abundance distribution patterns lead to negative associations with other organisms. In order to move forward in the biological interpretation of cooccurrence networks, an open-access extensive literature survey of diatom biotic interactions was compiled, of which 18.5% were recovered in the computed network. This result reveals the extent of what likely remains to be discovered in the field of planktonic biotic interactions, even for one of the best-known organismal groups. IMPORTANCE Diatoms are key phytoplankton in the modern ocean that are involved in numerous biotic interactions, ranging from symbiosis to predation and viral infection, which have considerable effects on global biogeochemical cycles. However, despite recent large-scale studies of plankton, we are still lacking a comprehensive picture of the diversity of diatom biotic interactions in the marine microbial community. Through the ecological interpretation of both inferred microbial association networks and available knowledge on diatom interactions compiled in an open-access database, we propose an ecosystems approach for exploring diatom interactions in the ocean.


2000 ◽  
Vol 57 (2) ◽  
pp. 291-307 ◽  
Author(s):  
T. PFEIFFER

The phylogenetic relationship of species within the Hypopterygium ‘rotulatum’ (Hedw.) Brid. s.l. complex is analysed by sequencing the trnL intron of cp DNA. Furthermore, the divergence in variable New Zealand H. ‘rotulatum’ samples is investigated along a latitudinal gradient. The presented data strongly support the delimitation of at least two distinct species within Hypopterygium ‘rotulatum’ s.l. in New Zealand, Australia and Tasmania, which correspond with the morphological species H. muelleri Hampe (possibly conspecific with H. debile Reichardt) and H. didictyon Müll. Hal., a species known from Chile. The distribution patterns of these species are discussed on a regional (New Zealand) and global scale; indicating an australasian distribution pattern of H. muelleri and a palaeoaustral pattern of H. didictyon.


2022 ◽  
Author(s):  
Amy Zanne ◽  
Habacuc Flores-Moreno ◽  
Jeff Powell ◽  
William Cornwell ◽  
James Dalling ◽  
...  

Abstract Animals, such as termites, have largely been overlooked as global-scale drivers of biogeochemical cycles1,2, despite site-specific findings3,4. Deadwood turnover, an important component of the carbon cycle, is driven by multiple decay agents. Studies have focused on temperate systems5,6, where microbes dominate decay7. Microbial decay is sensitive to temperature, typically doubling per 10°C increase (decay effective Q10 = ~2)8–10. Termites are important decayers in tropical systems3,11–13 and differ from microbes in their population dynamics, dispersal, and substrate discovery14–16, meaning their climate sensitivities also differ. Using a network of 133 sites spanning 6 continents, we report the first global field-based quantification of temperature and precipitation sensitivities for termites and microbes, providing novel understandings of their response to changing climates. Temperature sensitivity of microbial decay was within previous estimates. Termite discovery and consumption were both much more sensitive to temperature (decay effective Q10 = 6.53), leading to striking differences in deadwood turnover in areas with and without termites. Termite impacts were greatest in tropical seasonal forests and savannas and subtropical deserts. With tropicalization17 (i.e., warming shifts to a tropical climate), the termite contribution to global wood decay will increase as more of the earth’s surface becomes accessible to termites.


2013 ◽  
Vol 280 (1762) ◽  
pp. 20130680 ◽  
Author(s):  
Sara D. Leonhardt ◽  
Claus Rasmussen ◽  
Thomas Schmitt

Chemical compounds are highly important in the ecology of animals. In social insects, compounds on the body surface represent a particularly interesting trait, because they comprise different compound classes that are involved in different functions, such as communication, recognition and protection, all of which can be differentially affected by evolutionary processes. Here, we investigate the widely unknown and possibly antagonistic influence of phylogenetic and environmental factors on the composition of the cuticular chemistry of tropical stingless bees. We chose stingless bees because some species are unique in expressing not only self-produced compounds, but also compounds that are taken up from the environment. By relating the cuticular chemistry of 40 bee species from all over the world to their molecular phylogeny and geographical occurrence, we found that distribution patterns of different groups of compounds were differentially affected by genetic relatedness and biogeography. The ability to acquire environmental compounds was, for example, highly correlated with the bees' phylogeny and predominated in evolutionarily derived species. Owing to the presence of environmentally derived compounds, those species further expressed a higher chemical and thus functional diversity. In Old World species, chemical similarity of both environmentally derived and self-produced compounds was particularly high among sympatric species, even when they were less related to each other than to allopatric species, revealing a strong environmental effect even on largely genetically determined compounds. Thus, our findings do not only reveal an unexpectedly strong influence of the environment on the cuticular chemistry of stingless bees, but also demonstrate that even within one morphological trait (an insect's cuticular profile), different components (compound classes) can be differentially affected by different drivers (relatedness and biogeography), depending on the functional context.


2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Juan José Pierella Karlusich ◽  
Eric Pelletier ◽  
Fabien Lombard ◽  
Madeline Carsique ◽  
Etienne Dvorak ◽  
...  

AbstractNitrogen fixation has a critical role in marine primary production, yet our understanding of marine nitrogen-fixers (diazotrophs) is hindered by limited observations. Here, we report a quantitative image analysis pipeline combined with mapping of molecular markers for mining >2,000,000 images and >1300 metagenomes from surface, deep chlorophyll maximum and mesopelagic seawater samples across 6 size fractions (<0.2–2000 μm). We use this approach to characterise the diversity, abundance, biovolume and distribution of symbiotic, colony-forming and particle-associated diazotrophs at a global scale. We show that imaging and PCR-free molecular data are congruent. Sequence reads indicate diazotrophs are detected from the ultrasmall bacterioplankton (<0.2 μm) to mesoplankton (180–2000 μm) communities, while images predict numerous symbiotic and colony-forming diazotrophs (>20 µm). Using imaging and molecular data, we estimate that polyploidy can substantially affect gene abundances of symbiotic versus colony-forming diazotrophs. Our results support the canonical view that larger diazotrophs (>10 μm) dominate the tropical belts, while unicellular cyanobacterial and non-cyanobacterial diazotrophs are globally distributed in surface and mesopelagic layers. We describe co-occurring diazotrophic lineages of different lifestyles and identify high-density regions of diazotrophs in the global ocean. Overall, we provide an update of marine diazotroph biogeographical diversity and present a new bioimaging-bioinformatic workflow.


2019 ◽  
Author(s):  
Flora Vincent ◽  
Chris Bowler

ABSTRACTDiatoms are a major component of phytoplankton, believed to be responsible for around 20% of the annual primary production on Earth. As abundant and ubiquitous organisms, they are known to establish biotic interactions with many other members of the plankton. Through analysis of co-occurrence networks derived from the Tara Oceans expedition that take into account the importance of both biotic and abiotic factors in shaping the spatial distributions of species, we show that only 13% of diatom pairwise associations are driven by environmental conditions, whereas the vast majority are independent of abiotic factors. In contrast to most other plankton groups, at a global scale diatoms display a much higher proportion of negative correlations with other organisms, particularly towards potential predators and parasites, suggesting that their biogeography is constrained by top down pressure. Genus level analyses indicate that abundant diatoms are not necessarily the most connected, and that species-specific abundance distribution patterns lead to negative associations with other organisms. In order to move forward in the biological interpretation of co-occurrence networks, an open access extensive literature survey of diatom biotic interactions was compiled, of which 18.5% were recovered in the computed network. This result reveals the extent of what likely remains to be discovered in the field of planktonic biotic interactions, even for one of the best known organismal groups.ImportanceDiatoms are key phytoplankton in the modern ocean involved in numerous biotic interactions, ranging from symbiosis to predation and viral infection, which have considerable effects on global biogeochemical cycles. However, despite recent large-scale studies of plankton, we are still lacking a comprehensive picture of the diversity of diatom biotic interactions in the marine microbial community. Through the ecological interpretation of both inferred microbial association networks and available knowledge on diatom interactions compiled in an open access database, we propose an eco-systems level understanding of diatom interactions in the ocean.


2010 ◽  
Vol 108 (1) ◽  
pp. 220-225 ◽  
Author(s):  
Núria Roura-Pascual ◽  
Cang Hui ◽  
Takayoshi Ikeda ◽  
Gwénaël Leday ◽  
David M. Richardson ◽  
...  

Because invasive species threaten the integrity of natural ecosystems, a major goal in ecology is to develop predictive models to determine which species may become widespread and where they may invade. Indeed, considerable progress has been made in understanding the factors that influence the local pattern of spread for specific invaders and the factors that are correlated with the number of introduced species that have become established in a given region. However, few studies have examined the relative importance of multiple drivers of invasion success for widespread species at global scales. Here, we use a dataset of >5,000 presence/absence records to examine the interplay between climatic suitability, biotic resistance by native taxa, human-aided dispersal, and human modification of habitats, in shaping the distribution of one of the world's most notorious invasive species, the Argentine ant (Linepithema humile). Climatic suitability and the extent of human modification of habitats are primarily responsible for the distribution of this global invader. However, we also found some evidence for biotic resistance by native communities. Somewhat surprisingly, and despite the often cited importance of propagule pressure as a crucial driver of invasions, metrics of the magnitude of international traded commodities among countries were not related to global distribution patterns. Together, our analyses on the global-scale distribution of this invasive species provide strong evidence for the interplay of biotic and abiotic determinants of spread and also highlight the challenges of limiting the spread and subsequent impact of highly invasive species.


2019 ◽  
Author(s):  
Smruthi Karthikeyan ◽  
Luis M. Rodriguez-R ◽  
Patrick Heritier-Robbins ◽  
Janet K. Hatt ◽  
Markus Huettel ◽  
...  

ABSTRACTIndigenous microbial communities ultimately control the fate of petroleum hydrocarbons (PHCs) that enters the natural environment through natural seeps or accidental oil spills, but the interactions among microbes and with their chemical environment during oil biodegradation are highly complex and poorly understood. Genome-resolved metagenomics have the potential to help in unraveling these complex interactions. However, the lack of a comprehensive database that integrates existing genomic/metagenomic data from oiled environments with physicochemical parameters known to regulate the fate of PHCs currently limits data analysis and interpretations. Here, we present a curated, comprehensive, and searchable database that documents microbial populations in oiled ecosystems on a global scale, along with underlying physicochemical data, geocoded via GIS to reveal geographic distribution patterns of the populations. Analysis of the ~2,000 metagenome-assembled genomes (MAGs) available in the database revealed strong ecological niche specialization within habitats e.g., specialization to coastal sediments vs. water-column vs. deep-sea sediments. Over 95% of the recovered MAGs represented novel and uncultured species underscoring the limited representation of cultured organisms from oil-contaminated and oil reservoir ecosystems. The majority of MAGs linked to oiled ecosystems are members of the rare biosphere in non-oiled samples, except for the Gulf of Mexico (GoM) which appears to be primed for oil biodegradation. GROS should facilitate future work toward a more predictive understanding of the microbial taxa and their activities that control the fate of oil spills as well as serve as a model approach for building similar resources for additional environmental processes and omic data of interest.


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