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Taxonomy and phylogeny of poroid Hymenochaetaceae based on the most comprehensive phylogenetic analyses are presented. A phylogeny based on a combined dataset of ITS and nLSU sequences for accepted genera of Hymenochaetaceae was analyzed and multigene phylogenies for most species of ten large genera including Clotricia, Fomitiporella, Fomitiporia, Fulvifomes, Fuscoporia, Inonotus, Phylloporia, Porodaedalea, Sanghuangporus and Tropicoporus, were carried out. Based on samples from 37 countries of five continents, seven new genera, Meganotus, Neophellinus, Nothonotus, Pachynotus, Perenninotus, Pseudophylloporia and Rigidonotus, are introduced, 37 new species, Coltricia tibetica, Fomitiporella crassa, F. queenslandica, Fomitiporia eucalypti, F. gatesii, F. ovoidospora, Fulvifomes azonatus, F. caligoporus, F. costaricense, F. floridanus, F. jouzaii, F. nakasoneae, F. subindicus, Fuscoporia sinuosa, F. submurina, Inonotus subradiatus, I. vietnamensis, Neomensularia castanopsidis, Pachynotus punctatus, Phellinus cuspidatus, P. subellipsoideus, Phylloporia minutissima, P. tabernaemontanae, Porodaedalea occidentiamericana, P. orientoamericana, P. qilianensis, P. schrenkianae, Pseudophylloporia australiana, Sanghuangporus australianus, S. lagerstroemiae, Tropicoporus angustisulcatus, T. hainanicus, T. lineatus, T. minus, T. ravidus, T. substratificans and T. tenuis, are described, and 108 new combinations are proposed. In addition, one illegitimate name and two invalid names are renamed. The taxonomic relevance and limits of the new taxa are discussed. Photos and illustrations for 37 new species are presented, and a full description for each new species is given. Eventually, this study recognizes 672 species in 34 genera and provides a modern treatment of the poroid Hymenochaetaceae in the world. A key to the accepted poroid genera of Hymenochaetaceae is provided, and identification keys to the accepted species of 32 poroid genera worldwide are given. A synopsis description of each species is included in these keys.

The objective of this paper is to provide a taxonomic appraisal of the phytoseiids mainly from Apulia, Italy, through the examination of 1055 specimens collected in the areas of that district. Repo...

It is now indisputable that plastics are ubiquitous and problematic in ecosystems globally. Many suggestions have been made about the role that biofilms colonizing plastics in the environment—termed the “Plastisphere”—may play in the transportation and ecological impact of these plastics. By collecting and re-analyzing all raw 16S rRNA gene sequencing and metadata from 2,229 samples within 35 studies, we have performed the first meta-analysis of the Plastisphere in marine, freshwater, other aquatic (e.g., brackish or aquaculture) and terrestrial environments. We show that random forest models can be trained to differentiate between groupings of environmental factors as well as aspects of study design, but—crucially—also between plastics when compared with control biofilms and between different plastic types and community successional stages. Our meta-analysis confirms that potentially biodegrading Plastisphere members, the hydrocarbonoclastic Oceanospirillales and Alteromonadales are consistently more abundant in plastic than control biofilm samples across multiple studies and environments. This indicates the predilection of these organisms for plastics and confirms the urgent need for their ability to biodegrade plastics to be comprehensively tested. We also identified key knowledge gaps that should be addressed by future studies.

Broad-scale assessment of biodiversity is needed for detection of future changes across substantial regions of the Arctic. Presently, there are large data and information gaps in species composition and richness of the freshwater planktonic and meiobenthos communities of the Russian Arctic. Analysis of these data is very important for identifying the spatial distribution and temporal changes in species richness and diversity of rotifers, cladocerans, and copepods in the continental Russian Arctic. We investigated biogeographic patterns of freshwater plankton and meiobenthos fromc. 67 degrees to 73 degrees N by analysing data over the period 1960-2017. These data include information on the composition of rotifers, cladocerans, and copepods obtained from planktonic and meiobenthic samples, as well as from subfossil remains in bottom sediments of seven regions from the Kola Peninsula in the west, to the Indigirka River Basin (east Siberia) in the east. Total richness included 175 species comprised of 49 rotifer genera, 81 species from 40 cladoceran genera, and 101 species from 42 genera of calanoid, cyclopoid, and harpacticoid copepods. Longitudinal trends in rotifer and micro-crustacean diversity were revealed by change in species composition from Europe to eastern Siberia. The most common and widespread species were 19 ubiquitous taxa that includedKellicottia longispina(Rotifera),Chydorus sphaericuss. lat. (Cladocera),Heterocope borealis,Acanthocyclops vernalis, andMoraria duthiei(Copepoda). The highest number of rare species was recorded in the well-studied region of the Bolshezemelskaya tundra and in the Putorana Plateau. The total number of copepod and rotifer species in both Arctic lakes and ponds tended to increase with latitude. Relative species richness of copepods was positively associated with waterbody area, elevation, and precipitation, while relative species richness of cladocerans was positively related to temperature. This result is consistent with known thermophilic characteristics of cladocerans and the cold tolerance properties of copepods, with the former being dominant in shallow, warmer waterbodies of some western regions, and the latter being dominant in large cold lakes and waterbodies of eastern regions. Rotifers showed a negative association with these factors. Alpha- and beta-diversity of zooplankton in the Russian Arctic were strongly related to waterbody type. Lake zooplankton communities were more diverse than those in pond and pool systems. Moreover, the highest beta-diversity values were observed in regions that showed a greater breadth in latitude and highly heterogeneous environmental conditions and waterbody types (Bolshezemelskaya tundra and Putorana Plateau). Redistribution of freshwater micro-fauna caused by human activities occurred in the 1990s and 2000s. As a result of climate warming, a few cladoceran species appear to have extended their range northward. Nevertheless, the rotifer and micro-crustacean fauna composition and diversity of the majority of Arctic regions generally remain temporally conservative, and spatial differences in composition and species richness are chiefly associated with the differences between the warmer European and colder east Siberian climates.

Computational analysis of biosynthetic gene clusters (BGCs) has revolutionized natural product discovery by enabling the rapid investigation of secondary metabolic potential within microbial genome sequences. Grouping homologous BGCs into Gene Cluster Families (GCFs) facilitates mapping their architectural and taxonomic diversity and provides insights into the novelty of putative BGCs, through dereplication with BGCs of known function. While multiple databases exist for exploring BGCs from publicly available data, no public resources exist that focus on GCF relationships. Here, we present BiG-FAM, a database of 29,955 GCFs capturing the global diversity of 1,225,071 BGCs predicted from 209,206 publicly available microbial genomes and metagenome-assembled genomes (MAGs). The database offers rich functionalities, such as multi-criterion GCF searches, direct links to BGC databases such as antiSMASH-DB, and rapid GCF annotation of user-supplied BGCs from antiSMASH results. BiG-FAM can be accessed online at https://bigfam.bioinformatics.nl., Graphical Abstract Graphical AbstractConstructed based on a large-scale homology analysis of 1.2 million biosynthetic gene clusters, BiG-FAM provides a platform to explore their genomic diversity and to discover their relationships to newly sequenced ones.

Bacillus anthracis, the causative agent of anthrax, is a considerable global health threat affecting wildlife, livestock, and the general public. In this study whole-genome sequence analysis of over 350B. anthracisisolates was used to establish a new high-resolution global genotyping framework that is both biogeographically informative, and compatible with multiple genomic assays. The data presented in this study shed new light on the diverse global dissemination of this species and indicate that many lineages may be uniquely suited to the geographic regions in which they are found. In addition, we demonstrate that plasmid genomic structure for this species is largely consistent with chromosomal population structure, suggesting vertical inheritance in this bacterium has contributed to its evolutionary persistence. This classification methodology is the first based on population genomic structure for this species and has potential use for local and broader institutions seeking to understand both disease outbreak origins and recent introductions. In addition, we provide access to a newly developed genotyping script as well as the full whole genome sequence analyses output for this study, allowing future studies to rapidly employ and append their data in the context of this global collection. This framework may act as a powerful tool for public health agencies, wildlife disease laboratories, and researchers seeking to utilize and expand this classification scheme for further investigations intoB. anthracisevolution.

A leading strategy for developing a prophylactic HIV-1 vaccine is the elicitation of antibodies that can neutralize a large fraction of circulating HIV-1 variants. However, a major challenge that has limited the effectiveness of current vaccine candidates is the extensive global diversity of the HIV-1 envelope protein (Env), the sole target for HIV-neutralizing antibodies. To address this challenge, various strategies incorporating Env diversity into the vaccine formulation have been proposed. Here, we assessed the potential of two such strategies that utilize a nanoparticle-based vaccine platform to elicit broadly neutralizing antibody responses. The nanoparticle immunogens developed here consisted of different formulations of Envs from strains BG505 (clade A) and CZA97 (clade C), attached to the N-termini of bacterial ferritin. Single—antigen nanoparticle cocktails, as well as mosaic nanoparticles bearing both Env trimers, elicited high antibody titers in mice and guinea pigs. Furthermore, serum from guinea pigs immunized with nanoparticle immunogens achieved autologous, and in some cases heterologous, tier 2 neutralization, although significant differences between mosaic and single—antigen nanoparticles were not observed. These results provide insights into the ability of different vaccine strategies for incorporating Env sequence diversity to elicit neutralizing antibodies, with implications for the development of broadly protective HIV-1 vaccines.

The University of Pretoria, members of the Tree Protection Co-operative Program (TPCP), South Africa, and USDA Forest Service International Programs.

Insects collected in the light traps over a period of two years in the agroecosystems of GKVK campus represented 13 of the 21 orders of India. Among these orders collected, five orders viz., Coleoptera, Hemiptera, Hymenoptera, Lepidoptera and Diptera were the most predominant. We compared the relative proportions of these five speciose orders with those expected at national and at global levels to test if the light traps collections can be used as a surrogates of national and global diversity of these groups. We found that while orders Coleopteran and Hemipteran insects are over represented, those of Lepidoptera and Hymenoptera are under-represented. We discuss the possible reasons for these differentia representation.

With the biodiversity crisis continuing unchecked, we need to establish levels and drivers of extinction risk, and reassessments over time, to effectively allocate conservation resources and track progress towards global conservation targets. Given that threat appears particularly high in freshwaters, we assessed the extinction risk of 1428 randomly selected freshwater molluscs using the IUCN Red List Categories and Criteria, as part of the Sampled Red List Index project. We show that close to one-third of species in our sample are estimated to be threatened with extinction, with highest levels of threat in the Nearctic, Palearctic and Australasia and among gastropods. Threat levels were higher in lotic than lentic systems. Pollution (chemical and physical) and the modification of natural systems (e.g. through damming and water abstraction) were the most frequently reported threats to freshwater molluscs, with some regional variation. Given that we found little spatial congruence between species richness patterns of freshwater molluscs and other freshwater taxa, apart from crayfish, new additional conservation priority areas emerged from our study. We discuss the implications of our findings for freshwater mollusc conservation, the adequacy of a sampled approach and important next steps to estimate trends in freshwater mollusc extinction risk over time., The authors would like to acknowledge the Esme ́e Fairbairn Foundation (NIDR and MB) and the Rufford Foundation (MB) for their generous support. MV is supported by the Russian Fund for Basic Research (project No. 19-04-00270).

Although one quarter of the species of plants and vertebrates are threatened with extinction, little is known about how the potential effect of extinctions on the global diversity of ecological strategies. Using trait and phylogenetic information for more than 75,000 species of plants, mammals, birds, reptiles, amphibians and freshwater fishes, we characterized the global functional spectra of each of these groups. Mapping of extinction risk within these spectra revealed that larger species with slower pace of life are universally threatened. Simulated potential extinctions revealed extensive internal reorganizations in the global functional spectra, which are particularly severe for mammals and amphibians. Considering the disproportionate importance of the largest species for ecological processes, our results emphasize the importance of actions to prevent the extinction of the megabiota.

A new genus and new species of caprellid, Parapseudaeginella n. gen., and Parapseudaeginella australiensis n. sp., is described from shallow water of Ningaloo Reef, south of Tantabiddy, reef front, Western Australia. The new genus is very similar to Pseudaeginella Mayer, 1890, but can be easily distinguished by the pereonites 6 and 7 being clearly fused (separated in Pseudaeginella) and by the absence of a pair of proximal grasping spines on the propodus of pereopods 5-7 (present in Pseudaeginella). The new species is characterised by acute dorsal projections on head, pereonite 1 and 2, and acute lateral projections near the coxa of gnathopod 2 in males. The new taxon has probably been overlooked in the past due to its tiny size. Further efforts to sample and describe the smaller caprellids is needed to fully understand the global diversity and relationships of caprellids.

While the emerging amphibian disease chytridiomycosis is causing dramatic and ongoing biodiversity losses worldwide, sustainable strategies to mitigate this global threat to amphibians are currently missing. We here propose a conceptual framework for a novel biological mitigation strategy based on the increasing evidence that naturally occurring micropredators, such as protists, rotifers and crustaceans, are capable of using zoospores of the chytrid pathogens Batrachochytrium dendrobatidis (Bd) and Batrachochytrium salamandrivorans (Bsal) as a food source under controlled laboratory conditions. Pathogen predation may serve as a cost-efficient way to prevent chytridiomycosis outbreaks under natural conditions by reducing zoospore densities and thereby infection loads. This predator-pathogen relationship is not an isolated interaction, but is embedded in the aquatic food web structure that interacts with a wide range of environmental factors. Amphibian breeding ponds are increasingly associated to agricultural landscapes due to ongoing land use occupancy for food production, exposing these water bodies to a variety of environmental stressors such as agrochemical pollution, nutrient enrichment and cattle trampling. Environmental stressors may affect the composition and abundance of aquatic communities, while they can also exert sublethal effects that may reduce the zoospore removal efficiency of micropredators. By carefully controlling environmental stressors, trophic interactions may be steered to optimize chytrid predation with the aim of reducing zoospore densities to such extent that hosts and pathogens can sustainably coexist. We present a scientific outline of this novel concept and provide a framework for ongoing research to develop a complete mitigation strategy against chytridiomycosis based on such food web control.

Peanut allergy is one of the serious health concern and affects more than 1% of the world’s population mainly in Americas, Australia, and Europe. Peanut allergy is sometimes life-threatening and adversely affect the life quality of allergic individuals and their families. Consumption of hypoallergen peanuts is the best solution, however, not much effort has been made in this direction for identifying or developing hypoallergen peanut varieties. A highly diverse peanut germplasm panel was phenotyped using a recently developed monoclonal antibody-based ELISA protocol to quantify five major allergens. Results revealed a wide phenotypic variation for all the five allergens studied i.e., Ara h 1 (4–36,833 µg/g), Ara h 2 (41–77,041 µg/g), Ara h 3 (22–106,765 µg/g), Ara h 6 (829–103,892 µg/g), and Ara h 8 (0.01–70.12 µg/g). The hypoallergen peanut genotypes with low levels of allergen proteins for Ara h 1 (4 µg/g), Ara h 2 (41 µg/g), Ara h 3 (22 µg/g), Ara h 6 (829 µg/g), and Ara h 8 (0.01 µg/g) have paved the way for their use in breeding and genomics studies. In addition, these hypoallergen peanut genotypes are available for use in cultivation and industry, thus opened up new vistas for fighting against peanut allergy problem across the world.

Seoul virus (SEOV) poses a worldwide public health threat. This virus, which is harbored by Rattus norvegicus and R. rattus rats, is the causative agent of hemorrhagic fever with renal syndrome (HFRS) in humans, which has been reported in Asia, Europe, the Americas, and Africa. Defining SEOV genome sequences plays a critical role in development of preventive and therapeutic strategies against the unique worldwide hantavirus. We applied multiplex PCR–based next-generation sequencing to obtain SEOV genome sequences from clinical and reservoir host specimens. Epidemiologic surveillance of R. norvegicus rats in South Korea during 2000–2016 demonstrated that the serologic prevalence of enzootic SEOV infections was not significant on the basis of sex, weight (age), and season. Viral loads of SEOV in rats showed wide dissemination in tissues and dynamic circulation among populations. Phylogenetic analyses showed the global diversity of SEOV and possible genomic configuration of genetic exchanges.

In this work, we discuss the characterization and diversity analysis of 354 natural products (NPs) from Panama, systematically analyzed for the first time. The in-house database was compared to NPs from Brazil, compounds from Traditional Chinese Medicine, natural and semisynthetic collections used in high-throughput screening, and compounds from ChEMBL. An analysis of the "global diversity" was conducted using molecular properties of pharmaceutical interest, three molecular fingerprints of different design, molecular scaffolds, and molecular complexity. The global diversity was visualized using consensus diversity plots that revealed that the secondary metabolites in the Panamanian flora have a large scaffold diversity as compared to other composite databases and also have several unique scaffolds. The large scaffold diversity is in agreement with the broad range of biological activities that this collection of NPs from Panama has shown. This study also provided further quantitative evidence of the large structural complexity of NPs. The results obtained in this study support that NPs from Panama are promising candidates to identify selective molecules and are suitable sources of compounds for virtual screening campaigns.

How many parasites are there on Earth? Here, we use helminth parasites to highlight how little is known about parasite diversity, and how insufficient our current approach will be to describe the full scope of life on Earth. Using the largest database of host-parasite associations and one of the world’s largest parasite collections, we estimate a global total of roughly 100,000 to 350,000 species of helminth endoparasites of vertebrates, of which 85% to 95% are unknown to science. The parasites of amphibians and reptiles remain the most poorly described, but the majority of undescribed species are likely parasites of birds and bony fish. Missing species are disproportionately likely to be smaller parasites of smaller hosts in undersampled countries–species that have mostly been understudied over the last century. At current rates, it would take centuries to comprehensively sample, collect, and name vertebrate helminths. While some have suggested that macroecology can work around existing data limitations, we argue that patterns described from a small, biased sample of diversity aren’t necessarily reliable, especially as host-parasite networks are increasingly altered by global change. In the spirit of moonshots like the Human Genome Project and the Global Virome Project, we propose a global effort to transform parasitology and describe as much of global parasite diversity as possible. Significance Statement Roughly one in ten parasitic worms has been described by taxonomists, while the majority of species remain unknown to science. Data deficiencies are especially severe for some major groups (reptiles and amphibians) and regions (Africa and Southeast Asia). Decades of work have resulted in much larger datasets on host-parasite interactions, but their utility is limited by major data gaps. At current rates, those gaps could take hundreds of years to be filled. We propose that a globally-coordinated project could dramatically speed up this process, playing a critical role in tracking the disease impacts of global change. If successful, it could be a transformative opportunity for multilateral capacity building, and a path towards more equitable research benefit sharing.

Yellow fever virus (YFV) represents a re-emerging zoonotic pathogen, transmitted by mosquito vectors to humans from primate reservoirs. Sporadic outbreaks of YFV occur in endemic tropical regions, causing a viral hemorrhagic fever (VHF) associated with high mortality rates. Despite a highly effective vaccine, no antiviral treatments currently exist. Therefore, YFV represents a neglected tropical disease and is chronically understudied, with many aspects of YFV biology incompletely defined including host range, host–virus interactions and correlates of host immunity and pathogenicity. In this article, we review the current state of YFV research, focusing on the viral lifecycle, host responses to infection, species tropism and the success and associated limitations of the YFV-17D vaccine. In addition, we highlight the current lack of available treatments and use publicly available sequence and structural data to assess global patterns of YFV sequence diversity and identify potential drug targets. Finally, we discuss how technological advances, including real-time epidemiological monitoring of outbreaks using next-generation sequencing and CRISPR/Cas9 modification of vector species, could be utilized in future battles against this re-emerging pathogen which continues to cause devastating disease.

The changing trends in global diversity emphasize the need for skin type-specific expertize. This chapter explores structural variations in skin of color, from clinically apparent to microscopic differences, and examines how these contribute to the unique photobiological response exemplified in ethnic skin. Herein, we discuss the acute and chronic effects of the solar spectrum on skin of color, from ultraviolet and visible light to infrared radiation. In light of these structural and functional differences, we also review special considerations in the classification and management of photoaging in this population.

Review: 5 páginas, 1 figura, Two strains of Mycobacterium tuberculosis complex can be separated as much as 2500 single nucleotide differences (Coscolla and Gagneux, 2014). In that limited amount of diversity, we find an astonishing range of clinical, epidemiological and biological phenotypes. The most striking is the strong host preferences depending on the infecting strain while more subtle differences can be found looking at different human tuberculosis isolates. Those subtle differences are the most difficult to spot given that analysis methods for so little diversity are limited and phenotypes like virulence are difficult to define and measure. Recent genomics advances allow to study the pathogen diversity at a resolution not available before from comparative species level, to global diversity to transmission in local settings. Here, we will review some of these recent results to highlight how population genomics approaches can aid not only to understand how MTBC evolved but also to identify relevant biomedical targets., IC group is currently funded by projects of the European ResearchCouncil (ERC) research grant 638553-TB-ACCELERATE, Ministerio deEconomía y Competitividad (Spanish Government) research grant SAF2016-77346-R and Consellería de Educació, Investigació, Cultura iEsport (Valencian government) research grant AICO/2018/113. ACO isrecipient of a FPU fellowship from Ministerio de Ciencia, Innovación y Universidades FPU13/00913 (Spanish Government).

The unprecedented diversifications in the fossil record of the early Palaeozoic (541–419 million years ago) increased both within-sample (α) and global (γ) diversity, generating considerable ecological complexity. Faunal difference (β diversity), including spatial heterogeneity, is thought to have played a major role in early Palaeozoic marine diversification, although α diversity is the major determinant of γ diversity through the Phanerozoic. Drivers for this Phanerozoic shift from β to α diversity are not yet resolved. Here, we evaluate the impacts of environmental and faunal heterogeneity on diversity patterns using a global spatial grid. We present early Palaeozoic genus-level α, β and γ diversity curves for molluscs, brachiopods, trilobites and echinoderms and compare them with measures of spatial lithological heterogeneity, which is our proxy for environmental heterogeneity. We find that α and β diversity are associated with increased lithological heterogeneity, and that β diversity declines over time while α increases. We suggest that the enhanced dispersal of marine taxa from the Middle Ordovician onwards facilitated increases in α diversity by encouraging the occupation of narrow niches and increasing the prevalence of transient species, simultaneously reducing spatial β diversity. This may have contributed to a shift from β to α diversity as the major determinant of γ diversity increase over this critical evolutionary interval. The authors suggest that increased dispersal of marine animals from the Middle Ordovician onwards enhanced α diversity, providing a possible mechanism for the shift from β to α diversity as the major component of global diversity.

Botryosphaeriaceae-related diseases occur worldwide in a wide variety of plant hosts. The number of studies targeting the distribution, diversity, ecology, and pathogenicity of Botryosphaeriaceae species are consistently increasing. However, with the lack of consistency in species delimitation, the name of hosts, and the locations of studies, it is almost impossible to quantify the presence of these species worldwide, or the number of different host–fungus interactions that occur. In this review, we collected and organized Botryosphaeriaceae occurrences in a single cured dataset, allowing us to obtain for the first time a complete perspective on species’ global diversity, dispersion, host association, ecological niches, pathogenicity, communication efficiency of new occurrences, and new host–fungus associations. This dataset is freely available through an interactive and online application. The current release (version 1.0) contains 14,405 cured isolates and 2989 literature references of 12,121 different host–fungus interactions with 1692 different plant species from 149 countries.

In our ongoing study of the genus Cladonia, we have encountered several specimens that have proved to represent undescribed species. Four of them are described here as new. Cladonia camerunensis (Cameroon) resembles C. didyma (Fée) Vain., but the former has a coarsely granular surface and a melanotic podetial base; C. compressa (Bolivia) is distinguished by a dominant primary thallus and deeply divided and phyllopodiate podetia; C. longisquama (Seychelles) has well-developed squamules and contains barbatic acid; C. vescula (Bolivia, Peru) differs from C. peziziformis (With.) J. Laundon by an ecorticate podetial surface and the production of homosekikaic acid. The names C. aspera Ahti & Kashiw. and C. crinita (Delise ex Pers.) Ahti are shown to be illegitimate later homonyms and are replaced by the names C. asperula and C. perfoliata, respectively. The neglected name C. botryoides (Tuck.) Vain. is shown to be a synonym of C. squamosa. Another overlooked name, C. crinita Bertol., is shown to be the earliest name for C. evansii, but we propose to retain the latter through conservation. The typification of C. beaumontii Tuck. is amended. Cladonia conspicua is reinstated on the basis of new data. New range extensions in Canada and the United States are given for the poorly documented species C. oricola.

This research was funded by the Netherlands Organisation for Scientific Research VENI grant 863.13.003 (to A.L.P.), NASA Biodiversity grant NNX11AP72G and NSF grants NSF DBI 1262600, DBI 0960550 and DEB 1026764 (to W.J.), the Oxford Clarendon Fund and US-UK Fulbright Commission (to C.S.), and the John Fell Fund and NERC grant NE/I028068/1 (to J.A.T.). Ecological communities are assembled from the overlapping of species in geographic space, but the mechanisms facilitating or limiting such overlaps are difficult to resolve. Here, we combine phylogenetic, morphological and environmental data to model how multiple processes regulate the origin and maintenance of geographic range overlap across 1,115 pairs of avian sister species globally. We show that coexistence cannot be adequately predicted by either dispersal-assembly (that is, biogeographic) models or niche-assembly models alone. Instead, our results overwhelmingly support an integrated model with different assembly processes dominating at different stages of coexistence. The initial attainment of narrow geographic overlap is dictated by intrinsic dispersal ability and the time available for dispersal, whereas wider coexistence is largely dependent on niche availability, increasing with ecosystem productivity and divergence in niche-related traits, and apparently declining as communities become saturated with species. Furthermore, although coexistence of any individual pair of species is highly stochastic, we find that integrating assembly processes allows broad variation in the incidence and extent of coexistence to be predicted with reasonable accuracy. Our findings demonstrate how phylogenetic data coupled with environmental factors and functional traits can begin to clarify the multi-layered processes shaping the distribution of biodiversity at large spatial scales. Postprint

The integration of proteomics into precision oncology presents opportunities that may transform the molecular analysis of cancer and accelerate basic and clinical cancer research. This Commentary discusses the importance of international collaboration and data sharing inspired by the Cancer Moonshot to accelerate the progress of multi-omic precision medicine–an approach that addresses the global diversity of people and of cancers.

The genus Ptilophora currently includes 16 species occurring mostly in subtidal habitats of the Indo-Pacific Ocean, but its global diversity and biogeography are poorly understood. We analyzed mitochondrial cox1, plastid rbcL and plastid psbA sequences from specimens collected in southern Madagascar during the 2010 Atimo Vatae expedition and studied their morphologies. Both morphological and molecular data sets demonstrated the presence of five species in southern Madagascar: Ptilophora hildebrandtii, P. pterocladioides, and three new species described here, P. aureolusa, P. malagasya, and P. spongiophila. Ptilophora aureolusa is distinguished by its compound pinnae with uniformly spaced pinnules. Ptilophora malagasya has an indistinct midrib and irregularly spaced pinnules. Ptilophora spongiophila, heavily coated with sponges, has cylindrical to flattened main axes, lateral and surface proliferations, and spatulate tetrasporangial sori. The species of Ptilophora found in Madagascar are endemic, except P. hildebrandtii, which also occurs in eastern Africa. Ptilophora comprises four phylogenetic groups that map to eastern Australia, Japan, western Australia/Southeast Asia/Madagascar/eastern Africa, and Madagascar/eastern Africa/Aegean Sea. Biogeographical analysis revealed that the ancestor of Ptilophora originated in Australia, but most of the species radiated from Madagascar.

Rodents represent 42% of the world's mammalian biodiversity encompassing 2,277 species populating every continent (except Antarctica) and are reservoir hosts for a wide diversity of disease agents. Thus, knowing the identity, diversity, host-pathogen relationships, and geographic distribution of rodent-borne zoonotic pathogens, is essential for predicting and mitigating zoonotic disease outbreaks. Hantaviruses are hosted by numerous rodent reservoirs. However, the diversity of rodents harboring hantaviruses is likely unknown because research is biased toward specific reservoir hosts and viruses. An up-to-date, systematic review covering all known rodent hosts is lacking. Herein, we document gaps in our knowledge of the diversity and distribution of rodent species that host hantaviruses. Of the currently recognized 681 cricetid, 730 murid, 61 nesomyid, and 278 sciurid species, we determined that 11.3, 2.1, 1.6, and 1.1%, respectively, have known associations with hantaviruses. The diversity of hantaviruses hosted by rodents and their distribution among host species supports a reassessment of the paradigm that each virus is associated with a single-host species. We examine these host-virus associations on a global taxonomic and geographical scale with emphasis on the rodent host diversity and distribution. Previous reviews have been centered on the viruses and not the mammalian hosts. Thus, we provide a perspective not previously addressed.

We introduce this Branchiopoda Special Issue of the Journal of Crustacean Biology, providing a brief outline of the 13 research papers presented at the 8 th International Crustacean Congress in Frankfurt, Germany, August 2014. We also discuss the current status and direction of research on the large branchiopod crustaceans.

Competitive varieties of covered and naked oats resistant and/or tolerant to region-specific ecological factors limiting their productivity have been developed by selection and hybridization techniques using the germplasm from VIR’s oat collection. Among them there are oats varieties widely cultivated in Russia, such as Argamak, Krechet and Gunter, and new varieties Sapsan and Avatar combining high productivity (8-11.2 t/ha) with resistanceto biotic and abiotic stressors. From 250 up to 350 oat samples are evaluated annually in parallel collection nurseries on two cultivated (Kirov and Falenki) and one naturally acidified (Falenki, 13.45-17.23 mg-equiv. Al 3 + /100 g of soil) plots of soddy-podzolic soils. It is shown that expanding the spectrum of recombinations requires development of mixedhybrids on the basis of covered and naked genotypes. Thus, using covered and naked source materials in crossings, the naked oat cultivar Persheron has been released and included in the State Register of Breeding Achievements of the Russian Federation since 2013; and the covered oat cultivar Medved with high grain quality has been submitted to the State Crop Variety Trials.

Many drug discovery projects rely on commercial compounds to discover active leads. However, current commercial libraries, with mostly synthetic compounds, access a small fraction of the possible chemical diversity. Natural products, in contrast, possess a vast structural diversity and have proven to be an outstanding source of new drugs. Several chemoinformatic analyses of natural products have demonstrated their diversity and structural complexity. However, to our knowledge, the scaffold content and structural diversity of fungal secondary metabolites have never been studied. Herein, the scaffold diversity of 223 fungal metabolites was measured and compared to the diversity of approved drugs and commercial libraries for HTS containing natural, synthetic, and semi-synthetic compounds. In addition, the global diversity of the fungal isolates was assessed and compared to other reference data sets using Consensus Diversity Plots, a chemoinformatic tool recently developed. It was concluded that fungal secondary metabolites are cyclic systems with few ramifications and more diverse than the commercial libraries with natural products and semi-synthetic compounds. The fungal metabolites data set was one of the most structurally diverse, containing a large proportion of different and unique scaffolds not found in the other compound data sets including ChEMBL. Therefore, fungal metabolites offer a rich source of molecules suited for identifying diverse candidates for drug discovery.

The raphid pennates (order Bacillariales) are a diverse group of diatoms easily recognized by having a slit in the siliceous cell wall, called the raphe, with functions in cell motility. It has been hypothesized that this morphological innovation contributed to the evolutionary success of this relatively young but species-rich group of diatoms. However, owing to the incompleteness of the fossil record this hypothesis remains untested. Using the 18S ribosomal RNA gene, fossil calibrations, and Bayesian phylogenetic and diversification frameworks, we detect a shift in the speciation rate of marine raphid pennate diatoms in the Cretaceous, not detected in other diatom lineages nor previously recognized in the microfossil record. Our results suggest a positive link between the speciation of raphid pennate diatoms and the benefits derived from evolving motility skills, which could account for their outstanding present-day global diversity. The coincidence between the advent of the raphe and the increase in the speciation rate of raphid pennates supports the idea that simple morphological novelties can have important consequences on the evolutionary history of eukaryotic microorganisms.

WOS: 000388059500017, 27621130, Freshwater mussels of the order Unionida are key elements of freshwater habitats and are responsible for important ecological functions and services. Unfortunately, these bivalves are among the most threatened freshwater taxa in the world. However, conservation planning and management are hindered by taxonomic problems and a lack of detailed ecological data. This highlights the urgent need for advances in the areas of systematics and evolutionary relationships within the Unionida. This study presents the most comprehensive phylogeny to date of the larger Unionida family, i.e., the Unionidae. The phylogeny is based on a combined dataset of 1032 bp (COI + 28S) of 70 species in 46 genera, with 7 of this genera being sequenced for the first time. The resulting phylogeny divided the Unionidae into 6 supported subfamilies and 18 tribes, three of which are here named for the first time (i.e., Chamberlainiini nomen novum, Cristariini nomen novum and Lanceolariini nomen novum). Molecular analyses were complemented by investigations of selected morphological, anatomical and behavioral characters used in traditional phylogenetic studies. No single morphological, anatomical or behavioral character was diagnostic at the subfamily level and few were useful at the tribe level. However, within subfamilies, many tribes can be recognized based on a subset of these characters. The geographical distribution of each of the subfamilies and tribes is also presented. The present study provides important advances in the systematics of these extraordinary taxa with implications for future ecological and conservation studies. (C) 2016 Elsevier Inc. All rights reserved., Portuguese Foundation for Science and Technology (FCT) Grant [SFRH/BPD/108445/2015]; Vietnam Academy of Science and Technology [IEBR.CBT.TS07/2015]; Central Michigan University Poyang Lake Research Investment Fund; Key Laboratory of Poyang Lake Wetland and Watershed Research Director's Open Fund of Jiangxi Normal University, Financial support was provided by: the Portuguese Foundation for Science and Technology (FCT) Grant to EF (SFRH/BPD/108445/2015); the Vietnam Academy of Science and Technology under grant number IEBR.CBT.TS07/2015 for the Vietnamese field research; the Central Michigan University Poyang Lake Research Investment Fund and the Key Laboratory of Poyang Lake Wetland and Watershed Research Director's Open Fund of Jiangxi Normal University for procurement of and analysis of some Chinese specimens. The authors wish to thank: Jamie Smith, Collection manager of Mollusks, North Carolina Museum of Natural Sciences, Raleigh, North Carolina, for all of her efforts to ship tissue samples to be used in this project; the Confederated Tribes of the Umatilla Indian Reservation for providing access to specimens of A. nuttalliana.

18 páginas, 6 figuras, 1 tabla., The deficiency in the distributional data of invertebrate taxa is one of the major impediments acting on the bias towards the low awareness of its conservation status. The present study sets a basic framework to understand the large branchiopods distribution in the Iberian Peninsula and Balearic Islands. Since the extensive surveys performed in the late 1980s, no more studies existed updating the information for the whole studied area. The present study fills the gap, gathering together all available information on large branchiopods distribution since 1995, and analysing the effect of human population density and several landscape characteristics on their distribution, taking into consideration different spatial scales (100 m, 1 km and 10 km). In overall, 28 large branchiopod taxa (17 anostracans, 7 notostracans and 4 spinicaudatans) are known to occur in the area. Approximately 30% of the sites hosted multiple species, with a maximum of 6 species. Significant positive co-occurring species pairs were found clustered together, forming 4 different associations of large branchiopod species. In general, species clustered in the same group showed similar responses to analysed landscape characteristics, usually showing a better fit at higher spatial scales., MF is supported by a grant from the Brazilian Conselho Nacional de Desenvolvimento Cientı´fico e Tecnolo´gico—CNPq (401045/ 2014-5), program Cieˆncia sem Fronteiras. DC-M held a grant from the Spanish Ministry of Education, Culture and Sport (FPU014/06783).

The definitions of different types of mycorrhizas and problems with mycorrhizal diagnosis, especially for plants with sparse or inconsistent mycorrhizal colonisation, are discussed. These include plants which have arbuscular mycorrhizas (AM) in some habitats but have nonmycorrhizal (NM) roots in others (NM-AM plants). NM and NM-AM plants are most common in harsh environments where plant productivity is limited by soil infertility, disturbance, cold, salinity, waterlogging, etc. Revised estimates are provided for the total number of flowering plants and vascular plants with mycorrhizal or NM roots, confirming the overall importance of AM that occurs in 72% of vascular plants, while about 7% have inconsistent AM associations (NM-AM), 2% are ectomycorrhizal (EcM)

Based on percentages of undescribed species collected during intensive recent sampling campaigns in South America, tropical Africa, and the Caribbean, the current global total number of pholcid species is estimated to range from about 4,000 to 5,000. With the current rate of descriptions of about 570 pholcid species per decade, this suggests that a global inventory of the family could be completed within a few decades. However, I argue that a complete (or near-complete) inventory is neither realistic nor necessary and that knowing the majority of species of a particular group will answer most questions on that taxon's biology, while being a manageable task. At current rates of description, the majority of pholcid species might be known within 10–20 years.

Sexual dimorphism in the human pelvis has been studied widely for forensic purposes, but it is still unclear to what extent it varies among human populations. There is evidence that microevolutionary processes, both neutral (i.e., population history) and selective (e.g., thermoregulatory adaptation and size-related obstetrical constraints) contribute to explain pelvic variation among populations, but the extent to which these factors affect pelvic sexual dimorphism is unknown. In this study, I analyze sexual dimorphism of the os coxae in 20 globally distributed human populations, using 3D morphometric data to separate the size and shape components of sexual differences. After evaluating population differences in the degree and pattern of sexual dimorphism, I test for the effect of population history, climate, and body size in shaping global diversity. The results show that size and shape dimorphism follow different patterns. Coxal size dimorphism is generally quite consistent through populations, with males bigger than females, but it appears to be reduced in small-bodied populations, possibly in relation to obstetrically-related selective pressures for a spacious birth canal. Beyond a general species-wide pattern of shape dimorphism, commonly used for forensic sex determination, other aspects of sexual differences in coxal shape vary among human populations, reflecting the effects of neutral demographic processes and climatic adaptation.

Human immunodeficiency virus type 1 (HIV-1) is pandemic, but its contemporary global transmission network has not been characterized. A better understanding of the properties and dynamics of this network is essential for surveillance, prevention, and eventual eradication of HIV. Here, we apply a simple and computationally efficient network-based approach to all publicly available HIV polymerase sequences in the global database, revealing a contemporary picture of the spread of HIV-1 within and between countries. This approach automatically recovered well-characterized transmission clusters and extended other clusters thought to be contained within a single country across international borders. In addition, previously undescribed transmission clusters were discovered. Together, these clusters represent all known modes of HIV transmission. The extent of international linkage revealed by our comprehensive approach demonstrates the need to consider the global diversity of HIV, even when describing local epidemics. Finally, the speed of this method allows for near-real-time surveillance of the pandemic's progression.

6 pages, 7 figures, 2 tables, Theories of taxonomic diversification dispute whether global diversity has an upper limit set by the strength of biological interactions or grows in unlimited fashion until catastrophic events reset the system. We analyzed a global compendium of fossil planktic foraminifera from the early Cretaceous to the present after correcting for temporal differences in sampling effort. Our results show that their morphological diversity has increased exponentially through time in two different phases. The first phase collapsed at the Cretaceous-Paleogene boundary transition. The second phase developed through the Cenozoic era and declined during the Pliocene-Pleistocene interval, a period of time that was dominated by enhanced climatic and oceanographic instability. In none of these phases diversity reached an equilibrium level. Cenozoic faunas evolved faster than those inhabiting Cretaceous oceans, perhaps as a result of a higher environmental variability. Our results indicate that planktic foraminifera conform to an exponential diversification model. However, because catastrophic events have repeatedly reset the level of biological diversity and have kept it below the maximum, we cannot confirm whether the level of diversity is potentially unlimited. © 2013 Elsevier B.V., The research was funded by Xunta de Galicia through program Incite (10-PXIB-312058-PR)

The Nunn Member (early Osagean) of the Lake Valley Formation of New Mexico is known for its abundance and diversity of crinoids. Although crinoids were first reported in the late 1800s, no comprehensive study of the crinoids has been conducted and a complete list of the crinoid taxa does not exist. All subclasses of crinoids occur in the Lake Valley, but the camerates are by far the dominant group. Study of the Macurda collection from the University of Michigan, the Laudon collection from the University of New Mexico, and new collections provided more than 7000 specimens, 4,500 of which were identifiable camerates. Sixty-one species of camerates are recognized in the Nunn Member, including five new species: Blairocrinus macurdai, Iotacrinus novamexicanus, Agaricocrinus alamogordoensis, Uperocrinus kuesi, and Collicrinus laudoni. This camerate fauna is very similar to that of the lower Burlington Limestone of the Mississippi Valley. An update of the crinoid taxa in the Lake Valley Formation allows for a better understanding of the temporal and geographic relationships of crinoid faunas across North American during the Early Mississippian when camerates were at their global diversity maximum. The majority of the camerates come from the western New Mexico outcrops where the Nunn Member is thicker and the marine shelf was shallower, but several also occur in association with the deep-water Waulsortian mounds.

We evaluated the abundance and nature of simple sequence repeats (SSRs) in the causal agent of stem rust of wheat, Puccinia graminis f. sp. tritici, in order to characterize and develop SSR markers. A strategy was tested in which publicly available genome datasets extracted from genome sequences of P. graminis f. sp. tritici were searched for abundance and mined for candidate novel SSR markers that could be applied to a wide range of Puccinia species. The genome analysis from 393 supercontigs yielded a total of 34,359 SSR repeat motifs. A majority of these (98 %) were mononucleotide, dinucleotide, and trinucleotide repeats. The AG/GA dinucleotide motifs were the most common, and a TTGTT motif was the longest of all SSRs. From a total of 500 primer pairs designed, 460 produced bands within the expected size range and 56 SSR markers were eventually developed. Most of these were tetranucleotide and pentanucleotide motifs with PIC values ranging from 0.40 to 0.91 with an average PIC value of 0.71. The cross amplification of these markers in 11 isolates representing five Puccinia species and six formae speciales of P. graminis was also investigated. The frequency of PCR amplifications was lower for the species P. coronata, P. striiformis and P. triticina, and consequently, no significant polymorphisms were detected. In contrast 10, 10, and 11 polymorphic SSR loci were identified in P. graminis f. sp. secalis, P. graminis f. sp. avenae, and the “Scabrum” rust, respectively. The SSR markers reported here will be useful to characterize and profile global diversity in the important pathogen P. graminis.

Many decades of experimental and theoretical research on the origin of life have yielded important discoveries regarding the chemical and physical conditions under which organic compounds can be synthesized and polymerized. However, such conditions often seem mutually exclusive, because they are rarely encountered in a single environmental setting. As such, no convincing models explain how living cells formed from abiotic constituents. Here, we propose a new approach that considers the origin of life within the global context of the Hadean Earth. We review previous ideas and synthesize them in four central hypotheses: (i) Multiple microenvironments contributed to the building blocks of life, and these niches were not necessarily inhabitable by the first organisms; (ii) Mineral catalysts were the backbone of prebiotic reaction networks that led to modern metabolism; (iii) Multiple local and global transport processes were essential for linking reactions occurring in separate locations; (iv) Global diversity and local selection of reactants and products provided mechanisms for the generation of most of the diverse building blocks necessary for life. We conclude that no single environmental setting can offer enough chemical and physical diversity for life to originate. Instead, any plausible model for the origin of life must acknowledge the geological complexity and diversity of the Hadean Earth. Future research may therefore benefit from identifying further linkages between organic precursors, minerals, and fluids in various environmental contexts.

Viruses, once thought of only as purveyors of disease, take centre stage, from the human microbiome to the oceans, as archives of global diversity and drivers of biogeochemical cycles.

Scientific Reports 6: Article number: 25506; published online: 03 May 2016; updated: 27 June 2016. In this Article, all instances of “rs714598” should read “rs713598”.

Plants are clever green strategists (Horn, 1971). By plants, I mean those living on land-or vascular plants. Their evolutionary history goes back to the Silurian, some 430 million years ago. Their evolution in dramatically different environments over that time resulted in the formation of an impressive variety of forms and attributes, in a global diversity that today consists of approximately 260,000 species. Although exceedingly important (one can say, with some justi„cation, that biology is the study of plants and their parasites), our knowledge of them is far exceeded by that of animals. We are more connected to animals (we are animals), more concerned about their conservation, and have studied them much more. Because plants are poor models for human diseases, there is much less research funding available to study them. Some research on plants and biomiomicry has dealt with rapid movements from the storage of energy in tensile organs (Burghart and Franzl, 2009); we seem to be particularly fascinated by plants when they take on the animal-like characteristics of rapid movement (Edwards et al., 2005; Taylor et al., 2006).