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Morphological and genetic evidence supports the separation of two ants (Formicidae, Dolichoderinae) from the Atlantic Forest biome.

Zookeys 2021 22;1033:35-62. Epub 2021 Apr 22.

Facultad de Ciencias Básicas, Programa de Biología, Universidad del Magdalena, Carrera 32 # 22-08, Santa Marta, Magdalena, Colombia Universidad del Magdalena Santa Marta Colombia.

The taxonomic boundaries of many Neotropical ant species of the genus are still unclear. and are two morphologically similar taxa which occur sympatrically in the southern Atlantic Forest of Brazil. Some characters such as the scape length and head shape suggest that these taxa may be different species. Read More

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Whole-genome analysis of giraffe supports four distinct species.

Curr Biol 2021 Apr 28. Epub 2021 Apr 28.

Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt am Main, Germany; Institute for Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Straße 13, 60438 Frankfurt am Main, Germany; LOEWE Centre for Translational Biodiversity Genomics, Senckenberganlage 25, 60325 Frankfurt am Main, Germany. Electronic address:

Species is the fundamental taxonomic unit in biology and its delimitation has implications for conservation. In giraffe (Giraffa spp.), multiple taxonomic classifications have been proposed since the early 1900s. Read More

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Niche divergence contributes to geographical parthenogenesis in two dandelion taxa.

J Evol Biol 2021 May 6. Epub 2021 May 6.

Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, P.O. Box 94248, 1090GE, Amsterdam.

Many sexual-asexual complexes show a distinct pattern where the asexuals have larger and more northerly ranges than closely related sexuals. A prime candidate to explain this so-called "geographical parthenogenesis" is ecological niche divergence between the sexuals and asexuals. Modern niche modelling techniques allow testing niche divergence by directly comparing the niches of sexuals and asexuals. Read More

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Revisiting the hyperdominance of Neotropical tree species under a taxonomic, functional and evolutionary perspective.

Sci Rep 2021 May 5;11(1):9585. Epub 2021 May 5.

Department of Integrative Biology, University of California, Berkeley, CA, 94720-3140, USA.

Recent studies have leveraged large datasets from plot-inventory networks to report a phenomenon of hyperdominance in Amazonian tree communities, concluding that few species are common and many are rare. However, taxonomic hypotheses may not be consistent across these large plot networks, potentially masking cryptic diversity and threatened rare taxa. In the current study, we have reviewed one of the most abundant putatively hyperdominant taxa, Protium heptaphyllum (Aubl. Read More

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Community composition and functional prediction of prokaryotes associated with sympatric sponge species of southwestern Atlantic coast.

Sci Rep 2021 May 5;11(1):9576. Epub 2021 May 5.

Department of Physiology, Center for Marine Biology, Biosciences Institute and NP-Biomar, São Paulo University, São Paulo, Brazil.

Prokaryotes contribute to the health of marine sponges. However, there is lack of data on the assembly rules of sponge-associated prokaryotic communities, especially for those inhabiting biodiversity hotspots, such as ecoregions between tropical and warm temperate southwestern Atlantic waters. The sympatric species Aplysina caissara, Axinella corrugata, and Dragmacidon reticulatum were collected along with environmental samples from the north coast of São Paulo (Brazil). Read More

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Comparison of Different Soluble Dietary Fibers during the Fermentation Process.

J Agric Food Chem 2021 May 5. Epub 2021 May 5.

School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.

Soluble dietary fibers being fermented by gut microbiota constitute a pivotal prerequisite for soluble dietary fibers exhibiting physiological functions. However, the relationship between fiber type and gut microbiota metabolism remains unclear. The purpose of this study was to investigate and compare the effect of fiber types on short-chain fatty acid (SCFA) biosynthesis in a simulated colon. Read More

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Size, microhabitat, and loss of larval feeding drive cranial diversification in frogs.

Nat Commun 2021 05 4;12(1):2503. Epub 2021 May 4.

Department of Life Sciences, Natural History Museum, London, UK.

Habitat is one of the most important factors shaping organismal morphology, but it may vary across life history stages. Ontogenetic shifts in ecology may introduce antagonistic selection that constrains adult phenotype, particularly with ecologically distinct developmental phases such as the free-living, feeding larval stage of many frogs (Lissamphibia: Anura). We test the relative influences of developmental and ecological factors on the diversification of adult skull morphology with a detailed analysis of 15 individual cranial regions across 173 anuran species, representing every extant family. Read More

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Microbial iron and carbon metabolism as revealed by taxonomy-specific functional diversity in the Southern Ocean.

ISME J 2021 May 3. Epub 2021 May 3.

CNRS, Sorbonne Université, Laboratoire d'Océanographie Microbienne, LOMIC, F-66650, Banyuls/mer, France.

Marine microbes are major drivers of all elemental cycles. The processing of organic carbon by heterotrophic prokaryotes is tightly coupled to the availability of the trace element iron in large regions of the Southern Ocean. However, the functional diversity in iron and carbon metabolism within diverse communities remains a major unresolved issue. Read More

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An interpreted atlas of biosynthetic gene clusters from 1,000 fungal genomes.

Proc Natl Acad Sci U S A 2021 May;118(19)

Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208;

Fungi are prolific producers of natural products, compounds which have had a large societal impact as pharmaceuticals, mycotoxins, and agrochemicals. Despite the availability of over 1,000 fungal genomes and several decades of compound discovery efforts from fungi, the biosynthetic gene clusters (BGCs) encoded by these genomes and the associated chemical space have yet to be analyzed systematically. Here, we provide detailed annotation and analyses of fungal biosynthetic and chemical space to enable genome mining and discovery of fungal natural products. Read More

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Distinct patterns of abundant and rare subcommunities in paddy soil during wetting-drying cycles.

Sci Total Environ 2021 Apr 24;785:147298. Epub 2021 Apr 24.

Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, Fujian 361021, China. Electronic address:

Wetting-drying cycles typically result in a wide range of soil moistures and redox potentials (Eh) that significantly affect the soil microbial community. Although numerous studies have addressed the effects of soil moisture on soil microbial community structure and composition, the response of active microbes to the fluctuation in soil Eh is still largely unknown; this is especially true for the ecological roles of abundant and rare taxa. To explore the dynamics of active and total microbial communities in response to wetting-drying cycles, we conducted a microcosm experiment based on three wetting-drying cycles and 16S rRNA transcript (active) and 16S rRNA gene (total) amplicon sequencing. Read More

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Specialized pro-resolving mediator lipidome and 16S rRNA bacterial microbiome data associated with human chronic rhinosinusitis.

Data Brief 2021 Jun 1;36:107023. Epub 2021 Apr 1.

Department of Medicine, Division of Infectious Disease, University of Colorado Anschutz Medical Campus, Aurora, CO, United States.

Chronic rhinosinusitis (CRS) is a clinical syndrome defined by symptoms including nasal congestion, facial pain and pressure, anosmia, and rhinorrhea lasting more than 12 weeks. Several mechanistically distinct processes lead to the development of clinical symptoms in CRS including innate immune dysfunction, dysregulated eicosanoid metabolism and perturbations in host-microbiome interactions [1]. We developed a database comprised of patient demographic information, lipid mediator metabolomic profiles, and 16S bacterial rRNA gene sequence data from 66 patients undergoing endoscopic sinus surgery. Read More

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What prevents mainstream evolutionists teaching the whole truth about how genomes evolve?

Prog Biophys Mol Biol 2021 Apr 29. Epub 2021 Apr 29.

Department of Physiology, Anatomy & Genetics, University of Oxford, USA. Electronic address:

The common belief that the neo-Darwinian Modern Synthesis (MS) was buttressed by the discoveries of molecular biology is incorrect. On the contrary those discoveries have undermined the MS. This article discusses the many processes revealed by molecular studies and genome sequencing that contribute to evolution but nonetheless lie beyond the strict confines of the MS formulated in the 1940s. Read More

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Deep evolutionary diversification of semicircular canals in archosaurs.

Curr Biol 2021 Apr 27. Epub 2021 Apr 27.

Department of Geosciences, Virginia Tech, 926 West Campus Drive, Blacksburg, VA 24061, USA. Electronic address:

Living archosaurs (birds and crocodylians) have disparate locomotor strategies that evolved since their divergence ∼250 mya. Little is known about the early evolution of the sensory structures that are coupled with these changes, mostly due to limited sampling of early fossils on key stem lineages. In particular, the morphology of the semicircular canals (SCCs) of the endosseous labyrinth has a long-hypothesized relationship with locomotion. Read More

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Dinoflagellate symbionts escape vomocytosis by host cell immune suppression.

Nat Microbiol 2021 Apr 29. Epub 2021 Apr 29.

Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany.

Alveolata comprises diverse taxa of single-celled eukaryotes, many of which are renowned for their ability to live inside animal cells. Notable examples are apicomplexan parasites and dinoflagellate symbionts, the latter of which power coral reef ecosystems. Although functionally distinct, they evolved from a common, free-living ancestor and must evade their host's immune response for persistence. Read More

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Mycobiota Associated with the Vascular Wilt of Poplar.

Plants (Basel) 2021 Apr 28;10(5). Epub 2021 Apr 28.

Department of Forest Pathology, Poznań University of Life Sciences, Wojska Polskiego 71c, 60-625 Poznań, Poland.

In 2017, a 560-ha area of hybrid poplar plantation in northern Poland showed symptoms of tree decline. The leaves appeared smaller, yellow-brown, and were shed prematurely. Twigs and smaller branches died without distinct cankers. Read More

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The Microbiome of the Reef Macroalga in Singapore.

Microorganisms 2021 Apr 22;9(5). Epub 2021 Apr 22.

Yale-NUS College, National University of Singapore, 16 College Avenue West, Singapore 138527, Singapore.

The large canopy-forming macroalga, , provides shelter and food for numerous coral reef species, but it can also be detrimental at high abundances where it outcompetes other benthic organisms for light and space. Here, we investigate the microbial communities associated with in Singapore, where it is an abundant and important member of coral reef communities. We collected eight complete thalli from eight island locations along an approximate 14 km east-to-west transect. Read More

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Exploring the Species Diversity of Edible Mushrooms in Yunnan, Southwestern China, by DNA Barcoding.

J Fungi (Basel) 2021 Apr 17;7(4). Epub 2021 Apr 17.

State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, and Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming 650032, China.

Yunnan Province, China, is famous for its abundant wild edible mushroom diversity and a rich source of the world's wild mushroom trade markets. However, much remains unknown about the diversity of edible mushrooms, including the number of wild edible mushroom species and their distributions. In this study, we collected and analyzed 3585 mushroom samples from wild mushroom markets in 35 counties across Yunnan Province from 2010 to 2019. Read More

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Bovine Milk Oligosaccharides and Human Milk Oligosaccharides Modulate the Gut Microbiota Composition and Volatile Fatty Acid Concentrations in a Preclinical Neonatal Model.

Microorganisms 2021 Apr 21;9(5). Epub 2021 Apr 21.

Department of Food Science & Human Nutrition, University of Illinois, Urbana, IL 61801, USA.

Milk oligosaccharides (OS) shape microbiome structure and function, but their relative abundances differ between species. Herein, the impact of the human milk oligosaccharides (HMO) (2'-fucosyllactose [2'FL] and lacto-N-neotetraose [LNnT]) and OS isolated from bovine milk (BMOS) on microbiota composition and volatile fatty acid (VFA) concentrations in ascending colon (AC) contents and feces was assessed. Intact male piglets received diets either containing 6. Read More

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Human- and Infrastructure-associated Bacteria in Greywater.

J Appl Microbiol 2021 Apr 27. Epub 2021 Apr 27.

Office of Research and Development, United States Environmental Protection Agency, Cincinnati, OH, USA.

Greywater, the wastewater from sinks, showers, and laundry, is an understudied environment for bacterial communities. Most greywater studies focus on quantifying pathogens, often via proxies used in other wastewater, like fecal indicator bacteria; there is a need to identify more greywater-appropriate surrogates, like Staphylococcus sp. Sequencing-based studies have revealed distinct communities in different types of greywater as well as in different parts of greywater infrastructure, including biofilms on pipes, holding tanks, and filtration systems. Read More

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Functional redundancy and specific taxa modulate the contribution of prokaryotic diversity and composition to multifunctionality.

Mol Ecol 2021 Apr 27. Epub 2021 Apr 27.

Key Laboratory of Pollinating Insect Biology, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, 100093, China.

Observational and experimental evidence has revealed the functional importance of microbial diversity. However, microbial diversity loss effects on ecosystem functions are not consistent across studies, which are likely tempered by microbial functional redundancy, specific taxa, and functions evaluated. Here we conducted diversity manipulation experiments in two independent soils with distinct prokaryotic communities, and investigated how the initial community traits (e. Read More

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Genome-centric resolution of novel microbial lineages in an excavated Centrosaurus dinosaur fossil bone from the Late Cretaceous of North America.

Environ Microbiome 2020 Mar 19;15(1). Epub 2020 Mar 19.

Department of Geosciences, Princeton University, B88, Guyot Hall, Princeton University, Princeton, NJ, 08544, USA.

Background: Exceptional preservation of endogenous organics such as collagens and blood vessels has been frequently reported in Mesozoic dinosaur fossils. The persistence of these soft tissues in Mesozoic fossil bones has been challenged because of the susceptibility of proteins to degradation and because bone porosity allows microorganisms to colonize the inner microenvironments through geological time. Although protein lability has been studied extensively, the genomic diversity of microbiomes in dinosaur fossil bones and their potential roles in bone taphonomy remain underexplored. Read More

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Marine biodiversity refugia in a climate-sensitive subarctic shelf.

Glob Chang Biol 2021 Apr 25. Epub 2021 Apr 25.

Arctic Research Center, Hokkaido University, Sapporo, Japan.

The subarctic shelf of the Eastern Bering Sea (EBS) is one of the world's most productive marine environments, exposed to drastic climate changes characterized by extreme fluctuations in temperature, sea ice concentration, timing, and duration. These climatic changes elicit profound responses in species distribution, abundance, and community composition. Here, we examined the patterns of alpha and temporal beta diversity of 159 marine taxa (66 vertebrates and 93 invertebrate species) from 29 years (1990-2018) of species observations from the NOAA bottom trawl surveys in the EBS. Read More

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Two new species of Cephalogonimidae Looss, 1899 (Digenea: Plagiorchioidea) from Africa (Mozambique and Guinea), including a new phylogenetic hypothesis for related plagiorchioids.

Int J Parasitol Parasites Wildl 2021 Apr 9;14:228-240. Epub 2021 Mar 9.

Aquatic Parasitology Laboratory and Southeastern Cooperative Fish Parasite and Disease Project, School of Fisheries, Aquaculture, and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA.

Two new species of Cephalogonimidae Looss, 1899 (from Looss, 1900 and Chatterji, 1933) are described from African freshwater fishes. n. sp. Read More

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First record of (Monogenea: Polystomatidae) from tree frogs in Madagascar, with the description of five new species.

Int J Parasitol Parasites Wildl 2021 Apr 17;14:161-178. Epub 2021 Feb 17.

Unit for Environmental Sciences and Management, North-West University, Potchefstroom Campus, Private Bag X 6001, Potchefstroom, 2520, South Africa.

Although Madagascar has more than 350 frog species of which all but two are endemic to the island, the known polystome (Monogenea: Polystomatidae) diversity parasitizing Malagasy frogs is low, encompassing five species of , one species of and one . Investigating the parasite diversity of frog parasites at selected Malagasy localities led to the discovery of undescribed polystomes. Five treefrogs, , , , and were found to be infected and are reported here as hosts for new species. Read More

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Infant Feeding Alters the Longitudinal Impact of Birth Mode on the Development of the Gut Microbiota in the First Year of Life.

Front Microbiol 2021 7;12:642197. Epub 2021 Apr 7.

Department of Epidemiology, The Geisel School of Medicine at Dartmouth, Hanover, NH, United States.

Cesarean-delivered (CD) infants harbor a distinct gut microbiome from vaginally delivered (VD) infants, however, during infancy, the most important driver of infant gut microbial colonization is infant feeding. Earlier studies have shown that breastfeeding is associated with higher levels of health-promoting bacteria such and and via modulation of the immune system, and production of metabolites. As the infant gut matures and solid foods are introduced, it is unclear whether longer duration of breast feeding restore loss of beneficial taxa within the intestinal microbiota of operatively delivered infants. Read More

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Field multi-omics analysis reveals a close association between bacterial communities and mineral properties in the soybean rhizosphere.

Sci Rep 2021 Apr 23;11(1):8878. Epub 2021 Apr 23.

Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.

The plant root-associated environments such as the rhizosphere, rhizoplane, and endosphere are different from the outer soil region (bulk soil). They establish characteristic conditions including microbiota, metabolites, and minerals, and they can directly affect plant growth and development. However, comprehensive insights into those characteristic environments, especially the rhizosphere, and molecular mechanisms of their formation are not well understood. Read More

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Brockarchaeota, a novel archaeal phylum with unique and versatile carbon cycling pathways.

Nat Commun 2021 04 23;12(1):2404. Epub 2021 Apr 23.

Department of Marine Science, University of Texas Austin, Port Aransas, TX, 78373, USA.

Geothermal environments, such as hot springs and hydrothermal vents, are hotspots for carbon cycling and contain many poorly described microbial taxa. Here, we reconstructed 15 archaeal metagenome-assembled genomes (MAGs) from terrestrial hot spring sediments in China and deep-sea hydrothermal vent sediments in Guaymas Basin, Gulf of California. Phylogenetic analyses of these MAGs indicate that they form a distinct group within the TACK superphylum, and thus we propose their classification as a new phylum, 'Brockarchaeota', named after Thomas Brock for his seminal research in hot springs. Read More

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A fossil-calibrated time-tree of all Australian freshwater fishes.

Mol Phylogenet Evol 2021 Apr 20;161:107180. Epub 2021 Apr 20.

School of Life and Environmental Sciences, University of Sydney, Sydney, Australia.

Australian freshwater fishes are a relatively species-poor assemblage, mostly comprising groups derived from older repeated freshwater invasions by marine ancestors, plus a small number of Gondwanan lineages. These taxa are both highly endemic and highly threatened, but a comprehensive phylogeny for Australian freshwater fishes is lacking. This has hampered efforts to study their phylogenetic diversity, distribution of extinction risk, speciation rates, and rates of trait evolution. Read More

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Temperate and tropical coastal waters share relatively similar microbial biofilm communities while free-living or particle-attached communities are distinct.

Mol Ecol 2021 Apr 22. Epub 2021 Apr 22.

Laboratoire MAPIEM, Université de Toulon, EA, Toulon, France.

Free-living (FL) marine microbial communities differ from those attached to particles (PA). Likewise, biofilms (B) colonizing artificial surfaces, including plastics or ship hulls, hardly resemble their planktonic surroundings. However, few studies have examined the effect of the environment on these lifestyles and on the source of organisms colonizing marine surfaces. Read More

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Breastmilk, Stool, and Meconium: Bacterial Communities in South Africa.

Microb Ecol 2021 Apr 22. Epub 2021 Apr 22.

Center for Environmental Research and Children's Health, University of California Berkeley, Berkeley, CA, USA.

Human milk optimizes gut microbial richness and diversity, and is critical for proper immune development. Research has shown differing microbial composition based on geographic location, providing evidence that diverse biospecimen data is needed when studying human bacterial communities. Yet, limited research describes human milk and infant gut microbial communities in Africa. Read More

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