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Trinity L Hamilton, Judith M Klatt, Dirk de Beer, Jennifer L Macalady
We report the isolation of a pinnacle-forming cyanobacterium isolated from a microbial mat covering the sediment surface at Little Salt Spring-a flooded sinkhole in Florida with a perennially microoxic and sulfidic water column. The draft genome of the isolate encodes all of the enzymatic machinery necessary for both oxygenic and anoxygenic photosynthesis, as well as genes for methylating hopanoids at the C-2 position. The physiological response of the isolate to H2S is complex: (i) no induction time is necessary for anoxygenic photosynthesis; (ii) rates of anoxygenic photosynthesis are regulated by both H2S and irradiance; (iii) O2 production is inhibited by H2S concentrations as low as 1 μM and the recovery rate of oxygenic photosynthesis is dependent on irradiance; (iv) under the optimal light conditions for oxygenic photosynthesis, rates of anoxygenic photosynthesis are nearly double those of oxygenic photosynthesis...
January 12, 2018: ISME Journal
Kwaku Aduse-Poku, Freerk Molleman, William Oduro, Samuel K Oppong, David J Lohman, Rampal S Etienne
The unified neutral theory of biodiversity and biogeography has gained the status of a quantitative null model for explaining patterns in ecological (meta)communities. The theory assumes that individuals of trophically similar species are functionally equivalent. We empirically evaluate the relative contribution of neutral and deterministic processes in shaping fruit-feeding butterfly assemblages in three tropical forests in Africa, using both direct (confronting the neutral model with species abundance data) and indirect approaches (testing the predictions of neutral theory using data other than species abundance distributions)...
January 2018: Ecology and Evolution
Wei Dai, Ming Zou, Liandong Yang, Kang Du, Weitao Chen, Yanjun Shen, Richard L Mayden, Shunping He
The phylogeny of otocephalan fishes is the subject of broad controversy based on morphological and molecular evidence. The primary unresolved issue pertaining to this lineage relates to the origin of Characiphysi, especially the paraphyly of Characiformes. The considerable uncertainty associated with this lineage has precluded a greater understanding of the origin and evolution of the clade. Herein, a phylogenomic approach was applied to resolve this debate. By analyzing 10 sets of transcriptomic data generated in this study and 12 sets of high-throughput data available in public databases, we obtained 1,110 single-copy orthologous genes (935,265 sites for analysis) from 22 actinopterygians, including 14 otocephalan fishes from six orders: Clupeiformes, Gonorynchiformes, Cypriniformes, Siluriformes, Characiformes, and Gymnotiformes...
January 9, 2018: Scientific Reports
Ga Hun Boo, Line Le Gall, Il Ki Hwang, Kathy Ann Miller, Sung Min Boo
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 datasets demonstrated the presence of five species in southern Madagascar: Ptilophora hildebrandtii, P. pterocladioides, and three new species described here, P...
January 5, 2018: Journal of Phycology
William J Resetarits, Jason R Bohenek, Tyler Breech, Matthew R Pintar
Two of the most important factors determining community structure and diversity within and among habitat patches are patch size and patch quality. Despite the importance of patch size in existing paradigms in island biogeography, metapopulation biology, landscape ecology, and metacommunity ecology, and growing conservation concerns with habitat fragmentation, there has been little investigation into how patch size interacts with patch quality. We crossed three levels of patch size (1.13 m2 , 2.54 m2 and 5.73 m2 ) with two levels of patch quality [fish presence/absence - green sunfish (Lepomis cyanellus) and golden shiners (Notemigonus chrysoleucus) in 6 replicate experimental landscapes (3 x 2 x 6 = 36 patches)...
January 7, 2018: Ecology
Jennifer Pratscher, John Vollmers, Sandra Wiegand, Marc G Dumont, Anne-Kristin Kaster
Understanding of global methane sources and sinks is a prerequisite for the design of strategies to counteract global warming. Microbial methane oxidation in soils represents the largest biological sink for atmospheric methane. However, still very little is known about the identity, metabolic properties, and distribution of the microbial group proposed to be responsible for most of this uptake, the uncultivated upland soil cluster α (USCα). Here, we reconstructed a draft genome of USCα from a combination of targeted cell sorting and metagenomes from forest soil, providing the first insights into its metabolic potential and environmental adaptation strategies...
January 3, 2018: Environmental Microbiology
Mohamed A Almarri, Reem A Lootah
X-chromosomal short tandem repeats (X-STRs) are used to complement autosomal and Y-STRs in complex kinship testing, and can be of potential value when determining trace female DNA in male background. We analyzed extracted and directly-amplified samples of 501 males from the United Arab Emirates and report the forensic statistical parameters of 12 X-STRs and haplotypes of the four previously defined linkage groups using the Investigator Argus X-12 QS kit. Combined PDM, PDF, MEC Desmarais Trio and MEC Desmarais Duo based on allele (and haplotype) frequencies were 0...
December 29, 2017: Forensic Science International. Genetics
Sonia Fisch-Muller, Jan H A Mol, Raphaël Covain
Characterizing and naming species becomes more and more challenging due to the increasing difficulty of accurately delineating specific bounderies. In this context, integrative taxonomy aims to delimit taxonomic units by leveraging the complementarity of multiple data sources (geography, morphology, genetics, etc.). However, while the theoretical framework of integrative taxonomy has been explicitly stated, methods for the simultaneous analysis of multiple data sets are poorly developed and in many cases different information sources are still explored successively...
2018: PloS One
K Saravanan, P Puneeth Kumar, J Praveenraj, Arunjyoti Baruah, T Sivaramakrishnan, T Sathish Kumar, S Pramod Kumar, R Kiruba Sankar, S Dam Roy
White spot syndrome virus (WSSV) is one of the most prevalent, widespread and devastating pathogen associated with shrimp population. The present study was aimed at screening the wild caught shrimps from Andaman and Nicobar Islands (ANI) for WSSV infection. Shrimp samples of different penaeid species including Penaeus monodon, Penaeus indicus, Penaeus merguiensis and Metapenaeus monoceros collected from nine different landing centers across the coast of ANI were screened for WSSV infection. Presence of white spots, a typical clinical sign of white spot disease was observed on the exoskeleton of WSSV infected shrimp samples...
December 2017: Virusdisease
Siyan Zhao, Linjie Zhuang, Cheng Wang, Yifei Li, Shanyun Wang, Guibing Zhu
This study investigated the diversity, community composition, and abundance of anaerobic ammonium oxidation (anammox) bacteria along the altitudinal gradient in Qinghai-Tibet Plateau. Two types of soil samples (wetland and dryland soils, n = 123) were collected from 641 m to 5,033 m altitudes. Polymerase chain reaction (PCR) screening showed that anammox were not widespread, and were only detected in 9 sampling sites of the 50 sites tested by amplifying the 16S rRNA genes. Then, only samples collected from Linzhi (2,715 m), Rikaze (4,030 m), and Naqu (5,011 m), which were positive for the presence of anammox, were further processed to explore the biogeography of anammox bacteria in Qinghai-Tibet Plateau...
December 29, 2017: MicrobiologyOpen
Antônio Ralph Medeiros-Sousa, Aristides Fernandes, Walter Ceretti-Junior, André Barreto Bruno Wilke, Mauro Toledo Marrelli
Mosquitoes are well known for their epidemiological importance as vectors of a wide range of human pathogens. Despite the many studies on medically important species, little is known about the diversity patterns of these insects in urban green spaces, which serve as shelter and refuge for many native and invasive species. Here, we investigate drivers of mosquito richness and composition in nine urban parks in the city of São Paulo, Brazil. Using the equilibrium theory of island biogeography, we tested predictive models for species richness and composition and performed nestedness analysis...
December 19, 2017: Scientific Reports
C David Owen, Louise E Tailford, Serena Monaco, Tanja Šuligoj, Laura Vaux, Romane Lallement, Zahra Khedri, Hai Yu, Karine Lecointe, John Walshaw, Sandra Tribolo, Marc Horrex, Andrew Bell, Xi Chen, Gary L Taylor, Ajit Varki, Jesus Angulo, Nathalie Juge
Ruminococcus gnavus is a human gut symbiont wherein the ability to degrade mucins is mediated by an intramolecular trans-sialidase (RgNanH). RgNanH comprises a GH33 catalytic domain and a sialic acid-binding carbohydrate-binding module (CBM40). Here we used glycan arrays, STD NMR, X-ray crystallography, mutagenesis and binding assays to determine the structure and function of RgNanH_CBM40 (RgCBM40). RgCBM40 displays the canonical CBM40 β-sandwich fold and broad specificity towards sialoglycans with millimolar binding affinity towards α2,3- or α2,6-sialyllactose...
December 19, 2017: Nature Communications
Isa Schön, Janet Higuti, Tasnim Patel, Koen Martens
Cladogenesis is often driven by the interplay of dispersal and vicariance. The importance of long-distance dispersal in biogeography and speciation is increasingly recognised, but still ill-understood. Here, we study faunal interconnectivity between four large Brazilian floodplains, namely the Amazon, Araguaia, Pantanal (on Paraguay River) and Upper Paraná River floodplains, investigating a species complex of the non-marine ostracod genus Strandesia. We use DNA sequence data from the mitochondrial COI and the nuclear Elongation Factor 1 alpha genes to construct molecular phylogenies and minimum spanning networks, to identify genetic species, analyse biogeographic histories and provide preliminary age estimates of this species complex...
December 16, 2017: Molecular Phylogenetics and Evolution
Antonio Palomba, Alessandro Tanca, Cristina Fraumene, Marcello Abbondio, Francesco Fancello, Alberto Stanislao Atzori, Sergio Uzzau
The digestive functions of the pre-weaned lamb gastrointestinal tracts (GITs) have been the subject of much research in recent years, but the microbial and host functions underlying these complex processes remain largely unknown. Here, we undertook a proof-of-principle metaproteogenomic investigation on luminal and mucosal samples collected from 10 GITs of a 30-day-old pre-weaned lamb. We demonstrate that the analysis of the diverse ecological niches along the GITs can reveal microbiota composition and metabolic functions, although low amounts of microbial proteins could be identified in the small intestinal and mucosal samples...
December 18, 2017: Proteomes
Gregory F M Jongsma, Michael F Barej, Christopher D Barratt, Marius Burger, Werner Conradie, Raffael Ernst, Eli Greenbaum, Mareike Hirschfeld, Adam D Leaché, Johannes Penner, Daniel M Portik, Ange-Ghislain Zassi-Boulou, Mark-Oliver Rödel, David C Blackburn
Frogs in the genus Amnirana (family Ranidae) are widely distributed across sub-Saharan Africa and present a model system for exploring the relationship between diversification and geography across the continent. Using multiple loci from the mitochondrial (16S) and nuclear genomes (DISP2, FICD, KIAA2013, REV3L), we generated a strongly supported species-level phylogeny that provides insights into the continental biogeography of African species of Amnirana, which form a monophyletic group within the genus. Species delimitation analyses suggest that there may be as many as seven additional species of Amnirana in Africa...
December 12, 2017: Molecular Phylogenetics and Evolution
Douglas A Craig, John K Moulton, Douglas C Currie
The hitherto monotypic South American genus Paraustrosimulium Wygodzinsky & Coscarón is revised to accommodate two Australian species: Austrosimulium colboi Davies & Györkös and Paraustrosimulium obcidens n. sp. The generic diagnosis is updated and the eastern Australian species Paraustrosimulium colboi (Davies & Györkös) n. stat. is re-described, including the male for the first time. The Western, Australian sister species of P. colbo, namely P. obcidens Craig, Moulton Currie n. sp. is also fully described...
October 20, 2017: Zootaxa
Giovanni Nachtigall Maurício, Marcos Ricardo Bornschein
The Brazilian tapaculo Scytalopus speluncae species-group has been the subject of intense taxonomic work in the past 18 years, with six new species being named in that time lapse and other taxonomic problems having been highlighted (Bornschein et al. 1998, 2007; Maurício 2005; Raposo et al. 2006, 2012; Mata et al. 2009; Whitney et al. 2010; Maurício et al. 2010, 2014; Pulido-Santacruz et al. 2016). One of the most persistent of these problems involves the oldest name in this group, S. speluncae (Ménétriès), and the taxa it may represent...
November 20, 2017: Zootaxa
Bradley J Sinclair, Adrian R Plant
Seven new species of Dolichocephala Macquart from Thailand are described (D. bicolor sp. nov., D. curvata sp. nov., D. immaculata sp. nov., D. incus sp. nov., D. longicerca sp. nov., D. srisukai sp. nov., D. thailandensis sp. nov.). A key to species is provided, distributions mapped and phenology and biogeography discussed.
November 30, 2017: Zootaxa
Julio Rivera, Clorinda Vergara-Cobián
We present a preliminary checklist of the praying mantises (Insecta: Mantodea) of Peru. A total of 67 species are reported, nine of which constitute new records from that country. The following new nomenclatural procedures are introduced: Musoniella margharethae Battiston and Picciau, 2008 is transferred to Musonia as Musonia margharethae (Battiston and Picciau, 2008) (comb. n.), and Phyllovates brevicollis Orofino, Ippolito and Lombardo, 2006 is considered a new synonym (syn. n.) of Pseudovates peruviana (Rehn, 1911)...
October 19, 2017: Zootaxa
Robert C Thomson, Phillip Q Spinks, H Bradley Shaffer
The map turtles (genus Graptemys) comprise a morphologically diverse clade that forms a major component of the southeastern US hotspot of chelonian diversity. Map turtles have experienced both recent and rapid diversification resulting in long-standing uncertainty regarding species boundaries and phylogenetic relationships within the genus as well as timing of their divergence. We present a phylogeny for the group that includes geographically representative sampling for all described species and subspecies...
December 11, 2017: Molecular Phylogenetics and Evolution
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