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https://www.readbyqxmd.com/read/28448639/cryptic-diversity-of-the-subfamily-calaphidinae-hemiptera-aphididae-revealed-by-comprehensive-dna-barcoding
#1
Yerim Lee, Wonhoon Lee, Mariusz Kanturski, Robert G Foottit, Shin-Ichi Akimoto, Seunghwan Lee
Aphids are a species rich group comprising many important pests. However, species identification can be very difficult for aphids due to their morphological ambiguity. DNA barcoding has been widely adopted for rapid and reliable species identification as well as cryptic species detection. In this study, we investigated cryptic diversity in the subfamily Calaphidinae (Hemiptera: Aphididae) based on 899 sequences of cytochrome c oxidase I (COI) for 115 morphospecies (78 species collected in this study and sequences of 73 species downloaded from Genbank)...
2017: PloS One
https://www.readbyqxmd.com/read/28448620/correction-systematics-of-the-dendropsophus-leucophyllatus-species-complex-anura-hylidae-cryptic-diversity-and-the-description-of-two-new-species
#2
Marcel A Caminer, Borja Milá, Martin Jansen, Antoine Fouquet, Pablo J Venegas, Germán Chávez, Stephen C Lougheed, Santiago R Ron
[This corrects the article DOI: 10.1371/journal.pone.0171785.].
2017: PloS One
https://www.readbyqxmd.com/read/28448517/cryptic-chytridiomycosis-linked-to-climate-and-genetic-variation-in-amphibian-populations-of-the-southeastern-united-states
#3
Ariel A Horner, Eric A Hoffman, Matthew R Tye, Tyler D Hether, Anna E Savage
North American amphibians have recently been impacted by two major emerging pathogens, the fungus Batrachochytrium dendrobatidis (Bd) and iridoviruses in the genus Ranavirus (Rv). Environmental factors and host genetics may play important roles in disease dynamics, but few studies incorporate both of these components into their analyses. Here, we investigated the role of environmental and genetic factors in driving Bd and Rv infection prevalence and severity in a biodiversity hot spot, the southeastern United States...
2017: PloS One
https://www.readbyqxmd.com/read/28442735/novel-antibiotic-screening-methods-to-awaken-silent-or-cryptic-secondary-metabolic-pathways-in-actinomycetes
#4
REVIEW
Hiroyasu Onaka
Streptomyces have the potential to produce more than 30 secondary metabolites; however, the expression of most metabolite biosynthetic gene clusters is cryptic or silent. Indeed, the expression of these genes is conditional and dependent on culture conditions. To activate such gene clusters, many methods have been developed. In this review, I describe two activation approaches developed in my laboratory: use of the activation mediator goadsporin and combined-culture. Goadsporin is a chemical substance isolated from Streptomyces sp...
April 26, 2017: Journal of Antibiotics
https://www.readbyqxmd.com/read/28438699/cryptic-diversity-in-amazonian-frogs-integrative-taxonomy-of-the-genus-anomaloglossus-amphibia-anura-aromobatidae-reveals-a-unique-case-of-diversification-within-the-guiana-shield
#5
Jean-Pierre Vacher, Philippe J R Kok, Miguel T Rodrigues, Jucivaldo Dias Lima, Andy Lorenzini, Quentin Martinez, Manon Fallet, Elodie A Courtois, Michel Blanc, Philippe Gaucher, Maël Dewynter, Rawien Jairam, Paul Ouboter, Christophe Thébaud, Antoine Fouquet
Lack of resolution on species boundaries and distribution can hamper inferences in many fields of biology, notably biogeography and conservation biology. This is particularly true in megadiverse and under-surveyed regions such as Amazonia, where species richness remains vastly underestimated. Recently, integrative approaches using a combination of phenotypic and molecular phylogenetics evidence have proved extremely successful in reducing knowledge gaps, especially in animal groups displaying high levels of cryptic diversity like amphibians...
April 21, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28437732/weaving-through-a-cryptic-species-comparing-the-neotropical-ants-camponotus-senex-and-camponotus-textor-hymenoptera-formicidae
#6
Eduardo Gonçalves Paterson Fox, Daniel Russ Solis, Cristiano Lazoski, William Mackay
Camponotus senex (Fr. Smith 1858) and Camponotus textor Forel, 1899 are commonly confused species in the New World tropics. We provide morphological characteristics based on the larvae and adults, behavioural differences, together with evidence from molecular markers (cuticular hydrocarbon profiles, venom differences, nuclear ribosomal ITS-1, and mtDNA COI sequence comparisons) to separate the two species, demonstrating they are not immediately closely related. In conclusion we suggest new reliable morphological characters which can benefit from deeper phenetic analysis, and support the contextual usefulness of non-morphological tools in resolving sibling ant species...
April 3, 2017: Micron: the International Research and Review Journal for Microscopy
https://www.readbyqxmd.com/read/28431212/dna-barcoding-and-traditional-taxonomy-an-integrated-approach-for-biodiversity-conservation
#7
Bhavisha P Sheth, Vrinda S Thaker
Biological diversity is depleting at an alarming rate. Additionally, a vast amount of biodiversity still remains undiscovered. Taxonomy has been serving the purpose of describing, naming, and classifying species for more than 250 years. DNA taxonomy and barcoding have accelerated the rate of this process, thereby providing a tool for conservation practice. DNA barcoding and traditional taxonomy have their own inherent merits and demerits. The synergistic use of both methods, in the form of integrative taxonomy, has the potential to contribute to biodiversity conservation in a pragmatic timeframe and overcome their individual drawbacks...
April 21, 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28430780/the-importance-of-standardization-for-biodiversity-comparisons-a-case-study-using-autonomous-reef-monitoring-structures-arms-and-metabarcoding-to-measure-cryptic-diversity-on-mo-orea-coral-reefs-french-polynesia
#8
Emma Ransome, Jonathan B Geller, Molly Timmers, Matthieu Leray, Angka Mahardini, Andrianus Sembiring, Allen G Collins, Christopher P Meyer
The advancement of metabarcoding techniques, declining costs of high-throughput sequencing and development of systematic sampling devices, such as autonomous reef monitoring structures (ARMS), have provided the means to gather a vast amount of diversity data from cryptic marine communities. However, such increased capability could also lead to analytical challenges if the methods used to examine these communities across local and global scales are not standardized. Here we compare and assess the underlying biases of four ARMS field processing methods, preservation media, and current bioinformatic pipelines in evaluating diversity from cytochrome c oxidase I metabarcoding data...
2017: PloS One
https://www.readbyqxmd.com/read/28429797/sirtuins-in-the-phylum-basidiomycota-a-role-in-virulence-in-cryptococcus-neoformans
#9
Samantha D M Arras, Jessica L Chitty, Maha S I Wizrah, Paige E Erpf, Benjamin L Schulz, Milos Tanurdzic, James A Fraser
Virulence of Cryptococcus neoformans is regulated by a range of transcription factors, and is also influenced by the acquisition of adaptive mutations during infection. Beyond the temporal regulation of virulence factor production by transcription factors and these permanent microevolutionary changes, heritable epigenetic modifications such as histone deacetylation may also play a role during infection. Here we describe the first comprehensive analysis of the sirtuin class of NAD+ dependent histone deacetylases in the phylum Basidiomycota, identifying five sirtuins encoded in the C...
April 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28428843/rad-sequencing-reveals-genomewide-divergence-between-independent-invasions-of-the-european-green-crab-carcinus-maenas-in-the-northwest-atlantic
#10
Nicholas W Jeffery, Claudio DiBacco, Mallory Van Wyngaarden, Lorraine C Hamilton, Ryan R E Stanley, Renée Bernier, Jennifer FitzGerald, K Matheson, C H McKenzie, Praveen Nadukkalam Ravindran, Robert Beiko, Ian R Bradbury
Genomic studies of invasive species can reveal both invasive pathways and functional differences underpinning patterns of colonization success. The European green crab (Carcinus maenas) was initially introduced to eastern North America nearly 200 years ago where it expanded northwards to eastern Nova Scotia. A subsequent invasion to Nova Scotia from a northern European source allowed further range expansion, providing a unique opportunity to study the invasion genomics of a species with multiple invasions...
April 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28428147/title-high-genetic-diversities-between-isolates-of-the-fish-parasite-cryptocaryon-irritans-ciliophora-suggest-multiple-cryptic-species
#11
Hongshu Chi, Patricia Taik, Emily J Foley, Alycia C Racicot, Hilary M Gray, Katherine E Guzzetta, Hsin-Yun Lin, Yen-Ling Song, Che-Huang Tung, Kosuke Zenke, Tomoyoshi Yoshinaga, Chao-Yin Cheng, Wei-Jen Chang, Hui Gong
The ciliate protozoan Cryptocaryon irritans parasitizes marine fish and causes lethal white spot disease. Sporadic infections as well as large-scale outbreaks have been reported globally and the parasite's broad host range poses particular threat to the aquaculture and ornamental fish markets. In order to better understand C. irritans' population structure, we sequenced and compared mitochondrial cox-1, SSU rRNA, and ITS-1 sequences from 8 new isolates of C. irritans collected in China, Japan, and Taiwan. We detected two SSU rRNA haplotypes, which differ at three positions, separating the isolates into two main groups (I and II)...
April 18, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28427391/fish-with-red-fluorescent-eyes-forage-more-efficiently-under-dim-blue-green-light-conditions
#12
Ulrike Katharina Harant, Nicolaas Karel Michiels
BACKGROUND: Natural red fluorescence is particularly conspicuous in the eyes of some small, benthic, predatory fishes. Fluorescence also increases in relative efficiency with increasing depth, which has generated speculation about its possible function as a "light organ" to detect cryptic organisms under bluish light. Here we investigate whether foraging success is improved under ambient conditions that make red fluorescence stand out more, using the triplefin Tripterygion delaisi as a model system...
April 20, 2017: BMC Ecology
https://www.readbyqxmd.com/read/28425096/influence-of-coral-cover-and-structural-complexity-on-the-accuracy-of-visual-surveys-of-coral-reef-fish-communities
#13
D J Coker, J P Nowicki, N A J Graham
Using manipulated patch reefs with combinations of varying live-coral cover (low, medium and high) and structural complexity (low and high), common community metrics (abundance, diversity, richness and community composition) collected through standard underwater visual census techniques were compared with exhaustive collections using a fish anaesthetic (clove oil). This study showed that reef condition did not influence underwater visual census estimates at a community level, but reef condition can influence the detectability of some small and cryptic species and this may be exacerbated if surveys are conducted on a larger scale...
April 19, 2017: Journal of Fish Biology
https://www.readbyqxmd.com/read/28422973/camera-trap-arrays-improve-detection-probability-of-wildlife-investigating-study-design-considerations-using-an-empirical-dataset
#14
Kelly M O'Connor, Lucas R Nathan, Marjorie R Liberati, Morgan W Tingley, Jason C Vokoun, Tracy A G Rittenhouse
Camera trapping is a standard tool in ecological research and wildlife conservation. Study designs, particularly for small-bodied or cryptic wildlife species often attempt to boost low detection probabilities by using non-random camera placement or baited cameras, which may bias data, or incorrectly estimate detection and occupancy. We investigated the ability of non-baited, multi-camera arrays to increase detection probabilities of wildlife. Study design components were evaluated for their influence on wildlife detectability by iteratively parsing an empirical dataset (1) by different sizes of camera arrays deployed (1-10 cameras), and (2) by total season length (1-365 days)...
2017: PloS One
https://www.readbyqxmd.com/read/28422134/genetic-structure-and-signatures-of-selection-in-grey-reef-sharks-carcharhinus-amblyrhynchos
#15
P Momigliano, R Harcourt, W D Robbins, V Jaiteh, G N Mahardika, A Sembiring, A Stow
With overfishing reducing the abundance of marine predators in multiple marine ecosystems, knowledge of genetic structure and local adaptation may provide valuable information to assist sustainable management. Despite recent technological advances, most studies on sharks have used small sets of neutral markers to describe their genetic structure. We used 5517 nuclear single-nucleotide polymorphisms (SNPs) and a mitochondrial DNA (mtDNA) gene to characterize patterns of genetic structure and detect signatures of selection in grey reef sharks (Carcharhinus amblyrhynchos)...
April 19, 2017: Heredity
https://www.readbyqxmd.com/read/28412383/a-prospective-international-aspergillus-terreus-survey-an-efisg-isham-and-ecmm-joint-study
#16
Brigitte Risslegger, Tamara Zoran, Michaela Lackner, Maria Aigner, Ferran Sánchez-Reus, Antonio Rezusta, Anuradha Chowdhary, Saad Jaber Taj-Aldeen, Maiken C Arendrup, Salvatore Oliveri, Dimitrios P Kontoyiannis, Ana Alastruey-Izquierdo, Katrien Lagrou, Giuliana Lo Cascio, Jacques F Meis, Walter Buzina, Claudio Farina, Miranda Drogari-Apiranthitou, Anna Grancini, Anna Maria Tortorano, Birgit Willinger, Axel Hamprecht, Elizabeth Johnson, Lena Klingspor, Valentina Arsic-Arsenijevic, Oliver A Cornely, Joseph Meletiadis, Wolfgang Prammer, Vivian Tullio, Jörg-Janne Vehreschild, Laura Trovato, Russell E Lewis, Esther Segal, Peter-Michael Rath, Petr Hamal, Manuel Rodriguez-Iglesias, Emmanuel Roilides, Sevtap Arikan-Akdagli, Arunaloke Chakrabarti, Arnaldo L Colombo, Mariana S Fernández, M Teresa Martin-Gomez, Hamid Badali, Georgios Petrikkos, Nikolai Klimko, Sebastian M Heimann, Jos Houbraken, Omrum Uzun, Michael Edlinger, Sonia de la Fuente, Cornelia Lass-Flörl
OBJECTIVES: A prospective international multicentre surveillance study was conducted to investigate the prevalence and amphotericin B (AMB) susceptibility of Aspergillus terreus species complex infections. METHODS: Three hundred seventy cases from 21 countries were evaluated. RESULTS: The overall prevalence of A. terreus species complex among patients investigated and with mold positive cultures was 5.2% (370/7116). AMB MICs were ranging from 0...
April 13, 2017: Clinical Microbiology and Infection
https://www.readbyqxmd.com/read/28411161/a-reassessment-of-the-phylogeny-and-circumscription-of-zaluzianskya-scrophulariaceae
#17
Jenny K Archibald, Jacqueline Cook, Bruce Anderson, Steven D Johnson, Mark E Mort
The genus Zaluzianskya (Scrophulariaceae s.s.) encompasses a diversity of traits, such as flowers ranging from 4 to 60 mm in length with various patterns of color and indumentum. However, this diversity, as described by the current taxonomic circumscription of Zaluzianskya, is an underestimate. The boundaries of this genus require expansion via incorporation of species from other genera and recognition of unnamed species. This study advances prior molecular phylogenies for the southern African genus through the addition of DNA regions and an up to 70% increase in population sampling, targeting specific taxa...
April 11, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28404998/a-single-biochemical-activity-underlies-the-pleiotropy-of-the-aging-related-protein-clk-1
#18
Ju-Ling Liu, Callista Yee, Ying Wang, Siegfried Hekimi
The Caenorhabditis elegans clk-1 gene and the orthologous mouse gene Mclk1 encode a mitochondrial hydroxylase that is necessary for the biosynthesis of ubiquinone (UQ). Mutations in these genes produce broadly pleiotropic phenotypes in both species, including a lengthening of animal lifespan. A number of features of the C. elegans clk-1 mutants, including a maternal effect, particularly extensive pleiotropy, as well as unexplained differences between alleles have suggested that CLK-1/MCLK1 might have additional functions besides that in UQ biosynthesis...
April 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28404508/model-based-analyses-reveal-insular-population-diversification-and-cryptic-frog-species-in-the-ischnocnema-parva-complex-in-the-atlantic-forest-of-brazil
#19
Marcelo Gehara, Adriane Barth, Eliana Faria de Oliveira, Marco Antonio Costa, Célio Fernando Baptista Haddad, Miguel Vences
The Atlantic Forest (AF) of Brazil has long been recognized as a biodiversity conservation hotspot. Despite decades of studies the species inventory of this biome continues to increase with the discovery of cryptic diversity and the description of new species. Different diversification mechanisms have been proposed to explain the diversity in the region, including models of forest dynamics, barriers to gene flow and dispersal. Also, sea level change is thought to have influenced coastal diversification and isolated populations on continental islands...
April 9, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28403525/cyanomargarita-gen-nov-nostocales-cyanobacteria-convergent-evolution-resulting-in-a-cryptic-genus
#20
Sergei Shalygin, Regina Shalygina, Jeffrey R Johansen, Nicole Pietrasiak, Esther Berrendero, Markéta Bohunická, Jan Mareš, Christopher A Sheil
Two populations of Rivularia-like cyanobacteria were isolated from ecologically distinct and biogeographically distant sites. One population was from an unpolluted stream in the Kola Peninsula of Russia, whereas the other was from a wet wall in the Grand Staircase-Escalante National Monument, a desert park-land in Utah. Though both were virtually indistinguishable from Rivularia in field and cultured material, they were both phylogenetically distant from Rivularia and the Rivulariaceae based on both 16S rRNA and rbcLX phylogenies...
April 12, 2017: Journal of Phycology
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