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https://www.readbyqxmd.com/read/28734067/range-instability-leads-to-cytonuclear-discordance-in-a-morphologically-cryptic-ground-squirrel-species-complex
#1
Mark A Phuong, Ke Bi, Craig Moritz
The processes responsible for cytonuclear discordance frequently remain unclear. Here, we employed an exon capture dataset and demographic methods to test hypotheses generated by species distribution models to examine how contrasting histories of range stability vs. fluctuation have caused cytonuclear concordance and discordance in ground squirrel lineages from the Otospermophilus beecheyi species complex. Previous studies in O. beecheyi revealed three morphologically cryptic and highly divergent mitochondrial DNA lineages (named the Northern, Central, and Southern lineages based on geography) with only the Northern lineage exhibiting concordant divergence for nuclear genes...
July 22, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28731202/on-the-brink-the-highly-reduced-plastomes-of-nonphotosynthetic-ericaceae
#2
Thomas W A Braukmann, Michael B Broe, Saša Stefanović, John V Freudenstein
Ericaceae (the heather family) is a large and diverse group of plants that forms elaborate symbiotic relationships with mycorrhizal fungi, and includes several nonphotosynthetic lineages. Using an extensive sample of fully mycoheterotrophic (MH) species, we explored inter- and intraspecific variation as well as selective constraints acting on the plastomes of these unusual plants. The plastomes of seven MH genera were analysed in a phylogenetic context with two geographically disparate individuals sequenced for Allotropa, Monotropa, and Pityopus...
July 21, 2017: New Phytologist
https://www.readbyqxmd.com/read/28729611/cryptic-speciation-in-pan-tropical-sea-urchins-a-case-study-of-an-edge-of-range-population-of-tripneustes-from-the-kermadec-islands
#3
Omri Bronstein, Andreas Kroh, Barbara Tautscher, Libby Liggins, Elisabeth Haring
Tripneustes is one of the most abundant and ecologically significant tropical echinoids. Highly valued for its gonads, wild populations of Tripneustes are commercially exploited and cultivated stocks are a prime target for the fisheries and aquaculture industry. Here we examine Tripneustes from the Kermadec Islands, a remote chain of volcanic islands in the southwest Pacific Ocean that mark the boundary of the genus' range, by combining morphological and genetic analyses, using two mitochondrial (COI and the Control Region), and one nuclear (bindin) marker...
July 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28727788/oecomys-catherinae-sigmodontinae-cricetidae-evidence-for-chromosomal-speciation
#4
Stella Miranda Malcher, Julio Cesar Pieczarka, Lena Geise, Rogério Vieira Rossi, Adenilson Leão Pereira, Patricia Caroline Mary O'Brien, Paulo Henrique Asfora, Victor Fonsêca da Silva, Maria Iracilda Sampaio, Malcolm Andrew Ferguson-Smith, Cleusa Yoshiko Nagamachi
Among the Oryzomyini (Sigmodontinae), Oecomys is the most speciose, with 17 species. This genus presents high karyotypic diversity (2n = 54 to 2n = 86) and many taxonomic issues at the species level because of the presence of cryptic species and the overlap of morphological characters. For these reasons the real number of species of Oecomys may be underestimated. With the aim of verifying if the taxon Oecomys catherinae is composed of more than one species, we made comparative studies on two populations from two regions of Brazil, one from the Amazon and another from the Atlantic Forest using both classical cytogenetics (G- and C-banding) and comparative genomic mapping with whole chromosome probes of Hylaeamys megacephalus (HME), molecular data (cytochrome b mitochondrial DNA) and morphology...
2017: PloS One
https://www.readbyqxmd.com/read/28716927/nuclear-genomes-distinguish-cryptic-species-suggested-by-their-dna-barcodes-and-ecology
#5
Daniel H Janzen, John M Burns, Qian Cong, Winnie Hallwachs, Tanya Dapkey, Ramya Manjunath, Mehrdad Hajibabaei, Paul D N Hebert, Nick V Grishin
DNA sequencing brings another dimension to exploration of biodiversity, and large-scale mitochondrial DNA cytochrome oxidase I barcoding has exposed many potential new cryptic species. Here, we add complete nuclear genome sequencing to DNA barcoding, ecological distribution, natural history, and subtleties of adult color pattern and size to show that a widespread neotropical skipper butterfly known as Udranomia kikkawai (Weeks) comprises three different species in Costa Rica. Full-length barcodes obtained from all three century-old Venezuelan syntypes of U...
July 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28702376/nematode-species-identification-current-status-challenges-and-future-perspectives-for-cyathostomins
#6
Christina M Bredtmann, Jürgen Krücken, Jayaseelan Murugaiyan, Tetiana Kuzmina, Georg von Samson-Himmelstjerna
Human and animal health is globally affected by a variety of parasitic helminths. The impact of co-infections and development of anthelmintic resistance requires improved diagnostic tools, especially for parasitic nematodes e.g., to identify resistant species or attribute pathological effects to individual species or particular species combinations. In horses, co-infection with cyathostomins is rather a rule than an exception with typically 5 to 15 species (out of more than 40 described) per individual host...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28702067/quantifying-phenotype-environment-matching-in-the-protected-kerry-spotted-slug-mollusca-gastropoda-using-digital-photography-exposure-to-uv-radiation-determines-cryptic-colour-morphs
#7
Aidan O'Hanlon, Kristina Feeney, Peter Dockery, Michael J Gormally
BACKGROUND: Animal colours and patterns commonly play a role in reducing detection by predators, social signalling or increasing survival in response to some other environmental pressure. Different colour morphs can evolve within populations exposed to different levels of predation or environmental stress and in some cases can arise within the lifetime of an individual as the result of phenotypic plasticity. Skin pigmentation is variable for many terrestrial slugs (Mollusca: Gastropoda), both between and within species...
2017: Frontiers in Zoology
https://www.readbyqxmd.com/read/28695208/population-genomics-of-picophytoplankton-unveils-novel-chromosome-hypervariability
#8
Romain Blanc-Mathieu, Marc Krasovec, Maxime Hebrard, Sheree Yau, Elodie Desgranges, Joel Martin, Wendy Schackwitz, Alan Kuo, Gerald Salin, Cecile Donnadieu, Yves Desdevises, Sophie Sanchez-Ferandin, Hervé Moreau, Eric Rivals, Igor V Grigoriev, Nigel Grimsley, Adam Eyre-Walker, Gwenael Piganeau
Tiny photosynthetic microorganisms that form the picoplankton (between 0.3 and 3 μm in diameter) are at the base of the food web in many marine ecosystems, and their adaptability to environmental change hinges on standing genetic variation. Although the genomic and phenotypic diversity of the bacterial component of the oceans has been intensively studied, little is known about the genomic and phenotypic diversity within each of the diverse eukaryotic species present. We report the level of genomic diversity in a natural population of Ostreococcus tauri (Chlorophyta, Mamiellophyceae), the smallest photosynthetic eukaryote...
July 2017: Science Advances
https://www.readbyqxmd.com/read/28690814/barcoding-rotifer-biodiversity-in-mediterranean-ponds-using-diapausing-egg-banks
#9
Emilio Moreno, José M Conde-Porcuna, Africa Gómez
The biodiversity of Mediterranean freshwater bodies is among the most threatened worldwide; therefore, its accurate estimation is an urgent issue. However, traditional methods are likely to underestimate freshwater zooplankton biodiversity due to its high species seasonality and cryptic diversity. We test the value of applying DNA barcoding to diapausing egg banks, in combination with the creation of a reference collection of DNA barcodes using adult individual samples, to characterize rotifer communities. We use monogonont rotifers from two lakes in Doñana National Park and one from Ruidera Natural Park in Spain as models to create a reference collection of DNA barcodes for taxonomically diagnosed adult individuals sampled from the water column, to compare with the sequences obtained from individual eggs from the diapausing egg banks...
July 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28688201/contrasting-patterns-of-x-chromosome-divergence-underlie-multiple-sex-ratio-polymorphisms-in-stalk-eyed-flies
#10
Kimberly A Paczolt, Josephine A Reinhardt, Gerald S Wilkinson
Sex-linked segregation distorters cause offspring sex ratios to differ from equality. Theory predicts that such selfish alleles may either go to fixation and cause extinction, reach a stable polymorphism, or initiate an evolutionary arms race with genetic modifiers. The extent to which a sex ratio distorter follows any of these trajectories in nature is poorly known. Here we used X-linked sequence and simple tandem repeat data for three sympatric species of stalk-eyed flies (Teleopsis whitei and two cryptic species of T...
July 8, 2017: Journal of Evolutionary Biology
https://www.readbyqxmd.com/read/28687754/dna-barcoding-studies-on-thrips-in-india-cryptic-species-and-species-complexes
#11
Kaomud Tyagi, Vikas Kumar, Devkant Singha, Kailash Chandra, Boni Amin Laskar, Shantanu Kundu, Rajasree Chakraborty, Sumantika Chatterjee
Thrips are one of the major sucking pest and vector of plant viruses causing huge economic loss in agriculture. The accurate identification of thrips is crucial for effective pest management strategies. However, morphology based identification has limitations and warrants integration of molecular data. We attempted the largest DNA barcoding initiative on 370 sequences of 89 thrips morphospecies including 104 novel sequences from 39 morphospecies, including the type specimens of four species. The results of multiple species delimitation methods (BIN, ABGD, GMYC and bPTP) were consistent for 73 species (82%) with their morphological identifications...
July 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28685416/can-we-predict-diatoms-herbicide-sensitivities-with-phylogeny-influence-of-intraspecific-and-interspecific-variability
#12
Sara M Esteves, Franc Ois Keck, Salomé F P Almeida, Etelvina Figueira, Agne S Bouchez, Fre de Ric Rimet
Diatoms are used as indicators of freshwater ecosystems integrity. Developing diatom-based tools to assess impact of herbicide pollution is expected by water managers. But, defining sensitivities of all species to multiple herbicides would be unattainable. The existence of a phylogenetic signal of herbicide sensitivity was shown among diatoms and should enable prediction of new species sensitivity. However, diatoms present a cryptic diversity that may lead to variation in their sensitivity to herbicides that would need to be taken into account...
July 6, 2017: Ecotoxicology
https://www.readbyqxmd.com/read/28675688/whole-mitochondrial-genome-capture-from-fecal-samples-and-museum-preserved-specimens
#13
Tom van der Valk, Frida Lona Durazo, Love Dalén, Katerina Guschanski
Population-scale molecular studies of endangered and cryptic species are often limited by access to high-quality samples. The use of non-invasively collected samples or museum-preserved specimens reduces the pressure on modern populations by removing the need to capture and handle live animals. However, endogenous DNA content in such samples is low, making shotgun sequencing a financially prohibitive approach. Here, we apply a target enrichment method to retrieve mitochondrial genomes from 65 museum specimens and 56 non-invasively collected fecal samples of two endangered great ape species, Grauer's gorilla and the eastern chimpanzee...
July 4, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28674655/contrasting-biological-features-in-morphologically-cryptic-mediterranean-sponges
#14
Leire Garate, Andrea Blanquer, Maria J Uriz
Sponges are key organisms in the marine benthos where they play essential roles in ecological processes such as creating new niches, competition for resources, and organic matter recycling. Despite the increasing number of taxonomical studies, many sponge species remain hidden, whether unnoticed or cryptic. The occurrence of cryptic species may confound ecological studies by underestimating biodiversity. In this study, we monitored photographically growth, fusions, fissions, and survival of two morphologically cryptic species Hemimycale mediterranea Uriz, Garate & Agell, 2017 and H...
2017: PeerJ
https://www.readbyqxmd.com/read/28668078/population-genetic-structure-in-sabatieria-nematoda-reveals-intermediary-gene-flow-and-admixture-between-distant-cold-seeps-from-the-mediterranean-sea
#15
Annelies De Groote, Freija Hauquier, Ann Vanreusel, Sofie Derycke
BACKGROUND: There is a general lack of information on the dispersal and genetic structuring for populations of small-sized deep-water taxa, including free-living nematodes which inhabit and dominate the seafloor sediments. This is also true for unique and scattered deep-sea habitats such as cold seeps. Given the limited dispersal capacity of marine nematodes, genetic differentiation between such geographically isolated habitat patches is expected to be high. Against this background, we examined genetic variation in both mitochondrial (COI) and nuclear (18S and 28S ribosomal) DNA markers of 333 individuals of the genus Sabatieria, abundantly present in reduced cold-seep sediments...
July 1, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28667823/bordered-pits-in-xylem-of-vesselless-angiosperms-and-their-possible-misinterpretation-as-perforation-plates
#16
Ya Zhang, Matthias Klepsch, Steven Jansen
Vesselless wood represents a rare phenomenon within the angiosperms, characterizing Amborellaceae, Trochodendraceae, and Winteraceae. Anatomical observations of bordered pits and their pit membranes based on light, scanning and transmission electron microscopy (SEM, TEM) are required to understand functional questions surrounding vesselless angiosperms and the potential occurrence of cryptic vessels. Interconduit pit membranes in 11 vesselless species showed a similar ultrastructure as mesophytic vessel-bearing angiosperms, with a mean thickness of 245 nm (± 53, SD; n = 6 species)...
July 1, 2017: Plant, Cell & Environment
https://www.readbyqxmd.com/read/28667534/methods-for-posttranslational-induction-of-polyreactivity-of-antibodies
#17
Maxime Lecerf, Annaelle Jarossay, Srinivas V Kaveri, Sébastien Lacroix-Desmazes, Jordan D Dimitrov
An antibody molecule that recognizes multiple unrelated antigens is defined as polyreactive. Polyreactivity is an intrinsic characteristic of immune repertoires. Degenerated antigen binding diversifies the repertoire of specificities, thus contributing to immune defense and immune regulation. Immune repertoire contains also a fraction of immunoglobulins, which acquire polyreactivity only following contact with various protein-destabilizing or pro-oxidative substances. Posttranslational induction of the antibody polyreactivity may have important repercussion for laboratory practice, as well as in cases of pathological conditions accompanied by liberation of large quantities of pro-oxidative substances such as heme, labile iron, or reactive oxygen species...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28666786/phylogenetic-analysis-of-placobdella-hirudinea-rhynchobdellida-glossiphoniidae-with-consideration-of-coi-variation
#18
Danielle de Carle, Alejandro Oceguera-Figueroa, Michael Tessler, Mark E Siddall, Sebastian Kvist
Placobdella is a genus of blood-feeding leeches in the family Glossiphoniidae. Historically, species of Placobdella have posed difficulty for systematists owing to a lack of informative morphological characters and the preponderance of inadequate or incomplete species descriptions. Here, we conduct a phylogenetic analysis of 55 individuals representing 20 of the 24 currently recognized nominal taxa using COI, ND1, 12S rDNA and ITS sequences under parsimony, maximum likelihood and Bayesian inference. We also examine the isolated COI phylogeny for the genus using an expanded dataset encompassing three additional species not included in the concatenated dataset...
June 27, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28660362/antarctic-rocks-from-continental-antarctica-as-source-of-potential-human-opportunistic-fungi
#19
Vívian N Gonçalves, Fabio S Oliveira, Camila R Carvalho, Carlos E G R Schaefer, Carlos A Rosa, Luiz H Rosa
We assessed the diversity of culturable fungi associated with rocks of continental Antarctica to evaluate their physiological opportunistic virulence potential in vitro. The seventy fungal isolates obtained were identified as nine species of Acremonium, Byssochlamys, Cladosporium, Debaryomyces, Penicillium, and Rhodotorula. Acremonium sp., D. hansenii, P. chrysogenum, P. citrinum, P. tardochrysogenum, and R. mucilaginosa were able to grow at 37 °C; in addition, B. spectabilis displayed a high level of growth at 37 and 45 °C...
June 28, 2017: Extremophiles: Life Under Extreme Conditions
https://www.readbyqxmd.com/read/28654351/zz-z0-the-new-system-of-sex-chromosomes-in-eigenmannia-aff-trilineata-teleostei-gymnotiformes-sternopygidae-characterized-by-molecular-cytogenetics-and-dna-barcoding
#20
Cristian Araya-Jaime, Nadayca T Bonani Mateussi, Ricardo Utsunomia, Guilherme J Costa-Silva, Claudio Oliveira, Fausto Foresti
The cytogenetic characteristics of Eigenmannia aff. trilineata were analyzed by basic and molecular cytogenetics, applying fluorescent in situ hybridization, with 18S and 5S rDNA and U2 snRNA probes. The species revealed a kind of polymorphism associated to ZZ/Z0 type sex chromosomes, with 2n = 32 (8m+2sm+22a, NF = 42) in all males under analysis, whereas females evidenced 2n = 31 (8m+1sm+22a, NF = 40). C-banding showed constitutive heterochromatin restricted to the pericentromeric region of all chromosomes and single-nucleolus organized regions on pair 11...
June 27, 2017: Zebrafish
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