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https://www.readbyqxmd.com/read/28337395/isolation-and-characterization-of-microsatellite-loci-for-smilax-sieboldii-smilacaceae
#1
Yalu Ru, Ruijing Cheng, Jing Shang, Yunpeng Zhao, Pan Li, Chengxin Fu
PREMISE OF THE STUDY: Polymorphic microsatellite markers were developed for Smilax sieboldii (Smilacaceae), a member of the S. hispida group with a biogeographic disjunction between eastern Asia and North America, to study the phylogeography and incipient speciation of this species and its close relatives. METHODS AND RESULTS: Transcriptome sequencing produced 47,628 unigenes. Seventeen loci were developed from 122 randomly selected primer pairs. Polymorphism and genetic variation were evaluated for 68 accessions representing five populations of S...
March 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28330511/cytochrome-c-oxidase-subunit-i-haplotype-reveals-high-genetic-diversity-of-angiostrongylus-malaysiensis-nematoda-angiostrongylidae
#2
P Eamsobhana, H S Yong, S L Song, A Prasartvit, S Boonyong, A Tungtrongchitr
The rat lungworm Angiostrongylus malaysiensis is a metastrongyloid nematode parasite. It has been reported in Malaysia, Thailand, Laos, Myanmar, Indonesia and Japan. In this study, A. malaysiensis adult worms recovered from the lungs of wild rats in different geographical regions/provinces in Thailand were used to determine their haplotype by means of the mitochondrial partial cytochrome c oxidase subunit I (COI) gene sequence. The results revealed high COI haplotype diversity of A. malaysiensis from Thailand...
March 23, 2017: Journal of Helminthology
https://www.readbyqxmd.com/read/28315064/first-evidence-of-pezoloma-ericae-in-australia-using-the-biomes-of-australia-soil-environments-base-to-explore-the-australian-phylogeography-of-known-ericoid-mycorrhizal-and-root-associated-fungi
#3
David J Midgley, Paul Greenfield, Andrew Bissett, Nai Tran-Dinh
The prominent ericoid mycorrhizal fungus, Pezoloma ericae, has not been found in Australia to date. In the present study, internal transcribed spacer (ITS) data from the Biomes of Australia Soil Environments (BASE) was searched for evidence of P. ericae and other known ericoid mycorrhizal and root-associated taxa. ITS sequences with high identity to P. ericae, Meliniomyces bicolor, Meliniomyces variabilis, Cairneyella sp. 2, Cadophora finlandica and Woollsia mycorrhizal fungus VI were identified and their distribution in Australia visualised...
March 17, 2017: Mycorrhiza
https://www.readbyqxmd.com/read/28303189/islands-within-an-island-population-genetic-structure-of-the-endemic-sardinian-newt-euproctus-platycephalus
#4
Sarah E Ball, Stefano Bovero, Giuseppe Sotgiu, Giulia Tessa, Claudio Angelini, Jon Bielby, Christopher Durrant, Marco Favelli, Enrico Gazzaniga, Trenton W J Garner
The identification of historic and contemporary barriers to dispersal is central to the conservation of endangered amphibians, but may be hindered by their complex life history and elusive nature. The complementary information generated by mitochondrial (mtDNA) and microsatellite markers generates a valuable tool in elucidating population structure and the impact of habitat fragmentation. We applied this approach to the study of an endangered montane newt, Euproctus platycephalus. Endemic to the Mediterranean island of Sardinia, it is threatened by anthropogenic activity, disease, and climate change...
February 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28295830/interspecific-hybridization-causes-long-term-phylogenetic-discordance-between-nuclear-and-mitochondrial-genomes-in-freshwater-fishes
#5
Graham P Wallis, Sophia Cameron-Christie, Hannah L Kennedy, Gemma Palmer, Tessa R Sanders, David J Winter
Classification, phylogeography and the testing of evolutionary hypotheses rely on correct estimation of species phylogeny. Early molecular phylogenies often relied on mtDNA alone, which acts as a single linkage group with one history. Over the last decade, the use of multiple nuclear sequences has often revealed conflict among gene trees. This observation can be attributed to hybridization, lineage sorting, paralogy or selection. Here we use 54 groups of fishes from 48 studies to estimate the degree of concordance between mitochondrial and nuclear gene trees in two ecological grades of fishes: marine and freshwater...
March 12, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28295052/dynamic-circulation-and-genetic-exchange-of-a-shrew-borne-hantavirus-imjin-virus-in-the-republic-of-korea
#6
Seung-Ho Lee, Won-Keun Kim, Jin Sun No, Jeong-Ah Kim, Jin Il Kim, Se Hun Gu, Heung-Chul Kim, Terry A Klein, Man-Seong Park, Jin-Won Song
Hantaviruses (family Bunyaviridae) are enveloped negative-sense tripartite RNA viruses. The natural hosts of hantaviruses include rodents, shrews, moles, and bats. Imjin virus (MJNV) is a shrew-borne hantavirus identified from the Ussuri white-toothed shrews (Crocidura lasiura) in the Republic of Korea (ROK) and China. We have isolated MJNV and determined its prevalence and molecular diversity in Gyeonggi province, ROK. However, the distribution and phylogeography of MJNV in other regions of ROK remain unknown...
March 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28294452/phylogenetic-relationships-and-divergence-dates-of-softshell-turtles-testudines-trionychidae-inferred-from-complete-mitochondrial-genomes
#7
Haifeng Li, Juanjuan Liu, Lei Xiong, Huanhuan Zhang, Huaxing Zhou, Huazong Yin, Wanxing Jing, Jun Li, Qiong Shi, Yuqin Wang, Jianjun Liu, Liuwang Nie
The softshell turtles (Trionychidae) are one of the most widely distributed reptile groups in the world, and fossils have been found on all continents except Antarctica. The phylogenetic relationships among members of this group have been previously studied; however, there are disagreements regarding its taxonomy, its phylogeography and divergence times are still poorly understood as well. Here we present a comprehensive mitogenomic study of softshell turtles. We sequenced the complete mitochondrial genomes of 10 softshell turtles, in addition to the GenBank sequence of Dogania subplana, Lissemys punctata, Trionyx triunguis, which cover all extant genera within Trionychidae except for Cyclanorbis and Cycloderma...
March 15, 2017: Journal of Evolutionary Biology
https://www.readbyqxmd.com/read/28288943/cophylogenetics-and-biogeography-reveal-a-coevolved-relationship-between-sloths-and-their-symbiont-algae
#8
Emily D Fountain, Jonathan N Pauli, Jorge E Mendoza, Jenna Carlson, M Zachariah Peery
Specialized species, like arboreal folivores, often develop beneficial relationships with symbionts to exploit ecologically constrained lifestyles. Although coevolution can drive speciation by specialization of a symbiont to a host, a symbiotic relationship is not indicative of coevolution between host and symbiont. We tested for coevolved relationships between highly specialized two- and three-toed sloths (Choloepus spp. and Bradypus spp., respectively) and their symbiotic algae using cophylogenies and phylogeography...
March 10, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28282422/late-pleistocene-holocene-paleobiogeography-of-the-genus-apodemus-in-central-europe
#9
Markéta Knitlová, Ivan Horáček
Wood mice of the genus Apodemus are an essential component of small mammal communities throughout Europe. Molecular data suggest the postglacial colonization of current ranges from south European glacial refugia, different in particular species. Yet, details on the course of colonization and Holocene history of particular species are not available, partly because of a lack of reliable criteria for species identification in the fossil record. Using a sample of extant species, we analyzed variation patterns and between-species overlaps for a large set of metric and non-metric dental variables and established the criteria enabling the reliable species identification of fragmentary fossil material...
2017: PloS One
https://www.readbyqxmd.com/read/28271307/the-role-of-ecological-factors-in-determining-phylogeographic-and-population-genetic-structure-of-two-sympatric-island-skinks-plestiodon-kishinouyei-and-p-stimpsonii
#10
Kazuki Kurita, Mamoru Toda
We conducted comparative phylogeographic and population genetic analyses of Plestiodon kishinouyei and P. stimpsonii, two sympatric skinks endemic to islands in the southern Ryukyus, to explore different factors that have influenced population structure. Previous phylogenetic studies using partial mitochondrial DNA indicate similar divergence times from their respective closest relatives, suggesting that differences in population structure are driven by intrinsic attributes of either species rather than the common set of extrinsic factors that both presumably have been exposed to throughout their history...
March 7, 2017: Genetica
https://www.readbyqxmd.com/read/28267807/phylogeography-and-genetic-structure-of-the-oriental-river-prawn-macrobrachium-nipponense-crustacea-decapoda-palaemonidae-in-east-asia
#11
Po-Cheng Chen, Chun-Han Shih, Ta-Jen Chu, Ying-Chou Lee, Tzong-Der Tzeng
The oriental river prawn (Macrobrachium nipponense) is mainly distributed in East Asia. The phylogeography, population genetic structure and historical demography of this species in the East Asia were examined by using partial sequences of the cytochrome oxidase subunit I (COI) and 16S rRNA in mitochondrial DNA. Ten populations that included 239 individuals were collected from Taiwan (Shihmen Reservoir, SMR, Mingte Reservoir, MTR and Chengching Lake Reservoir, CLR), mainland China (Taihu Lake, TLC, Min River, MRC, Jiulong River, JRC and Shenzhen Reservoir, SRC), Japan (Biwa Lake, BLJ and Kasumigaura Lake, KLJ) and Korea (Han River, HRK)...
2017: PloS One
https://www.readbyqxmd.com/read/28264699/recent-range-expansion-of-an-intermediate-host-for-animal-schistosome-parasites-in-the-indo-australian-archipelago-phylogeography-of-the-freshwater-gastropod-indoplanorbis-exustus-in-south-and-southeast-asia
#12
Pauline Gauffre-Autelin, Thomas von Rintelen, Björn Stelbrink, Christian Albrecht
BACKGROUND: The planorbid snail Indoplanorbis exustus is the sole intermediate host for the Schistosoma indicum species group, trematode parasites responsible for cattle schistosomiasis and human cercarial dermatitis. This freshwater snail is widely distributed in Southern Asia, ranging from Iran to China eastwards including India and from the southeastern Himalayas to Southeast Asia southwards. The veterinary and medical importance of this snail explains the interest in understanding its geographical distribution patterns and evolutionary history...
March 6, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/28262789/iteration-expansion-and-regional-evolution-phylogeography-of-dendrobium-officinale-and-four-related-taxa-in-southern-china
#13
Beiwei Hou, Jing Luo, Yusi Zhang, Zhitao Niu, Qingyun Xue, Xiaoyu Ding
The genus Dendrobium was used as a case study to elucidate the evolutionary history of Orchidaceae in the Sino-Japanese Floristic Region (SJFR) and Southeast Asia region. These evolutionary histories remain largely unknown, including the temporal and spatial distribution of the evolutionary events. The present study used nuclear and plastid DNA to determine the phylogeography of Dendrobium officinale and four closely related taxa. Plastid DNA haplotype and nuclear data were shown to be discordant, suggesting reticulate evolution drove the species' diversification...
March 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28251872/phylogeography-of-human-y-chromosome-haplogroup-q3-l275-from-an-academic-citizen-science-collaboration
#14
Oleg Balanovsky, Vladimir Gurianov, Valery Zaporozhchenko, Olga Balaganskaya, Vadim Urasin, Maxat Zhabagin, Viola Grugni, Rebekah Canada, Nadia Al-Zahery, Alessandro Raveane, Shao-Qing Wen, Shi Yan, Xianpin Wang, Pierre Zalloua, Abdullah Marafi, Sergey Koshel, Ornella Semino, Chris Tyler-Smith, Elena Balanovska
BACKGROUND: The Y-chromosome haplogroup Q has three major branches: Q1, Q2, and Q3. Q1 is found in both Asia and the Americas where it accounts for about 90% of indigenous Native American Y-chromosomes; Q2 is found in North and Central Asia; but little is known about the third branch, Q3, also named Q1b-L275. Here, we combined the efforts of population geneticists and genetic genealogists to use the potential of full Y-chromosome sequencing for reconstructing haplogroup Q3 phylogeography and suggest possible linkages to events in population history...
February 7, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28247095/genome-sequencing-of-an-indian-peste-des-petits-ruminants-virus-isolate-izatnagar-94-and-its-implications-for-virus-diversity-divergence-and-phylogeography
#15
Amit Ranjan Sahu, Sajad Ahmad Wani, M Saminathan, Kaushal Kishor Rajak, Aditya Prasad Sahoo, Aruna Pandey, Shikha Saxena, Sonam Kanchan, Ashok Kumar Tiwari, Bina Mishra, D Muthuchelvan, R P Singh, Yaspal Singh, Mumtaz Baig, Bishnu Prasad Mishra, Raj Kumar Singh, Ravi Kumar Gandham
Peste des petits ruminants is an important transboundary disease infecting small ruminants. Genome or gene sequence analysis enriches our knowledge about the evolution and transboundary nature of the causative agent of this disease, peste des petits ruminants virus (PPRV). Although analysis using whole genome sequences of pathogens leads to more precise phylogenetic relationships, when compared to individual genes or partial sequences, there is still a need to identify specific genes/genomic regions that can provide evolutionary assessments consistent with those predicted with full-length genome sequences...
February 28, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28215350/species-delimitation-and-phylogeography-of-the-pectenia-species-complex-a-misunderstood-case-of-species-pairs-in-lichenized-fungi-where-reproduction-mode-does-not-delimit-lineages
#16
Mónica A G Otálora, Isabel Martínez, Gregorio Aragón, Mats Wedin
The main goal of this work was to study species boundaries in the genus Pectenia and elucidate the biogeographic history of the four currently accepted species. To accomplish this, we included 92 specimens across the range of Pectenia in Europe and northern Africa. We used three nuclear loci and assessed species circumscription using two Bayesian coalescent-based methods and the Bayes Factor approach. We reviewed the value of reproductive mode and other morphological features as predictors of monophyletic groups...
March 2017: Fungal Biology
https://www.readbyqxmd.com/read/28199442/phylogeographic-history-of-south-american-populations-of-the-silky-anteater-cyclopes-didactylus-pilosa-cyclopedidae
#17
Raphael Teodoro Franciscani Coimbra, Flávia Regina Miranda, Camila Clozato Lara, Marco Antônio Alves Schetino, Fabrício Rodrigues Dos Santos
Cyclopes didactylus, commonly called silky anteater, is the smallest and least studied of the anteaters. It is an arboreal species occurring in rainforests, ranging from southern Mexico to Central and South America, with an apparently disjoint distribution between Amazon and Atlantic rainforests in Brazil. Although seven subspecies are recognized, little is known about its geographical variation. Thus, to evaluate the population dynamics and evolutionary history of the South American silky anteater, we analyzed 1542 bp sequences of the mitochondrial control region (CR), COI and Cyt-b genes of 32 individuals...
February 13, 2017: Genetics and Molecular Biology
https://www.readbyqxmd.com/read/28187126/from-east-to-west-across-the-palearctic-phylogeography-of-the-invasive-lime-leaf-miner-phyllonorycter-issikii-lepidoptera-gracillariidae-and-discovery-of-a-putative-new-cryptic-species-in-east-asia
#18
Natalia Kirichenko, Paolo Triberti, Issei Ohshima, Julien Haran, Bong-Kyu Byun, Houhun Li, Sylvie Augustin, Alain Roques, Carlos Lopez-Vaamonde
Knowing the phylogeographic structure of invasive species is important for understanding the underlying processes of invasion. The micromoth Phyllonorycter issikii, whose larvae damage leaves of lime trees Tilia spp., was only known from East Asia. In the last three decades, it has been recorded in most of Europe, Western Russia and Siberia. We used the mitochondrial cytochrome c oxidase subunit I (COI) gene region to compare the genetic variability of P. issikii populations between these different regions...
2017: PloS One
https://www.readbyqxmd.com/read/28182721/correction-what-do-pneumocystis-organisms-tell-us-about-the-phylogeography-of-their-hosts-the-case-of-the-woodmouse-apodemus-sylvaticus-in-continental-europe-and-western-mediterranean-islands
#19
Christine Demanche, Manjula Deville, Johan Michaux, Véronique Barriel, Claire Pinçon, Cécile Marie Aliouat-Denis, Muriel Pottier, Christophe Noël, Eric Viscogliosi, El Moukhtar Aliouat, Eduardo Dei-Cas, Serge Morand, Jacques Guillot
[This corrects the article DOI: 10.1371/journal.pone.0120839.].
2017: PloS One
https://www.readbyqxmd.com/read/28176339/phylogeographic-insights-on-the-evolutionary-breakdown-of-heterostyly
#20
Wei Zhou, Spencer C H Barrett, Hai-Dong Li, Zhi-Kun Wu, Xin-Jia Wang, Hong Wang, De-Zhu Li
The breakdown of heterostyly to homostyly is a classic system for the investigation of evolutionary transitions from outcrossing to selfing. Loss of sexual polymorphism is characterized by changes to population morph structure and floral morphology. Here, we used molecular phylogeography to investigate the geographical context for the breakdown process in Primula chungensis, a species with distylous and homostylous populations. We genotyped plants from 20 populations throughout the entire range in south-west China using the chloroplast intergenic spacer (trnL-trnF), nuclear internal transcribed spacer (ITS) and 10 nuclear microsatellite loci, and determined the genetic relationships among populations and the variation in floral traits associated with homostyle evolution...
February 8, 2017: New Phytologist
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