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Bin Zhang, Kai He, Tao Wan, Peng Chen, Guozheng Sun, Shaoying Liu, Truong Son Nguyen, Liangkong Lin, Xuelong Jiang
BACKGROUND: Niviventer is a genus of white-bellied rats that are among the most common rodents in the Indo-Sundaic region. The taxonomy of the genus has undergone extensive revisions and remains controversial. The current phylogeny is unresolved and was developed primarily on the basis of mitochondrial genes. Identification is extremely difficult, and a large number of GenBank sequences seem to be problematic. We extensively sampled specimens of Niviventer in China and neighboring northern Vietnam, including topotypes of the most reported species (n = 6), subspecies (n = 8), and synonyms (n = 4)...
December 1, 2016: BMC Evolutionary Biology
Julieta M Manrique, Leandro R Jones
This work set out to shed light on the phylogeography of the SAR11 clade of Alphaproteobacteria, which is probably the most abundant group of heterotrophic bacteria on Earth. In particular, we assessed the degree to which empirical evidence (environmental DNA sequences) supports the concept that SAR11 lineages evolve faster than they are dispersed thus generating vicariant distributions, as predicted by recent simulation efforts. We generated 16S rRNA gene sequences from surface seawater collected at the South West Atlantic Ocean and combined these data with previously published sequences from similar environments from elsewhere...
November 25, 2016: Molecular Phylogenetics and Evolution
Christophe Dufresnes, Spartak N Litvinchuk, Amaël Borzée, Yikweon Jang, Jia-Tang Li, Ikuo Miura, Nicolas Perrin, Matthias Stöck
BACKGROUND: In contrast to the Western Palearctic and Nearctic biogeographic regions, the phylogeography of Eastern-Palearctic terrestrial vertebrates has received relatively little attention. In East Asia, tectonic events, along with Pleistocene climatic conditions, likely affected species distribution and diversity, especially through their impact on sea levels and the consequent opening and closing of land-bridges between Eurasia and the Japanese Archipelago. To better understand these effects, we sequenced mitochondrial and nuclear markers to determine phylogeographic patterns in East-Asian tree frogs, with a particular focus on the widespread H...
November 23, 2016: BMC Evolutionary Biology
Alexander N Lukashev, Alexander S Klimentov, Svetlana E Smirnova, Tamara K Dzagurova, Jan Felix Drexler, Anatoly P Gmyl
Crimean Congo hemorrhagic fever virus (CCHFV) is one of the most severe viral zoonozes. It is prevalent throughout Africa, Asia and southern Europe. Limited availability of sequence data has hindered phylogeographic studies. The complete genomic sequence of all three segments of 14 Crimean Congo hemorrhagic fever virus strains isolated from 1958-2000 in Russia, Central Asia and Africa was identified. Each genomic segment was independently subjected to continuous Bayesian phylogeographic analysis. The origin of each genomic segment was traced to Africa about 1,000-5,000 years ago...
2016: PloS One
Mohamed A Daw, Abdallah A El-Bouzedi, Mohamed O Ahmed, Aghnyia A Dau, Mohamed M Agnan, Aisha M Drah
AIM: To assess hepatitis C virus (HCV) geographic integration, evaluate the spatial and temporal evolution of HCV worldwide and propose how to diminish its burden. METHODS: A literature search of published articles was performed using PubMed, MEDLINE and other related databases up to December 2015. A critical data assessment and analysis regarding the epidemiological integration of HCV was carried out using the meta-analysis method. RESULTS: The data indicated that HCV has been integrated immensely over time and through various geographical regions worldwide...
November 12, 2016: World Journal of Virology
Jessica J Wadley, Damien A Fordham, Vicki A Thomson, Euan G Ritchie, Jeremy J Austin
The distribution of antilopine wallaroo, Macropus antilopinus, is marked by a break in the species' range between Queensland and the Northern Territory, coinciding with the Carpentarian barrier. Previous work on M. antilopinus revealed limited genetic differentiation between the Northern Territory and Queensland M. antilopinus populations across this barrier. The study also identified a number of divergent lineages in the Northern Territory, but was unable to elucidate any geographic structure. Here, we re-examine these results to (1) determine phylogeographic patterns across the range of M...
November 2016: Ecology and Evolution
Anshuman Mishra, Sheikh Nizammuddin, Chandana Basu Mallick, Sakshi Singh, Satya Prakash, Niyamat Ali Siddiqui, Niraj Rai, S Justin Carlus, D V S Sudhakar, Vishnu P Tripathi, Märt Möls, Xana Kim-Howard, Hemlata Dewangan, Abhishek Mishra, Alla G Reddy, Biswajit Roy, Krishna Pandey, Gyaneshwer Chaubey, Pradeep Das, Swapan K Nath, Lalji Singh, Kumarasamy Thangaraj
Our understanding of genetics of skin pigmentation has been largely skewed towards populations of European ancestry imparting much less attention to South Asian populations, who behold huge pigmentation diversity. Here, we investigate the skin pigmentation variation in a cohort of 1167 individuals in Middle Gangetic Plain of Indian subcontinent. Our data confirms the association of rs1426654 with skin pigmentation among South Asians, consistent with previous studies and also reveals association for rs2470102 SNP...
November 17, 2016: Journal of Investigative Dermatology
Philippe Gaubert, Flobert Njiokou, Gabriel Ngua, Komlan Afiademanyo, Sylvain Dufour, Jean Malekani, Sery Gonedelé Bi, Christelle Tougard, Ayodeji Olayemi, Emmanuel Danquah, Chabi A M S Djagoun, Prince Kaleme, Casimir Nebesse Mololo, William Stanley, Shu-Jin Luo, Agostinho Antunes
Knowledge on faunal diversification in African rainforests remains scarce. We used phylogeography to assess (i) the role of Pleistocene climatic oscillations in the diversification of the African common pangolin (Manis tricuspis) and (ii) the utility of our multilocus approach for taxonomic delineation and trade tracing of this heavily poached species. We sequenced 101 individuals for two mitochondrial DNA (mtDNA), two nuclear DNA and one Y-borne gene fragments (totalizing 2602 bp). We used a time-calibrated, Bayesian inference phylogenetic framework and conducted character-based, genetic and phylogenetic delineation of species hypotheses within African common pangolins...
December 2016: Molecular Ecology
David B Lowry, Sean Hoban, Joanna L Kelley, Katie E Lotterhos, Laura K Reed, Michael F Antolin, Andrew Storfer
Understanding how and why populations evolve is of fundamental importance to molecular ecology. RADseq (Restriction site-Associated DNA sequencing), a popular reduced representation method, has ushered in a new era of genome-scale research for assessing population structure, hybridization, demographic history, phylogeography, and migration. RADseq has also been widely used to conduct genome scans to detect loci involved in adaptive divergence among natural populations. Here, we examine the capacity of those RADseq-based genome scan studies to detect loci involved in local adaptation...
November 12, 2016: Molecular Ecology Resources
C Rune Stensvold, C Graham Clark
Several typing methods have been used in studies aiming to unravel the molecular epidemiology of Blastocystis, which is one of the most common intestinal parasites in human and many non-human hosts. Such studies have the potential to add to knowledge on Blastocystis transmission, host specificity, phylogeography, and clinical and public health significance, but rely on robust, standardized methods by which data can be generated and compared directly between studies. One of the most used methods is "barcoding,", which involves single-round PCR amplification and sequencing of partial small subunit ribosomal RNA genes of the parasites...
November 18, 2016: Current Protocols in Microbiology
Javier Bobo-Pinilla, Sara B Barrios de León, Jaume Seguí Colomar, Giuseppe Fenu, Gianluigi Bacchetta, Julio Peñas de Giles, María Montserrat Martínez-Ortega
Although it has been traditionally accepted that Arenaria balearica (Caryophyllaceae) could be a relict Tertiary plant species, this has never been experimentally tested. Nor have the palaeohistorical reasons underlying the highly fragmented distribution of the species in the Western Mediterranean region been investigated. We have analysed AFLP data (213) and plastid DNA sequences (226) from a total of 250 plants from 29 populations sampled throughout the entire distribution range of the species in Majorca, Corsica, Sardinia, and the Tuscan Archipelago...
2016: PeerJ
Ingi Agnarsson, Stephanie M LeQuier, Matjaž Kuntner, Ren-Chung Cheng, Jonathan A Coddington, Greta Binford
The Caribbean islands harbor rich biodiversity with high levels of single island endemism. Stretches of ocean between islands represent significant barriers to gene-flow. Yet some native species are widespread, indicating dispersal across oceans, even in wingless organisms like spiders. Argiope argentata (Fabricius, 1775) is a large, charismatic, and widespread species of orb-weaving spider ranging from the United States to Argentina and is well known to balloon. Here we explore the phylogeography of Argiope argentata in the Caribbean as a part of the multi-lineage CarBio project, through mtDNA haplotype and multi-locus phylogenetic analyses...
2016: ZooKeys
Patricia Marrero, Khaled K Abu-Amero, Jose M Larruga, Vicente M Cabrera
BACKGROUND: From a mtDNA dominant perspective, the exit from Africa of modern humans to colonize Eurasia occurred once, around 60 kya, following a southern coastal route across Arabia and India to reach Australia short after. These pioneers carried with them the currently dominant Eurasian lineages M and N. Based also on mtDNA phylogenetic and phylogeographic grounds, some authors have proposed the coeval existence of a northern route across the Levant that brought mtDNA macrohaplogroup N to Australia...
November 10, 2016: BMC Evolutionary Biology
Taiadjana M Fortuna, Alodie Snirc, Hélène Badouin, Jérome Gouzy, Sophie Siguenza, Diane Esquerre, Stéphanie Le Prieur, Jacqui A Shykoff, Tatiana Giraud
BACKGROUND: Anther-smut fungi belonging to the genus Microbotryum sterilize their host plants by aborting ovaries and replacing pollen by fungal spores. Sibling Microbotryum species are highly specialized on their host plants and they have been widely used as models for studies of ecology and evolution of plant pathogenic fungi. However, most studies have focused, so far, on M. lychnidis-dioicae that parasitizes the white campion Silene latifolia. Microbotryum saponariae, parasitizing mainly Saponaria officinalis, is an interesting anther-smut fungus, since it belongs to a tetrapolar lineage (i...
2016: PloS One
Carla C Stout, Milton Tan, Alan R Lemmon, Emily Moriarty Lemmon, Jonathan W Armbruster
BACKGROUND: Cypriniformes (minnows, carps, loaches, and suckers) is the largest group of freshwater fishes in the world (~4300 described species). Despite much attention, previous attempts to elucidate relationships using molecular and morphological characters have been incongruent. In this study we present the first phylogenomic analysis using anchored hybrid enrichment for 172 taxa to represent the order (plus three out-group taxa), which is the largest dataset for the order to date (219 loci, 315,288 bp, average locus length of 1011 bp)...
November 9, 2016: BMC Evolutionary Biology
Vasily V Grebennikov, Katsura Morimoto
The herein reported beetles (Figs 1, 2) were repeatedly sampled by the first author since 2008 by sifting leaf litter in two forested localities in Southwest China: Cang Shan Mountain Range in Yunnan and Mount Emei in Sichuan (Fig. 3). The specimens' characteristic appearance and edaphic way of life were consistent with those of various members of the subfamily Cossoninae (Morimoto 1973, 1993, 1995), although a more precise taxonomic assignment remained elusive. In 2015 the second author saw images of these beetles and suggested their affinities to the genus Cotasterosoma Konishi, 1962...
October 28, 2016: Zootaxa
Mandev S Gill, Lam Si Tung Ho, Guy Baele, Philippe Lemey, Marc A Suchard
Understanding the processes that give rise to quantitative measurements associated with molecular sequence data remains an important issue in statistical phylogenetics. Examples of such measurements include geographic coordinates in the context of phylogeography and phenotypic traits in the context of comparative studies. A popular approach is to model the evolution of continuously varying traits as a Brownian diffusion process acting on a phylogenetic tree. However, standard Brownian diffusion is quite restrictive and may not accurately characterize certain trait evolutionary processes...
October 18, 2016: Systematic Biology
Emily E Puckett, Jane Park, Matthew Combs, Michael J Blum, Juliet E Bryant, Adalgisa Caccone, Federico Costa, Eva E Deinum, Alexandra Esther, Chelsea G Himsworth, Peter D Keightley, Albert Ko, Åke Lundkvist, Lorraine M McElhinney, Serge Morand, Judith Robins, James Russell, Tanja M Strand, Olga Suarez, Lisa Yon, Jason Munshi-South
Native to China and Mongolia, the brown rat (Rattus norvegicus) now enjoys a worldwide distribution. While black rats and the house mouse tracked the regional development of human agricultural settlements, brown rats did not appear in Europe until the 1500s, suggesting their range expansion was a response to relatively recent increases in global trade. We inferred the global phylogeography of brown rats using 32 k SNPs, and detected 13 evolutionary clusters within five expansion routes. One cluster arose following a southward expansion into Southeast Asia...
October 26, 2016: Proceedings. Biological Sciences
Anahí Espíndola, Megan Ruffley, Megan L Smith, Bryan C Carstens, David C Tank, Jack Sullivan
Identifying units of biological diversity is a major goal of organismal biology. An increasing literature has focused on the importance of cryptic diversity, defined as the presence of deeply diverged lineages within a single species. While most discoveries of cryptic lineages proceed on a taxon-by-taxon basis, rapid assessments of biodiversity are needed to inform conservation policy and decision-making. Here, we introduce a predictive framework for phylogeography that allows rapidly identifying cryptic diversity...
October 26, 2016: Proceedings. Biological Sciences
Irene Lema-Suárez, Elvira Sahuquillo, Neus Marí-Mena, Manuel Pimentel
PREMISE OF THE STUDY: Nonplastid microsatellite primers were developed for the first time in the Euro-Siberian complex of Anthoxanthum (Poaceae), a genus of temperate grasses in which reticulate evolution is common. METHODS AND RESULTS: A microsatellite-enriched genomic DNA library allowed the detection of 500 fragments containing a microsatellite motif. Fifteen primer pairs were selected for an extended primer test. A preliminary analysis was conducted on the Eurasian diploid lineages of Anthoxanthum, with special emphasis on three populations of the Mediterranean A...
October 2016: Applications in Plant Sciences
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