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https://www.readbyqxmd.com/read/28704536/phylogeography-in-nassarius-mud-snails-complex-patterns-in-congeneric-species
#1
Chuanliang Pu, Haitao Li, Aijia Zhu, Yiyong Chen, Yan Zhao, Aibin Zhan
One major goal for phylogeographical studies is to elucidate respective roles of multiple evolutionary and ecological forces that shape the current distribution patterns. In marine and coastal ecosystems, it has been generated a common realization that species with enormous population size and pelagic larval stages can disperse across broad geographical scales, leading to weak or even no phylogeographical structure across large geographical scales. However, the violation of such realization has been frequently reported, and it remains largely unexplored on mechanisms responsible for various phylogeographical patterns observed in different species at varied geographical scales...
2017: PloS One
https://www.readbyqxmd.com/read/28690819/molecular-genetic-analysis-of-two-native-desert-palm-genera-washingtonia-and-brahea-from-the-baja-california-peninsula-and-guadalupe-island
#2
Anastasia Klimova, Joseph I Hoffman, Jesus N Gutierrez-Rivera, Jose Leon de la Luz, Alfredo Ortega-Rubio
The complex geological and ecological processes that have generated high levels of biodiversity and endemism in the Baja California Peninsula have been the subject of intensive study. However, relatively little is known about phylogeography of the iconic endemic palm species of this region. We therefore analyzed a total of 2,294 bp of chloroplast and 738 bp of nuclear sequence data in 169 samples of five native palm species from Baja California, Sonora and Guadalupe Island. We found that Washingtonia and Brahea palms had low levels of genetic diversity and were highly structured, with the majority of species and major geographic regions being characterized by distinct haplotypes...
July 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28680070/whole-mitogenomes-reveal-the-history-of-swamp-buffalo-initially-shaped-by-glacial-periods-and-eventually-modelled-by-domestication
#3
S Wang, N Chen, M R Capodiferro, T Zhang, H Lancioni, H Zhang, Y Miao, V Chanthakhoun, M Wanapat, M Yindee, Y Zhang, H Lu, L Caporali, R Dang, Y Huang, X Lan, M Plath, H Chen, J A Lenstra, A Achilli, C Lei
The newly sequenced mitochondrial genomes of 107 Asian swamp buffalo (Bubalus bubalis carabensis) allowed the reconstruction of the matrilineal divergence since ~900 Kya. Phylogenetic trees and Bayesian skyline plots suggest a role of the glacial periods in the demographic history of swamp buffalo. The ancestral swamp-buffalo mitogenome is dated ~232 ± 35 Kya. Two major macro-lineages diverged during the 2(nd) Pleistocene Glacial Period (~200-130 Kya), but most (~99%) of the current matrilines derive from only two ancestors (SA1'2 and SB) that lived around the Last Glacial Maximum (~26-19 Kya)...
July 5, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28678837/reconstructing-the-recent-west-nile-virus-lineage-2-epidemic-in-europe-and-italy-using-discrete-and-continuous-phylogeography
#4
Gianguglielmo Zehender, Carla Veo, Erika Ebranati, Valentina Carta, Francesca Rovida, Elena Percivalle, Ana Moreno, Davide Lelli, Mattia Calzolari, Antonio Lavazza, Chiara Chiapponi, Laura Baioni, Gioia Capelli, Silvia Ravagnan, Graziana Da Rold, Enrico Lavezzo, Giorgio Palù, Fausto Baldanti, Luisa Barzon, Massimo Galli
West Nile virus lineage 2 (WNV-2) was mainly confined to sub-Saharan Africa until the early 2000s, when it was identified for the first time in Central Europe causing outbreaks of human and animal infection. The aim of this study was to reconstruct the origin and dispersion of WNV-2 in Central Europe and Italy on a phylodynamic and phylogeographical basis. To this aim, discrete and continuous space phylogeographical models were applied to a total of 33 newly characterised full-length viral genomes obtained from mosquitoes, birds and humans in Northern Italy in the years 2013-2015 aligned with 64 complete sequences isolated mainly in Europe...
2017: PloS One
https://www.readbyqxmd.com/read/28674651/a-new-parrot-taxon-from-the-yucat%C3%A3-n-peninsula-mexico-its-position-within-genus-amazona-based-on-morphology-and-molecular-phylogeny
#5
Tony Silva, Antonio Guzmán, Adam D Urantówka, Paweł Mackiewicz
Parrots (Psittaciformes) are a diverse group of birds which need urgent protection. However, many taxa from this order have an unresolved status, which makes their conservation difficult. One species-rich parrot genus is Amazona, which is widely distributed in the New World. Here we describe a new Amazona form, which is endemic to the Yucatán Peninsula. This parrot is clearly separable from other Amazona species in eleven morphometric characters as well as call and behavior. The clear differences in these features imply that the parrot most likely represents a new species...
2017: PeerJ
https://www.readbyqxmd.com/read/28672032/mountaintops-phylogeography-a-case-study-using-small-mammals-from-the-andes-and-the-coast-of-central-chile
#6
R Eduardo Palma, Pablo Gutiérrez-Tapia, Juan F González, Dusan Boric-Bargetto, Fernando Torres-Pérez
We evaluated if two sigmodontine rodent taxa (Abrothrix olivacea and Phyllotis darwini) from the Andes and Coastal mountaintops of central Chile, experienced distributional shifts due to altitudinal movements of habitat and climate change during and after the Last Glacial Maximum (LGM). We tested the hypothesis that during LGM populations of both species experienced altitudinal shifts from the Andes to the lowlands and the coastal Cordillera, and then range retractions during interglacial towards higher elevations in the Andes...
2017: PloS One
https://www.readbyqxmd.com/read/28659474/phylogeography-of-coxsackievirus-a16-reveals-global-transmission-pathways-and-recent-emergence-and-spread-of-a-recombinant-genogroup
#7
Chervin Hassel, Audrey Mirand, Agnes Farkas, Sabine Diedrich, Hartwig P Huemer, Hélène Peigue-Lafeuille, Christine Archimbaud, Cécile Henquell, Jean-Luc Bailly
Coxsackievirus A16 (CV-A16; Picornaviridae) is an enterovirus (EV) type associated with hand-foot-and-mouth disease (HFMD) in children. To investigate the spatial spread of CV-A16, we used viral sequence data sampled during a prospective sentinel surveillance of HFMD in France (2010--2014) and phylogenetic reconstruction. A dataset of 168 VP1 sequences was assembled with 416 publicly available sequences of various geographic origins. The CV-A16 sequences reported were assigned to two clades, genogroup B and a previously uncharacterized clade D...
June 28, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28649336/phylogeography-of-a-widespread-small-carnivore-the-western-spotted-skunk-spilogale-gracilis-reveals-temporally-variable-signatures-of-isolation-across-western-north-america
#8
Adam W Ferguson, Molly M McDonough, Gema I Guerra, Margaret Rheude, Jerry W Dragoo, Loren K Ammerman, Robert C Dowler
We analyzed phylogeographic patterns in the western spotted skunk, Spilogale gracilis Merriam, 1890 (Carnivora: Mephitidae) in relation to historical events associated with Pre-Pleistocene Divergence (PPD) and Quaternary climate change (QCC) using mitochondrial DNA from 97 individuals distributed across Western North America. Divergence times were generated using BEAST to estimate when isolation in putative refugia occurred. Patterns and timing of demographic expansion was performed using Bayesian skyline plot...
June 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28640885/phylogeography-of-a-tough-rock-survivor-in-european-dry-grasslands
#9
Daniela Listl, Peter Poschlod, Christoph Reisch
Phylogeographic analyses of plants in Europe have revealed common glacial refugia and migration routes for several trees and herbs with arctic-alpine distributions. The postglacial histories of dry grassland species in central Europe have rarely been analyzed, even though the extremely species-rich habitat is threatened. Sedum album (Crassulaceae) is a common inhabitant of rocky sites in central European dry grasslands. We inferred the phylogeographic history of S. album over its distribution range in Europe...
2017: PloS One
https://www.readbyqxmd.com/read/28637254/phylogeography-of-lionfishes-pterois-indicate-taxonomic-over-splitting-and-hybrid-origin-of-the-invasive-pterois-volitans
#10
Christie L Wilcox, Hiroyuki Motomura, Mizuki Matsunuma, Brian W Bowen
The lionfish is an iconic marine fish, and recently renowned for a disastrous introduction into the West Atlantic. Genetic surveys of the putative invaders (Pterois volitans and P. miles) in their natural Indo-Pacific range can illuminate both topics. Previous research indicated that P. volitans and P. miles are sister species that hybridize in the invasive range, but hybridization in the native range is unknown. Here we apply mtDNA COI and two nuclear introns (S7 RP1 and Gpd2) from 229 lionfish including the two invaders and two closely-related taxa (44 P...
June 16, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/28633358/phylogeography-of-herbarium-specimens-of-asexually-propagated-paper-mulberry-broussonetia-papyrifera-l-l-h%C3%A3-r-ex-vent-moraceae-reveals-genetic-diversity-across-the-pacific
#11
Claudia Payacan, Ximena Moncada, Gloria Rojas, Andrew Clarke, Kuo-Fang Chung, Robin Allaby, Daniela Seelenfreund, Andrea Seelenfreund
Background and Aims: Paper mulberry or Broussonetia papyrifera (L.) L'Hér. ex Vent. (Moraceae) is a dioecious species native to continental South-east Asia and East Asia, including Taiwan, that was introduced to the Pacific by pre-historic voyagers and transported intentionally and propagated asexually across the full range of Austronesian expansion from Taiwan to East Polynesia. The aim of this study was to gain insight into the dispersal of paper mulberry into Oceania through the genetic analysis of herbaria samples which represent a more complete coverage of the historical geographical range of the species in the Pacific before later introductions and local extinctions occurred...
June 14, 2017: Annals of Botany
https://www.readbyqxmd.com/read/28628442/phylogeography-of-burkholderia-pseudomallei-isolates-western-hemisphere
#12
Jay E Gee, Christopher A Gulvik, Mindy G Elrod, Dhwani Batra, Lori A Rowe, Mili Sheth, Alex R Hoffmaster
The bacterium Burkholderia pseudomallei causes melioidosis, which is mainly associated with tropical areas. We analyzed single-nucleotide polymorphisms (SNPs) among genome sequences from isolates of B. pseudomallei that originated in the Western Hemisphere by comparing them with genome sequences of isolates that originated in the Eastern Hemisphere. Analysis indicated that isolates from the Western Hemisphere form a distinct clade, which supports the hypothesis that these isolates were derived from a constricted seeding event from Africa...
July 2017: Emerging Infectious Diseases
https://www.readbyqxmd.com/read/28616188/life-history-predicts-past-and-present-population-connectivity-in-two-sympatric-sea-stars
#13
Jonathan B Puritz, Carson C Keever, Jason A Addison, Sergio S Barbosa, Maria Byrne, Michael W Hart, Richard K Grosberg, Robert J Toonen
Life-history traits, especially the mode and duration of larval development, are expected to strongly influence the population connectivity and phylogeography of marine species. Comparative analysis of sympatric, closely related species with differing life histories provides the opportunity to specifically investigate these mechanisms of evolution but have been equivocal in this regard. Here, we sample two sympatric sea stars across the same geographic range in temperate waters of Australia. Using a combination of mitochondrial DNA sequences, nuclear DNA sequences, and microsatellite genotypes, we show that the benthic-developing sea star, Parvulastra exigua, has lower levels of within- and among-population genetic diversity, more inferred genetic clusters, and higher levels of hierarchical and pairwise population structure than Meridiastra calcar, a species with planktonic development...
June 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28611408/phylogeography-of-petrolisthes-armatus-an-invasive-species-with-low-dispersal-ability
#14
Alexandra Hiller, Harilaos A Lessios
Theoretically, species with high population structure are likely to expand their range, because marginal populations are free to adapt to local conditions; however, meta-analyses have found a negative relation between structure and invasiveness. The crab Petrolisthes armatus has a wide native range, which has expanded in the last three decades. We sequenced 1718 bp of mitochondrial DNA from native and recently established populations to determine the population structure of the former and the origin of the latter...
June 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28602572/the-near-east-as-a-cradle-of-biodiversity-a-phylogeography-of-banded-newts-genus-ommatotriton-reveals-extensive-inter-and-intraspecific-genetic-differentiation
#15
Isolde van Riemsdijk, Jan W Arntzen, Sergé Bogaerts, Michael Franzen, Spartak N Litvinchuk, Kurtuluş Olgun, Ben Wielstra
The banded newt (genus Ommatotriton) is widely distributed in the Near East (Anatolia, Caucasus and the Levant) - an understudied region from the perspective of phylogeography. The genus is polytypic, but the number of species included and the phylogenetic relationships between them are not settled. We sequenced two mitochondrial and two nuclear DNA markers throughout the range of Ommatotriton. For mtDNA we constructed phylogenetic trees, estimated divergence times using fossil calibration, and investigated changes in effective population size with Bayesian skyline plots and mismatch analyses...
June 13, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28600759/whole-genome-enrichment-using-rna-probes-and-sequencing-of-chlamydia-trachomatis-directly-from-clinical-samples
#16
Amanda Claire Brown, Mette T Christiansen
Whole-genome sequencing is a powerful, high-resolution tool that can be used to generate accurate data on bacterial population structure, phylogeography, and mutations associated with antimicrobial resistance. The ability to sequence pathogen genomes directly from clinical specimens, without the requirement for in vitro culturing, is attractive in terms of time- and labor-saving, especially in the case of slow-growing, or obligate intracellular pathogens, such as Chlamydia trachomatis. However clinical samples typically contain too low levels of pathogen nucleic acid, plus relatively high levels of human and natural microbiota DNA/RNA, to make this a viable option...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28594840/phylogeography-on-the-rocks-the-contribution-of-current-and-historical-factors-in-shaping-the-genetic-structure-of-chthamalus-montagui-crustacea-cirripedia
#17
Federica G Pannacciulli, Ferruccio Maltagliati, Christian de Guttry, Yair Achituv
The model marine broadcast-spawner barnacle Chthamalus montagui was investigated to understand its genetic structure and quantify levels of population divergence, and to make inference on historical demography in terms of time of divergence and changes in population size. We collected specimens from rocky shores of the north-east Atlantic Ocean (4 locations), Mediterranean Sea (8) and Black Sea (1). The 312 sequences 537 bp) of the mitochondrial cytochrome c oxidase I allowed to detect 130 haplotypes. High within-location genetic variability was recorded, with haplotype diversity ranging between h = 0...
2017: PloS One
https://www.readbyqxmd.com/read/28588562/phylogeography-and-coevolution-of-bamboo-mosaic-virus-and-its-associated-satellite-rna
#18
Ing-Nang Wang, Wen-Bin Yeh, Na-Sheng Lin
Bamboo mosaic virus (BaMV), a plant potexvirus, has been found only in infected bamboo species. It is frequently associated with a large, linear single-stranded satellite RNA (satBaMV) that encodes a non-structural protein. Decades of collecting across a wide geographic area in Asia have accumulated a sizable number of BaMV and satBaMV isolates. In this study, we reconstructed the BaMV phylogeny and satBaMV phylogeny with partial coat protein gene sequences and partial genomic sequences, respectively. The evolutionary relationships allowed us to infer the phylogeography of BaMV and satBaMV on the Asian continent and its outlying islands...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28587867/spatiotemporal-dynamics-of-influenza-a-h1n1-pdm09-in-brazil-during-the-pandemic-and-post-pandemic-periods
#19
Alessandra C B Manito, Tiago Gräf, Vagner R Lunge, Nilo Ikuta
Influenza A(H1N1)pdm09 was responsible for the first global flu pandemic in 21st century affecting all the world. In Brazil, A(H1N1)pdm09 is still circulating as a seasonal virus, causing deaths every year. Nevertheless, the viral diffusion process that yearly seeds new influenza strains in the country was not investigated yet. The aim of the current study was to describe the phylodynamics and phylogeography of influenza A(H1N1)pdm09 in Brazil between 2009 and 2014. Neuraminidase sequences from Brazil and other regions of the World were retrieved and analyzed...
June 3, 2017: Virus Research
https://www.readbyqxmd.com/read/28583078/the-conquering-of-north-america-dated-phylogenetic-and-biogeographic-inference-of-migratory-behavior-in-bee-hummingbirds
#20
Yuyini Licona-Vera, Juan Francisco Ornelas
BACKGROUND: Geographical and temporal patterns of diversification in bee hummingbirds (Mellisugini) were assessed with respect to the evolution of migration, critical for colonization of North America. We generated a dated multilocus phylogeny of the Mellisugini based on a dense sampling using Bayesian inference, maximum-likelihood and maximum parsimony methods, and reconstructed the ancestral states of distributional areas in a Bayesian framework and migratory behavior using maximum parsimony, maximum-likelihood and re-rooting methods...
June 5, 2017: BMC Evolutionary Biology
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