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https://www.readbyqxmd.com/read/29906638/the-benefits-of-analysing-complete-mitochondrial-genomes-deep-insights-into-the-phylogeny-and-population-structure-of-echinococcus-granulosus-sensu-lato-genotypes-g6-and-g7
#1
Teivi Laurimäe, Liina Kinkar, Thomas Romig, Rihab A Omer, Adriano Casulli, Gérald Umhang, Robin B Gasser, Abdul Jabbar, Mitra Sharbatkhori, Hossein Mirhendi, Francisco Ponce-Gordo, Lorena E Lazzarini, Silvia V Soriano, Antonio Varcasia, Mohammad Rostami Nejad, Vanessa Andresiuk, Pablo Maravilla, Luis Miguel González, Monika Dybicz, Jakub Gawor, Mindaugas Šarkūnas, Viliam Šnábel, Tetiana Kuzmina, Urmas Saarma
Cystic echinococcosis (CE) is a zoonotic disease caused by the larval stage of the species complex Echinococcus granulosus sensu lato. Within this complex, genotypes G6 and G7 have been frequently associated with human CE worldwide. Previous studies exploring the genetic variability and phylogeography of genotypes G6 and G7 have been based on relatively short mtDNA sequences, and the resolution of these studies has often been low. Moreover, using short sequences, the distinction between G6 and G7 has in some cases remained challenging...
June 12, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29906604/barcoding-and-multi-locus-phylogeography-of-the-globally-distributed-calcareous-tubeworm-genus-hydroides-gunnerus-1768-annelida-polychaeta-serpulidae
#2
Yanan Sun, Eunice Wong, Shane T Ahyong, Jane E Williamson, Pat A Hutchings, Elena K Kupriyanova
Hydroides is a large and diverse group of calcareous tubeworms (Serpulidae, Annelida) recognised by a distinctive but variable two-tiered operculum. Despite considerable research using several species of Hydroides as models in ecological and biofouling studies, phylogenetic and biogeographic relationships within the genus are still poorly understood. Using combined mitochondrial (COI, cytochrome b) and nuclear (18S, 28S and ITS) gene markers for 284 individuals of 45 morphospecies of Hydroides, we investigated the global phylogenetic and biogeographic relationships within the genus...
June 12, 2018: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29904267/exploring-monacha-cantiana-montagu-1803-phylogeography-cryptic-lineages-and-new-insights-into-the-origin-of-the-english-populations-eupulmonata-stylommatophora-hygromiidae
#3
Joanna R Pieńkowska, Giuseppe Manganelli, Folco Giusti, Alessandro Hallgass, Andrzej Lesicki
Molecular analysis of nucleotide sequences of mitochondrial cytochrome oxidase subunit 1 (COI) and 16S ribosomal DNA (16SrDNA) as well as nuclear histone 3 (H3) and internal transcribed spacer 2 of rDNA (ITS2) gene fragments together with morphological analysis of shell and genitalia features showed that English, French and Italian populations usually assigned to Monacha cantiana consist of four distinct lineages (CAN-1, CAN-2, CAN-3, CAN-4). One of these lineages (CAN-1) included most of the UK (five sites) and Italian (five sites) populations examined...
2018: ZooKeys
https://www.readbyqxmd.com/read/29889225/nuclear-genetic-analysis-of-the-red-fox-across-its-trans-pacific-range
#4
Benjamin N Sacks, Zachary T Lounsberry, Mark J Statham
The red fox (Vulpes vulpes) occurs on multiple continents in diverse habitats, making it an informative system for evolutionary genomic research. However, its phylogeography remains unclear. Previously, mitochondrial DNA and small numbers of nuclear loci provided discordant views. Both markers indicated deep divergence (~ 0.5 MY) between Eurasian and southern North American populations but differed in the apparent continental affinity of Alaskan red foxes, implying some degree of gene exchange during secondary contact (~0...
June 7, 2018: Journal of Heredity
https://www.readbyqxmd.com/read/29888129/in-quest-of-contact-phylogeography-of-helmeted-terrapins-pelomedusa-galeata-p-subrufa-sensu-stricto
#5
Melita Vamberger, Margaretha D Hofmeyr, Flora Ihlow, Uwe Fritz
Based on rangewide sampling and three mitochondrial and two nuclear markers (together up to 1,850 bp and 1,840 bp, respectively), we examine the phylogeography of two helmeted terrapin species ( Pelomedusa galeata and P. subrufa sensu stricto) and infer shifts of climatically suitable spaces since the Last Glacial Maximum using a modeling approach. Whilst P. galeata displays significant phylogeographic structuring across its range and consists of two deeply divergent lineages that could represent distinct species, P...
2018: PeerJ
https://www.readbyqxmd.com/read/29876070/evolutionary-and-demographic-processes-shaping-geographic-patterns-of-genetic-diversity-in-a-keystone-species-the-african-forest-elephant-loxodonta-cyclotis
#6
Yasuko Ishida, Natalie A Gugala, Nicholas J Georgiadis, Alfred L Roca
The past processes that have shaped geographic patterns of genetic diversity may be difficult to infer from current patterns. However, in species with sex differences in dispersal, differing phylogeographic patterns between mitochondrial (mt) and nuclear (nu) DNA may provide contrasting insights into past events. Forest elephants ( Loxodonta cyclotis ) were impacted by climate and habitat change during the Pleistocene, which likely shaped phylogeographic patterns in mitochondrial (mt) DNA that have persisted due to limited female dispersal...
May 2018: Ecology and Evolution
https://www.readbyqxmd.com/read/29873754/a-haplotype-information-theory-method-reveals-genes-of-evolutionary-interest-in-european-vs-asian-pigs
#7
Nicholas J Hudson, Marina Naval-Sánchez, Laercio Porto-Neto, Miguel Pérez-Enciso, Antonio Reverter
Asian and European wild boars were independently domesticated ca. 10,000 years ago. Since the 17th century, Chinese breeds have been imported to Europe to improve the genetics of European animals by introgression of favourable alleles, resulting in a complex mosaic of haplotypes. To interrogate the structure of these haplotypes further, we have run a new haplotype segregation analysis based on information theory, namely compression efficiency (CE). We applied the approach to sequence data from individuals from each phylogeographic region (n = 23 from Asia and Europe) including a number of major pig breeds...
June 5, 2018: Journal of Animal Science
https://www.readbyqxmd.com/read/29872442/phylogeography-and-ecological-niche-modeling-reveal-reduced-genetic-diversity-and-colonization-patterns-of-skunk-cabbage-symplocarpus-foetidus-araceae-from-glacial-refugia-in-eastern-north-america
#8
Seon-Hee Kim, Myong-Suk Cho, Pan Li, Seung-Chul Kim
Alternating glacial and interglacial periods during the Quaternary have dramatically affected the distribution and population genetic structure of plant and animal species throughout the northern hemisphere. Surprisingly, little is known about the post-glacial recolonization history of wetland herbaceous perennials that are widely distributed in the understory of deciduous or mixed deciduous-evergreen forests in eastern North America. In this study, we investigated infraspecific variation among 32 populations of skunk cabbage, Symplocarpus foetidus , to test the hypothesis that the extant species diversity of skunk cabbage is the result of a post-glacial range expansion from southern refugia during the Quaternary Ice Age...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29868119/phylogeography-of-parasyncalathium-souliei-asteraceae-and-its-potential-application-in-delimiting-phylogeoregions-in-the-qinghai-tibet-plateau-qtp-hengduan-mountains-hdm-hotspot
#9
Nan Lin, Tao Deng, Michael J Moore, Yanxia Sun, Xianhan Huang, Wenguang Sun, Dong Luo, Hengchang Wang, Jianwen Zhang, Hang Sun
Biogeographic regionalization can help to better understand diversity in biogeography, conservation, and macroecology. Historical regionalization schemes typically focus on species distributions, often rarely considering the rich context that phylogeographic information can provide. We investigated whether phylogeographic data could help to delineate floristic regions in the Qinghai-Tibet Plateau (QTP)-Hengduan Mountains (HDM) region by analyzing phylogeographic structure in the herb Parasyncalathium souliei (Asteraceae)...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29805298/reconstructed-historical-distribution-and-phylogeography-unravels-non-steppic-origin-of-caucasotachea-vindobonensis-gastropoda-helicidae
#10
Łukasz Kajtoch, Angus Davison, Adele Grindon, Tamás Deli, Gábor Sramkó, Mariusz Gwardjan, Sergei Kramarenko, Dominika Mierzwa-Szymkowiak, Rafał Ruta, Radosław Ścibior, János Pál Tóth, Chris Wade, Michał Kolasa, Roman V Egorov, Zoltán Fehér
Existing data on the phylogeography of European taxa of steppic provenance suggests that species were widely distributed during glacial periods but underwent range contraction and fragmentation during interglacials into "warm-stage refugia." Among the steppe-related invertebrates that have been examined, the majority has been insects, but data on the phylogeography of snails is wholly missing. To begin to fill this gap, phylogeographic and niche modeling studies on the presumed steppic snail Caucasotachea vindobonensis were conducted...
September 2017: Organisms, Diversity & Evolution
https://www.readbyqxmd.com/read/29801429/phylogeographic-patterns-of-the-desert-poplar-in-northwest-china-shaped-by-both-geology-and-climatic-oscillations
#11
Yan-Fei Zeng, Jian-Guo Zhang, Bawerjan Abuduhamiti, Wen-Ting Wang, Zhi-Qing Jia
BACKGROUND: The effects of historical geology and climatic events on the evolution of plants around the Qinghai-Tibetan Plateau region have been at the center of debate for years. To identify the influence of the uplift of the Tianshan Mountains and/or climatic oscillations on the evolution of plants in arid northwest China, we investigated the phylogeography of the Euphrates poplar (Populus euphratica) using chloroplast DNA (cpDNA) sequences and nuclear microsatellites, and estimated its historical distribution using Ecological Niche Modeling (ENM)...
May 25, 2018: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29782829/global-phylogeography-and-genetic-diversity-of-the-zoonotic-tapeworm-echinococcus-granulosus-sensu-stricto-genotype-g11
#12
Liina Kinkar, Teivi Laurimäe, Gerardo Acosta-Jamett, Vanessa Andresiuk, Ibrahim Balkaya, Adriano Casulli, Robin B Gasser, Joke van der Giessen, Luis Miguel González, Karen L Haag, Houria Zait, Malik Irshadullah, Abdul Jabbar, David J Jenkins, Eshrat Beigom Kia, Maria Teresa Manfredi, Hossein Mirhendi, Selim M'rad, Mohammad Rostami-Nejad, Myriam Oudni-M'rad, Nora Beatriz Pierangeli, Francisco Ponce-Gordo, Steffen Rehbein, Mitra Sharbatkhori, Sami Simsek, Silvia Viviana Soriano, Hein Sprong, Viliam Šnábel, Gérald Umhang, Antonio Varcasia, Urmas Saarma
Echinococcus granulosus sensu stricto (s.s.) is the major cause of human cystic echinococcosis worldwide and is listed among the most severe parasitic diseases of humans. To date, numerous studies have investigated the genetic diversity and population structure of E. granulosus s.s. in various geographic regions. However, there has been no global study. Recently, using mitochondrial DNA, it was shown that E. granulosus s.s. G1 and G3 are distinct genotypes, but a larger dataset is required to confirm the distinction of these genotypes...
May 18, 2018: International Journal for Parasitology
https://www.readbyqxmd.com/read/29773336/seasonal-dynamics-geographical-range-size-hosts-genetic-diversity-and-phylogeography-of-amblyomma-sculptum-in-argentina
#13
Evelina L Tarragona, Patrick S Sebastian, María N Saracho Bottero, Emilia I Martinez, Valeria N Debárbora, Atilio J Mangold, Alberto A Guglielmone, Santiago Nava
The aim of this work was to generate knowledge on ecological aspects of Amblyomma sculptum in Argentina, such as seasonal dynamics, geographical range size, hosts, genetic diversity and phylogeography. Adult and immature A. sculptum ticks were collected in different localities of Argentina to know the geographical range size and hosts. The genetic diversity of this tick was studied through analyses of 16S rDNA sequences. To describe the seasonal dynamics, free-living ticks were monthly collected from October 2013 to October 2015...
April 27, 2018: Ticks and Tick-borne Diseases
https://www.readbyqxmd.com/read/29770273/westwards-and-northwards-dispersal-of-triosteum-himalayanum-caprifoliaceae-from-the-hengduan-mountains-region-based-on-chloroplast-dna-phylogeography
#14
Hai-Rui Liu, Qing-Bo Gao, Fa-Qi Zhang, Gulzar Khan, Shi-Long Chen
The varying topography and environment that resulted from paleoorogeny and climate fluctuations of the Himalaya-Hengduan Mountains (HHM) areas had a considerable impact on the evolution of biota during the Quaternary. To understand the phylogeographic pattern and historical dynamics of Triosteum himalayanum (Caprifoliaceae), we sequenced three chloroplast DNA fragments ( rbcL-accD , rps15-ycf1 , and trnH-psbA ) from 238 individuals representing 20 populations. Nineteen haplotypes (H1-H19) were identified based on 23 single-site mutations and eight indels...
2018: PeerJ
https://www.readbyqxmd.com/read/29765686/phylogeography-of-hydrothermal-vent-stalked-barnacles-a-new-species-fills-a-gap-in-the-indian-ocean-dispersal-corridor-hypothesis
#15
Hiromi Kayama Watanabe, Chong Chen, Daniel P Marie, Ken Takai, Katsunori Fujikura, Benny K K Chan
Phylogeography of animals provides clues to processes governing their evolution and diversification. The Indian Ocean has been hypothesized as a 'dispersal corridor' connecting hydrothermal vent fauna of Atlantic and Pacific oceans. Stalked barnacles of the family Eolepadidae are common associates of deep-sea vents in Southern, Pacific and Indian oceans, and the family is an ideal group for testing this hypothesis. Here, we describe Neolepas marisindica sp. nov. from the Indian Ocean, distinguished from N. zevinae and N...
April 2018: Royal Society Open Science
https://www.readbyqxmd.com/read/29765639/structure-and-phylogeography-of-two-tropical-predators-spinner-stenella-longirostris-and-pantropical-spotted-s-attenuata-dolphins-from-snp-data
#16
Matthew S Leslie, Phillip A Morin
Little is known about global patterns of genetic connectivity in pelagic dolphins, including how circumtropical pelagic dolphins spread globally following the rapid and recent radiation of the subfamily delphininae. In this study, we tested phylogeographic hypotheses for two circumtropical species, the spinner dolphin ( Stenella longirostris ) and the pantropical spotted dolphin ( Stenella attenuata ), using more than 3000 nuclear DNA single nucleotide polymorphisms (SNPs) in each species. Analyses for population structure indicated significant genetic differentiation between almost all subspecies and populations in both species...
April 2018: Royal Society Open Science
https://www.readbyqxmd.com/read/29748665/a-finely-resolved-phylogeny-of-y-chromosome-hg-j-illuminates-the-processes-of-phoenician-and-greek-colonizations-in-the-mediterranean
#17
Andrea Finocchio, Beniamino Trombetta, Francesco Messina, Eugenia D'Atanasio, Nejat Akar, Aphrodite Loutradis, Emmanuel I Michalodimitrakis, Fulvio Cruciani, Andrea Novelletto
In order to improve the phylogeography of the male-specific genetic traces of Greek and Phoenician colonizations on the Northern coasts of the Mediterranean, we performed a geographically structured sampling of seven subclades of haplogroup J in Turkey, Greece and Italy. We resequenced 4.4 Mb of Y-chromosome in 58 subjects, obtaining 1079 high quality variants. We did not find a preferential coalescence of Turkish samples to ancestral nodes, contradicting the simplistic idea of a dispersal and radiation of Hg J as a whole from the Middle East...
May 10, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29747573/global-evolution-and-phylogeography-of-brucella-melitensis-strains
#18
Sergey V Pisarenko, Dmitry A Kovalev, Anna S Volynkina, Dmitry G Ponomarenko, Diana V Rusanova, Nina V Zharinova, Anna A Khachaturova, Lyudmila E Tokareva, Irina G Khvoynova, Alexander N Kulichenko
BACKGROUND: Brucellosis is a bacterial zoonotic disease. Annually in the world more than 500,000 new cases of brucellosis in humans are registered. In this study, we propose an evolutionary model of the historical distribution of B. melitensis based on the full-genomic SNP analysis of 98 strains. RESULTS: We performed an analysis of the SNP of the complete genomes of 98 B. melitensis strains isolated in different geographical regions of the world to obtain relevant information on the population structure, genetic diversity and the evolution history of the species...
May 10, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29746563/ancient-genomes-reveal-a-high-diversity-of-mycobacterium-leprae-in-medieval-europe
#19
Verena J Schuenemann, Charlotte Avanzi, Ben Krause-Kyora, Alexander Seitz, Alexander Herbig, Sarah Inskip, Marion Bonazzi, Ella Reiter, Christian Urban, Dorthe Dangvard Pedersen, G Michael Taylor, Pushpendra Singh, Graham R Stewart, Petr Velemínský, Jakub Likovsky, Antónia Marcsik, Erika Molnár, György Pálfi, Valentina Mariotti, Alessandro Riga, M Giovanna Belcastro, Jesper L Boldsen, Almut Nebel, Simon Mays, Helen D Donoghue, Sonia Zakrzewski, Andrej Benjak, Kay Nieselt, Stewart T Cole, Johannes Krause
Studying ancient DNA allows us to retrace the evolutionary history of human pathogens, such as Mycobacterium leprae, the main causative agent of leprosy. Leprosy is one of the oldest recorded and most stigmatizing diseases in human history. The disease was prevalent in Europe until the 16th century and is still endemic in many countries with over 200,000 new cases reported annually. Previous worldwide studies on modern and European medieval M. leprae genomes revealed that they cluster into several distinct branches of which two were present in medieval Northwestern Europe...
May 2018: PLoS Pathogens
https://www.readbyqxmd.com/read/29729946/the-probability-of-reciprocal-monophyly-of-gene-lineages-in-three-and-four-species
#20
Rohan S Mehta, Noah A Rosenberg
Reciprocal monophyly, a feature of a genealogy in which multiple groups of descendant lineages each consist of all of the descendants of their respective most recent common ancestors, has been an important concept in studies of species delimitation, phylogeography, population history reconstruction, systematics, and conservation. Computations involving the probability that reciprocal monophyly is observed in a genealogy have played a key role in criteria for defining taxonomic groups and inferring divergence times...
May 3, 2018: Theoretical Population Biology
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