keyword
MENU ▼
Read by QxMD icon Read
search

phylogeography

keyword
https://www.readbyqxmd.com/read/29691995/phylogeography-of-h5n1-avian-influenza-virus-in-indonesia
#1
E N Njoto, M Scotch, C M Bui, D C Adam, A A Chughtai, C R MacIntyre
Highly pathogenic avian influenza (HPAI) viruses of the H5N1 subtype are a major concern to human and animal health in Indonesia. This study aimed to characterize transmission dynamics of H5N1 over time using novel Bayesian phylogeography methods to identify factors which have influenced the spread of H5N1 in Indonesia. We used publicly available hemagglutinin sequence data sampled between 2003 and 2016 to model ancestral state reconstruction of HPAI H5N1 evolution. We found strong support for H5N1 transmission routes between provinces in Java Island and inter-island transmissions, such as between Nusa Tenggara and Kalimantan Islands, not previously described...
April 24, 2018: Transboundary and Emerging Diseases
https://www.readbyqxmd.com/read/29686692/new-geographical-insights-of-the-latest-expansion-of-fusarium-oxysporum-f-sp-cubense-tropical-race-4-into-the-greater-mekong-subregion
#2
Si-Jun Zheng, Fernando A García-Bastidas, Xundong Li, Li Zeng, Tingting Bai, Shengtao Xu, Kesuo Yin, Hongxiang Li, Gang Fu, Yanchun Yu, Liu Yang, Huy Chung Nguyen, Bounneuang Douangboupha, Aye Aye Khaing, Andre Drenth, Michael F Seidl, Harold J G Meijer, Gert H J Kema
Banana is the most popular and most exported fruit and also a major food crop for millions of people around the world. Despite its importance and the presence of serious disease threats, research into this crop is limited. One of those is Panama disease or Fusarium wilt. In the previous century Fusarium wilt wiped out the "Gros Michel" based banana industry in Central America. The epidemic was eventually quenched by planting "Cavendish" bananas. However, 50 years ago the disease recurred, but now on "Cavendish" bananas...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29678646/inferring-spatial-patterns-and-drivers-of-population-divergence-of-neolitsea-sericea-lauraceae-based-on-molecular-phylogeography-and-landscape-genomics
#3
Ya-Nan Cao, Ian J Wang, Lu-Yao Chen, Yan-Qian Ding, Lu-Xian Liu, Ying-Xiong Qiu
The relative roles of geography, climate and ecology in driving population divergence and (incipient) speciation has so far been largely neglected in studies addressing the evolution of East Asia's island flora. Here, we employed chloroplast and ribosomal DNA sequences and restriction site-associated DNA sequencing (RADseq) loci to investigate the phylogeography and drivers of population divergence of Neolitsea sericea. These data sets support the subdivision of N. sericea populations into the Southern and Northern lineages across the 'Tokara gap'...
April 17, 2018: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29675939/markers-in-time-and-space-a-review-of-the-last-decade-of-plant-phylogeographic-approaches
#4
Ashley B Morris, Joey Shaw
Plant studies comprise a relatively small proportion of the phylogeographic literature, likely as a consequence of the fundamental challenges posed by the complex genomic structures and life history strategies of these organisms. Comparative plastomics (i.e., comparisons of mutation rates within and among regions of the chloroplast genome) across plant lineages has led to an increased understanding of which markers are likely to provide the most information at low taxonomic levels. However, the extent to which the results of such work have influenced the literature have not been fully assessed, nor has the extent to which plant phylogeographers explicitly analyze markers in time and space, both of which are integral components of the field...
April 19, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29675902/demography-or-selection-on-linked-cultural-traits-or-genes-investigating-the-driver-of-low-mtdna-diversity-in-the-sperm-whale-using-complementary-mitochondrial-and-nuclear-genome-analyses
#5
Phillip A Morin, Andrew D Foote, C Scott Baker, Brittany L Hancock-Hanser, Kristin Kaschner, Bruce R Mate, Sarah L Mesnick, Victoria L Pease, Patricia E Rosel, Alana Alexander
Mitochondrial DNA has been heavily utilized in phylogeography studies for several decades. However, underlying patterns of demography and phylogeography may be misrepresented due to coalescence stochasticity, selection, variation in mutation rates, and cultural hitchhiking (linkage of genetic variation to culturally transmitted traits affecting fitness). Cultural hitchhiking has been suggested as an explanation for low genetic diversity in species with strong social structures, counteracting even high mobility, abundance and limited barriers to dispersal...
April 19, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29673217/genetic-evaluation-of-natural-populations-of-the-endangered-conifer-thuja-koraiensis-using-microsatellite-markers-by-restriction-associated-dna-sequencing
#6
Lu Hou, Yanhong Cui, Xiang Li, Wu Chen, Zhiyong Zhang, Xiaoming Pang, Yingyue Li
Thuja koraiensis Nakai is an endangered conifer of high economic and ecological value in Jilin Province, China. However, studies on its population structure and conservation genetics have been limited by the lack of genomic data. Here, 37,761 microsatellites (simple sequence repeat, SSR) were detected based on 875,792 de novo-assembled contigs using a restriction-associated DNA (RAD) approach. Among these SSRs, 300 were randomly selected to test for polymorphisms and 96 obtained loci were able to amplify a fragment of expected size...
April 17, 2018: Genes
https://www.readbyqxmd.com/read/29661261/genetic-diversity-and-phylogeography-of-the-elusive-but-epidemiologically-important-echinococcus-granulosus-sensu-stricto-genotype-g3
#7
Liina Kinkar, Teivi Laurimäe, Ibrahim Balkaya, Adriano Casulli, Houria Zait, Malik Irshadullah, Mitra Sharbatkhori, Hossein Mirhendi, Mohammad Rostami-Nejad, Francisco Ponce-Gordo, Steffen Rehbein, Eshrat Beigom Kia, Sami Simsek, Viliam Šnábel, Gérald Umhang, Antonio Varcasia, Urmas Saarma
Cystic echinococcosis (CE) is a severe parasitic disease caused by the species complex Echinococcus granulosus sensu lato. Human infections are most commonly associated with E. granulosus sensu stricto (s.s.), comprising genotypes G1 and G3. The objective of the current study was to provide first insight into the genetic diversity and phylogeography of genotype G3. Despite the epidemiological importance of the genotype, it has remained poorly explored due to the ambiguity in the definition of the genotype. However, it was recently demonstrated that long sequences of mitochondrial DNA (mtDNA) provide a reliable method to discriminate G1 and G3 from each other...
April 17, 2018: Parasitology
https://www.readbyqxmd.com/read/29651124/the-effects-of-sampling-location-and-predictor-point-estimate-certainty-on-posterior-support-in-bayesian-phylogeographic-generalized-linear-models
#8
Daniel Magee, Jesse E Taylor, Matthew Scotch
The use of generalized linear models in Bayesian phylogeography has enabled researchers to simultaneously reconstruct the spatiotemporal history of a virus and quantify the contribution of predictor variables to that process. However, little is known about the sensitivity of this method to the choice of the discrete state partition. Here we investigate this question by analyzing a data set containing 299 sequences of the West Nile virus envelope gene sampled in the United States and fifteen predictors aggregated at four spatial levels...
April 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29642852/parapatric-genetic-divergence-among-deep-evolutionary-lineages-in-the-mediterranean-green-crab-carcinus-aestuarii-brachyura-portunoidea-carcinidae-accounts-for-a-sharp-phylogeographic-break-in-the-eastern-mediterranean
#9
Temim Deli, Evrim Kalkan, Selahattin Ünsal Karhan, Sonya Uzunova, Alireza Keikhosravi, Raşit Bilgin, Christoph D Schubart
BACKGROUND: Recently, population genetic studies of Mediterranean marine species highlighted patterns of genetic divergence and phylogeographic breaks, due to the interplay between impacts of Pleistocene climate shifts and contemporary hydrographical barriers. These factors markedly shaped the distribution of marine organisms and their genetic makeup. The present study is part of an ongoing effort to understand the phylogeography and evolutionary history of the highly dispersive Mediterranean green crab, Carcinus aestuarii (Nardo, 1847), across the Mediterranean Sea...
April 11, 2018: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29593854/expansive-reed-populations-alien-invasion-or-disturbed-wetlands
#10
Kim Canavan, Iain D Paterson, Carla Lambertini, Martin P Hill
The tall-statured grasses in the genus Phragmites are dominant vegetation in wetlands worldwide and thus play a vital role in ecosystem functioning. As a result, Phragmites spp. are some of the most widely studied plants; particularly in areas where changes to their abundances have occurred, most notably in Europe and North America. In southern Africa a pattern of reed expansion has occurred in recent decades that has shown a similar trend to cryptic invasions reported in North America. This study used molecular techniques to explore the phylogeography of P...
March 2018: AoB Plants
https://www.readbyqxmd.com/read/29577497/pliocene-pleistocene-ecological-niche-evolution-shapes-the-phylogeography-of-a-mediterranean-plant-group
#11
C Benítez-Benítez, M Escudero, F Rodríguez-Sánchez, S Martín-Bravo, P Jiménez-Mejías
Estimating species ability to adapt to environmental changes is crucial to understand their past and future response to climate change. The Mediterranean basin has experienced remarkable climatic changes since the Miocene, which have greatly influenced the evolution of the Mediterranean flora. Here we examine the evolutionary history and biogeographic patterns of two sedge sister species (Carex, Cyperaceae) restricted to the western Mediterranean basin, but with Pliocene fossil record in central Europe. In particular, we estimated the evolution of climatic niches through time and its influence in lineage differentiation...
March 25, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29575777/phylogeography-of-diaphorina-citri-hemiptera-liviidae-and-its-primary-endosymbiont-candidatus-carsonella-ruddii-an-evolutionary-approach-to-host-endosymbiont-interaction
#12
Yanjing Wang, Jinming Lu, G Andrew C Beattie, Md Rashidul Islam, Namgay Om, Hang Thi Dao, Liem Van Nguyen, Syed Muhammad Zaka, Jun Guo, Mingyi Tian, Xiaoling Deng, Shunyun Tan, Paul Holford, Yurong He, Yijing Cen
BACKGROUND: In insects, little is known about the coevolution between their primary endosymbionts and hosts at the intraspecific level, and this study has examined codiversification between the notorious agricultural pest Diaphorina citri and its P-endosymbiont, 'Candidatus Carsonella ruddii' at the population level. RESULTS: Maximum likelihood, haplotype network, principal components and Bayesian clustering identified three lineages for D. citri and its P-endosymbiont: a Western clade containing individuals from Pakistan, Bhutan (Phuentsholing), Vietnam (Son La), USA, Myanmar and China (Ruili, Yunnan); a Central clade, with accessions originating from Southwest China, Bhutan (Tsirang) and Bangladesh; and an Eastern clade containing individuals from Southeast Asian countries, and East and South China...
March 25, 2018: Pest Management Science
https://www.readbyqxmd.com/read/29574273/resolving-complex-phylogeographic-patterns-in-the-balkan-peninsula-using-closely-related-wall-lizard-species-as-a-model-system
#13
Nikolaos Psonis, Aglaia Antoniou, Emmanouela Karameta, Adam D Leaché, Panayiota Kotsakiozi, Diego Darriba, Alexey Kozlov, Alexandros Stamatakis, Dimitris Poursanidis, Oleg Kukushkin, Daniel Jablonski, Jelka Crnobrnja-Isailović, Iulian Gherghel, Petros Lymberakis, Nikos Poulakakis
The Balkan Peninsula constitutes a biodiversity hotspot with high levels of species richness and endemism. The complex geological history of the Balkans in conjunction with the climate evolution are hypothesized as the main drivers generating this biodiversity. We investigated the phylogeography, historical demography, and population structure of closely related wall-lizard species from the Balkan Peninsula and southeastern Europe to better understand diversification processes of species with limited dispersal ability, from Late Miocene to the Holocene...
March 21, 2018: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29562307/hyde-a-python-package-for-genome-scale-hybridization-detection
#14
Paul D Blischak, Julia Chifman, Andrea D Wolfe, Laura S Kubatko
The analysis of hybridization and gene flow among closely related taxa is a common goal for researchers studying speciation and phylogeography. Many methods for hybridization detection use simple site pattern frequencies from observed genomic data and compare them to null models that predict an absence of gene flow. The theory underlying the detection of hybridization using these site pattern probabilities exploits the relationship between the coalescent process for gene trees within population trees and the process of mutation along the branches of the gene trees...
March 19, 2018: Systematic Biology
https://www.readbyqxmd.com/read/29543844/phylogeography-of-daphnia-magna-straus-crustacea-cladocera-in-northern-eurasia-evidence-for-a-deep-longitudinal-split-between-mitochondrial-lineages
#15
Eugeniya I Bekker, Dmitry P Karabanov, Yan R Galimov, Christoph R Haag, Tatiana V Neretina, Alexey A Kotov
Species with a large geographic distributions present a challenge for phylogeographic studies due to logistic difficulties of obtaining adequate sampling. For instance, in most species with a Holarctic distribution, the majority of studies has concentrated on the European or North American part of the distribution, with the Eastern Palearctic region being notably understudied. Here, we study the phylogeography of the freshwater cladoceran Daphnia magna Straus, 1820 (Crustacea: Cladocera), based on partial mitochondrial COI sequences and using specimens from populations spread longitudinally from westernmost Europe to easternmost Asia, with many samples from previously strongly understudied regions in Siberia and Eastern Asia...
2018: PloS One
https://www.readbyqxmd.com/read/29538303/phylogeny-and-phylogeography-of-rhizobial-symbionts-nodulating-legumes-of-the-tribe-genisteae
#16
REVIEW
Tomasz Stępkowski, Joanna Banasiewicz, Camille E Granada, Mitchell Andrews, Luciane M P Passaglia
The legume tribe Genisteae comprises 618, predominantly temperate species, showing an amphi-Atlantic distribution that was caused by several long-distance dispersal events. Seven out of the 16 authenticated rhizobial genera can nodulate particular Genisteae species. Bradyrhizobium predominates among rhizobia nodulating Genisteae legumes. Bradyrhizobium strains that infect Genisteae species belong to both the Bradyrhizobium japonicum and Bradyrhizobium elkanii superclades. In symbiotic gene phylogenies, Genisteae bradyrhizobia are scattered among several distinct clades, comprising strains that originate from phylogenetically distant legumes...
March 14, 2018: Genes
https://www.readbyqxmd.com/read/29531714/comparative-phylogeography-of-aedes-mosquitoes-and-the-role-of-past-climatic-change-for-evolution-within-africa
#17
Kelly Louise Bennett, Martha Kaddumukasa, Fortunate Shija, Rousseau Djouaka, Gerald Misinzo, Julius Lutwama, Yvonne Marie Linton, Catherine Walton
The study of demographic processes involved in species diversification and evolution ultimately provides explanations for the complex distribution of biodiversity on earth, indicates regions important for the maintenance and generation of biodiversity, and identifies biological units important for conservation or medical consequence. African and forest biota have both received relatively little attention with regard to understanding their diversification, although one possible mechanism is that this has been driven by historical climate change...
March 2018: Ecology and Evolution
https://www.readbyqxmd.com/read/29531683/phylogeography-and-taxonomic-status-of-trout-and-salmon-from-the-ponto-caspian-drainages-with-inferences-on-european-brown-trout-evolution-and-taxonomy
#18
Levan Ninua, David Tarkhnishvili, Elguja Gvazava
Current taxonomy of western Eurasian trout leaves a number of questions open; it is not clear to what extent some species are distinct genetically and morphologically. The purpose of this paper was to explore phylogeography and species boundaries in freshwater and anadromous trout from the drainages of the Black and the Caspian Seas (Ponto-Caspian). We studied morphology and mitochondrial phylogeny, combining samples from the western Caucasus within the potential range of five nominal species of trout that are thought to inhabit this region, and using the sequences available from GenBank...
March 2018: Ecology and Evolution
https://www.readbyqxmd.com/read/29527409/the-little-shrimp-that-could-phylogeography-of-the-circumtropical-stenopus-hispidus-crustacea-decapoda-reveals-divergent-atlantic-and-pacific-lineages
#19
'Ale'alani Dudoit, Matthew Iacchei, Richard R Coleman, Michelle R Gaither, William E Browne, Brian W Bowen, Robert J Toonen
The banded coral shrimp, Stenopus hispidus (Crustacea: Decapoda: Stenopodidea) is a popular marine ornamental species with a circumtropical distribution. The planktonic larval stage lasts ∼120-253 days, indicating considerable dispersal potential, but few studies have investigated genetic connectivity on a global scale in marine invertebrates. To resolve patterns of divergence and phylogeography of S. hispidus , we surveyed 525 bp of mitochondrial cytochrome c oxidase subunit I (COI) from 198 individuals sampled at 10 locations across ∼27,000 km of the species range...
2018: PeerJ
https://www.readbyqxmd.com/read/29522515/on-geographic-barriers-and-pleistocene-glaciations-tracing-the-diversification-of-the-russet-crowned-warbler-myiothlypis-coronata-along-the-andes
#20
David A Prieto-Torres, Andrés M Cuervo, Elisa Bonaccorso
We studied the phylogeography and plumage variation of the Russet-crowned Warbler (Myiothlypis coronata), from Venezuela to Bolivia, with focus on populations from Ecuador and northern Peru. We analyzed sequences of mitochondrial and nuclear genes, geographic distributions, as well as photographs of specimens deposited at museum collections. Phylogenetic analyses identified three major lineages formed by populations from: Venezuela and Colombia (M. c. regulus), Ecuador and northern Peru (M. elata, M. castaneiceps, M...
2018: PloS One
keyword
keyword
39224
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"