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https://www.readbyqxmd.com/read/28542160/the-phylogeography-of-myotis-bat-associated-rabies-viruses-across-canada
#1
Susan Nadin-Davis, Noor Alnabelseya, M Kimberly Knowles
As rabies in carnivores is increasingly controlled throughout much of the Americas, bats are emerging as a significant source of rabies virus infection of humans and domestic animals. Knowledge of the bat species that maintain rabies is a crucial first step in reducing this public health problem. In North America, several bat species are known to be rabies virus reservoirs but the role of bats of the Myotis genus has been unclear due to the scarcity of laboratory confirmed cases and the challenges encountered in species identification of poorly preserved diagnostic submissions by morphological traits alone...
May 19, 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28539631/phylogeography-of-the-tyrrhenian-red-deer-cervus-elaphus-corsicanus-resolved-using-ancient-dna-of-radiocarbon-dated-subfossils
#2
K Doan, F E Zachos, B Wilkens, J-D Vigne, N Piotrowska, A Stanković, B Jędrzejewska, K Stefaniak, M Niedziałkowska
We present ancient mitochondrial DNA analyses of 31 complete cytochrome b gene sequences from subfossil red deer remains from the Tyrrhenian islands (Corsica and Sardinia) and mainland Italy in a European-wide phylogeographic framework. Tyrrhenian and North African red deer, both going back to human introductions, were previously the only red deer to harbour the mitochondrial B lineage whose origin, however, remained unknown. Our ancient Italian samples from the central part of the peninsula that were radiocarbon-dated to an age of ca...
May 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28535779/carriers-of-mitochondrial-dna-macrohaplogroup-r-colonized-eurasia-and-australasia-from-a-southeast-asia-core-area
#3
Jose M Larruga, Patricia Marrero, Khaled K Abu-Amero, Maria V Golubenko, Vicente M Cabrera
BACKGROUND: The colonization of Eurasia and Australasia by African modern humans has been explained, nearly unanimously, as the result of a quick southern coastal dispersal route through the Arabian Peninsula, the Indian subcontinent, and the Indochinese Peninsula, to reach Australia around 50 kya. The phylogeny and phylogeography of the major mitochondrial DNA Eurasian haplogroups M and N have played the main role in giving molecular genetics support to that scenario. However, using the same molecular tools, a northern route across central Asia has been invoked as an alternative that is more conciliatory with the fossil record of East Asia...
May 23, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28533084/gene-flow-and-genetic-drift-contribute-to-high-genetic-diversity-with-low-phylogeographical-structure-in-european-hoopoes-upupa-epops
#4
Erjia Wang, Rien E Van Wijk, Markus Santhosh Braun, Michael Wink
The Hoopoe (Upupa epops epops) breeds widely in Eurasia and most populations migrate to Africa during the boreal winter. To date, data regarding its phylogeography in Europe are missing. In this study, we investigated the phylogeography and population genetics of Hoopoes by means of mitochondrial DNA (mtDNA) sequencing as well as microsatellite genotyping. Our analyses revealed 32 haplotypes in the cytochrome c oxidase subunit I (COI) (269 individuals) and 50 haplotypes in cytochrome b (cyt b) (233 individuals)...
May 19, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28529834/development-and-characterization-of-est-ssr-markers-for-begonia-luzhaiensis-begoniaceae
#5
Yu-Hsin Tseng, Han-Yau Huang, Wei-Bin Xu, Hsun-An Yang, Yan Liu, Ching-I Peng, Kuo-Fang Chung
PREMISE OF THE STUDY: Microsatellite primers were developed for Begonia luzhaiensis (Begoniaceae) to assess genetic diversity and population genetic structure. METHODS AND RESULTS: Based on the transcriptome data of B. luzhaiensis, 60 primer pairs were selected for initial validation, of which 16 yielded polymorphic microsatellite loci in 57 individuals. The number of alleles observed for these 16 loci ranged from one to nine. The observed and expected heterozygosity ranged from 0...
May 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28526725/phylogeography-and-genetic-structure-of-endemic-acmispon-argophyllus-and-a-dendroideus-fabaceae-across-the-california-channel-islands
#6
Lisa E Wallace, Gregory L Wheeler, Mitchell E McGlaughlin, Gerald Bresowar, Kaius Helenurm
PREMISE OF THE STUDY: Taxa inhabiting the California Channel Islands exhibit variation in their degree of isolation, but few studies have considered patterns across the entire archipelago. We studied phylogeography of insular Acmispon argophyllus and A. dendroideus to determine whether infraspecific taxa are genetically divergent and to elucidate patterns of diversification across these islands. METHODS: DNA sequences were collected from nuclear (ADH) and plastid genomes (rpL16, ndhA, psbD-trnT) from >450 samples on the Channel Islands and California...
May 19, 2017: American Journal of Botany
https://www.readbyqxmd.com/read/28525307/exploiting-genetic-information-to-trace-plant-virus-dispersal-in-landscapes
#7
Coralie Picard, Sylvie Dallot, Kirstyn Brunker, Karine Berthier, Phillipe Roumagnac, Samuel Soubeyrand, Emmanuel Jacquot, Gaël Thébaud
During the past decade, knowledge of pathogen life history has greatly benefited from the advent and development of molecular epidemiology. This branch of epidemiology uses information on pathogen variation at the molecular level to gain insights into a pathogen's niche and evolution and to characterize pathogen dispersal within and between host populations. Here, we review molecular epidemiology approaches that have been developed to trace plant virus dispersal in landscapes. In particular, we highlight how virus molecular epidemiology, nourished with powerful sequencing technologies, can provide novel insights at the crossroads between the blooming fields of landscape genetics, phylogeography, and evolutionary epidemiology...
May 19, 2017: Annual Review of Phytopathology
https://www.readbyqxmd.com/read/28515896/a-worldwide-phylogeography-of-the-whiteworm-lichens-thamnolia-reveals-three-lineages-with-distinct-habitats-and-evolutionary-histories
#8
Ioana Onuţ-Brännström, Leif Tibell, Hanna Johannesson
Thamnolia is a lichenized fungus with an extremely wide distribution, being encountered in arctic and alpine environments in most continents. In this study, we used molecular markers to investigate the population structure of the fungal symbiont and the associated photosynthetic partner of Thamnolia. By analyzing molecular, morphological, and chemical variation among 253 specimens covering the species distribution range, we revealed the existence of three mycobiont lineages. One lineage (Lineage A) is confined to the tundra region of Siberia and the Aleutian Islands, a second (Lineage B) is found in the high alpine region of the Alps and the Carpathians Mountains, and a third (Lineage C) has a worldwide distribution and covers both the aforementioned ecosystems...
May 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28498987/genetic-structure-and-phylogeography-of-the-leopard-cat-prionailurus-bengalensis-inferred-from-mitochondrial-genomes
#9
Riddhi P Patel, Saskia Wutke, Dorina Lenz, Shomita Mukherjee, Uma Ramakrishnan, Géraldine Veron, Jörns Fickel, Andreas Wilting, Daniel W Förster
The Leopard cat Prionailurus bengalensis is a habitat generalist that is widely distributed across Southeast Asia. Based on morphological traits, this species has been subdivided into 12 subspecies. Thus far, there have been few molecular studies investigating intraspecific variation, and those had been limited in geographic scope. For this reason, we aimed to study the genetic structure and evolutionary history of this species across its very large distribution range in Asia. We employed both PCR-based (short mtDNA fragments, 94 samples) and high throughput sequencing based methods (whole mitochondrial genomes, 52 samples) on archival, noninvasively collected and fresh samples to investigate the distribution of intraspecific genetic variation...
June 1, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/28498961/range-wide-snow-leopard-phylogeography-supports-three-subspecies
#10
Jan E Janecka, Jan E Janecka, Zhang Yu-Guang, Li Di-Qiang, Bariushaa Munkhtsog, Munkhtsog Bayaraa, Naranbaatar Galsandorj, Tshewang R Wangchuk, Dibesh Karmacharya, Thomas McCarthy, Juan Li, Lu Zhi, Kubanychbek Zhumabai Uulu, Ajay Gaur, Satish Kumar, B Kesav Kumar, Shafqat Hussain, Ghulam Muhammad, Matthew Jevit, Charlotte Hacker, Pamela Burger, Claudia Wultsch, Mary J Janecka, Kristofer Helgen, William J Murphy, Rodney Jackson
The snow leopard, Panthera uncia, is an elusive high-altitude specialist that inhabits vast, inaccessible habitat across Asia. We conducted the first range-wide genetic assessment of snow leopards based on noninvasive scat surveys. Thirty-three microsatellites were genotyped and a total of 683-bp of mitochondrial DNA sequenced in 70 individuals. Snow leopards exhibited low genetic diversity at microsatellites (AN = 5.8, HO = 0.433, HE = 0.568), virtually no mtDNA variation, and underwent a bottleneck in the Holocene (~8,000 years ago) coinciding with increased temperatures, precipitation, and upward treeline shift in the Tibetan Plateau...
May 4, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/28487260/pinpointing-cryptic-borders-fine-scale-phylogeography-and-genetic-landscape-analysis-of-the-hormogaster-elisae-complex-oligochaeta-hormogastridae
#11
Daniel F Marchán, Rosa Fernández, Irene de Sosa, Darío J Díaz Cosín, Marta Novo
Spatial and temporal aspects of the evolution of cryptic species complexes have received less attention than species delimitation within them. The phylogeography of the cryptic complex Hormogaster elisae (Oligochaeta, Hormogastridae) lacks knowledge on several aspects, including the small-scale distribution of its lineages or the palaeogeographic context of their diversification. To shed light on these topics, a dense specimen collection was performed in the center of the Iberian Peninsula - resulting in 28 new H...
May 6, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28479995/genetic-structure-among-greater-white-fronted-goose-populations-of-the-pacific-flyway
#12
Craig R Ely, Robert E Wilson, Sandra L Talbot
An understanding of the genetic structure of populations in the wild is essential for long-term conservation and stewardship in the face of environmental change. Knowledge of the present-day distribution of genetic lineages (phylogeography) of a species is especially important for organisms that are exploited or utilize habitats that may be jeopardized by human intervention, including climate change. Here, we describe mitochondrial (mtDNA) and nuclear genetic (microsatellite) diversity among three populations of a migratory bird, the greater white-fronted goose (Anser albifrons), which breeds discontinuously in western and southwestern Alaska and winters in the Pacific Flyway of North America...
May 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28479611/genetic-variation-and-geographic-differentiation-in-the-marine-triclad-bdelloura-candida-platyhelminthes-tricladida-maricola-ectocommensal-on-the-american-horseshoe-crab-limulus-polyphemus
#13
Ana Riesgo, Emily A Burke, Christopher Laumer, Gonzalo Giribet
Bdelloura candida (Platyhelminthes, Tricladida, Maricola) is an ectocommensal symbiont on the American horseshoe crab Limulus polyphemus, living on the book gills and appendages, where it spends its entire life. Given its limited dispersal capabilities and its inability to live outside of the host, we hypothesized a genetic structure that parallels that of its host. We obtained 84 planarian individuals from 19 horseshoe crabs collected from 10 sites from Massachusetts to Florida. We amplified the mitochondrial 16S rRNA and the nuclear internal transcribed spacer 2 and conducted phylogeographic and population genetic analyses, which show a clear and strong genetic break between the populations in the Atlantic and the Gulf coasts...
2017: Marine Biology
https://www.readbyqxmd.com/read/28479280/pelagic-and-benthic-communities-of-the-antarctic-ecosystem-of-potter-cove-genomics-and-ecological-implications
#14
REVIEW
D Abele, S Vazquez, A G J Buma, E Hernandez, C Quiroga, C Held, S Frickenhaus, L Harms, J L Lopez, E Helmke, W P Mac Cormack
Molecular technologies are more frequently applied in Antarctic ecosystem research and the growing amount of sequence-based information available in databases adds a new dimension to understanding the response of Antarctic organisms and communities to environmental change. We apply molecular techniques, including fingerprinting, and amplicon and metagenome sequencing, to understand biodiversity and phylogeography to resolve adaptive processes in an Antarctic coastal ecosystem from microbial to macrobenthic organisms and communities...
May 4, 2017: Marine Genomics
https://www.readbyqxmd.com/read/28476494/diversity-and-phylogeography-of-northeast-asian-brown-frogs-allied-to-rana-dybowskii-anura-ranidae
#15
Bao-Tian Yang, Yu Zhou, Mi-Sook Min, Masafumi Matsui, Bing-Jun Dong, Pi-Peng Li, Jonathan J Fong
We investigated the species diversity and phylogeography of the Northeast Asian brown frogs allied to Rana dybowskii (the R. dybowskii species complex: R. dybowskii, R. pirica, and R. uenoi) using four mitochondrial and three nuclear loci. Phylogenetic analyses confirmed the existence of three distinct species in this complex; using extensive molecular data, we confirm the validity of Rana uenoi recognized as a distinct species, and infer R. dybowskii and R. pirica to be sister species. Also, we included populations from previously unsampled regions in Northeast China, and identified them to be R...
May 2, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28462020/asymmetrical-dispersal-and-putative-isolation-by-distance-of-an-intertidal-blenniid-across-the-atlantic-mediterranean-divide
#16
Rita Castilho, Regina L Cunha, Cláudia Faria, Eva M Velasco, Joana I Robalo
Transition zones are of high evolutionary interest because unique patterns of spatial variation are often retained. Here, we investigated the phylogeography of the peacock blenny, Salaria pavo, a small marine intertidal fish that inhabits rocky habitats of the Mediterranean and the adjacent Atlantic Ocean. We screened 170 individuals using mitochondrial and nuclear sequence data from eight locations. Four models of genetic structure were tested: panmixia, isolation-by-distance, secondary contact and phylogeographic break...
2017: PeerJ
https://www.readbyqxmd.com/read/28449263/multi-dice-r-package-for-comparative-population-genomic-inference-under-hierarchical-co-demographic-models-of-independent-single-population-size-changes
#17
Alexander T Xue, Michael J Hickerson
Population genetic data from multiple taxa can address comparative phylogeographic questions about community-scale response to environmental shifts, and a useful strategy to this end is to employ hierarchical co-demographic models that directly test multi-taxa hypotheses within a single, unified analysis while benefiting in statistical power from aggregating datasets. This approach has been applied to classical phylogeographic datasets such as mitochondrial barcodes as well as reduced-genome polymorphism datasets that can yield 10,000s of SNPs, produced by emergent technologies such as RAD-seq and GBS...
April 27, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28437593/tabula-rasa-in-the-patagonian-channels-the-phylogeography-of-oreobolus-obtusangulus-cyperaceae
#18
Simon Pfanzelt, Dirk C Albach, Klaus Bernhard von Hagen
The extent of the Pleistocene glaciations in the Patagonian Channel region (southwesternmost South America) and their impact on the vegetation there is largely unknown. Whether the regional flora was wiped out completely (tabula rasa) or survived in ice-free pockets (in situ survival) is still an open question. The molecular imprint of either scenario should still be visible in extant populations. Therefore, DNA sequence data of Oreobolus obtusangulus Gaudich. (Cyperaceae) were analyzed. This species is an abundant constitutent of Patagonian cushion peat bogs, one of the Patagonian Channel region's major vegetation types...
April 24, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28437589/the-roles-of-ecology-behavior-and-effective-population-size-in-the-evolution-of-a-community
#19
Chih-Ming Hung, Sergei V Drovetski, Robert M Zink
Organismal traits such as ecological specialization and migratory behavior may affect colonization potential, population persistence, and degree of isolation, factors that determine the composition and genetic structure of communities. However, studies focusing on community assembly rarely consider these factors jointly. We sequenced 16 nuclear and one mitochondrial genes from Caucasian and European populations of 30 forest-dwelling avian species that represent diverse ecological (specialist-generalist) and behavioral (migratory-resident) backgrounds...
April 24, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28437560/phylogeography-and-population-structure-analysis-reveals-diversity-by-mutations-in-lasiodiplodia-theobromae-with-distinct-sources-of-selection
#20
P H D Santos, B M Carvalho, K P Aguiar, F A S Aredes, T P S Poltronieri, J M S Vivas, V Mussi Dias, G A Bezerra, D B Pinho, M G Pereira, S F Silveira
Lasiodiplodia theobromae is a plant pathogen with a worldwide distribution, with low host specificity, causing stem cankers, dieback diseases, and fruit rot in several species of plants. In coconut, this pathogen is reported as the etiological agent of "coconut leaf blight" (CLB) disease, causing several losses in fruit production. The CLB is an important disease for this crop in Brazil. In our study, we used a phylogeographic approach through the molecular characterization of the translation elongation factor 1-α (TEF1-α) to elucidate the pathogen distribution in Brazil and other countries, besides, search information about diversity sources of this pathogen in coconut palm tree at Brazilian northern, northeast, and southeast...
April 20, 2017: Genetics and Molecular Research: GMR
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