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Joseph W Saelens, Dalia Lau-Bonilla, Anneliese Moller, Ana M Xet-Mull, Narda Medina, Brenda Guzmán, Maylena Calderón, Raúl Herrera, Jason E Stout, Eduardo Arathoon, Blanca Samayoa, David M Tobin
Whole-genome sequencing has resulted in new insights into the phylogeography of Mycobacterium tuberculosis However, only limited genomic data are available from M. tuberculosis strains in Guatemala. Here we report 16 complete genomes of clinical strains belonging to the Euro-American lineage 4, the most common lineage found in Guatemala and Central America.
February 15, 2018: Genome Announcements
Peng Qiao, Wei Tian, Peigui Liu, Fuqiang Yu, Juan Chen, Xiaojuan Deng, Shanping Wan, Ran Wang, Yun Wang, Hongen Guo
Tuber indicum is an ectomycorrhizal ascomycete that produces edible ascocarps. Based on a number of specimens with known exact origin, we investigate the speciation of the Tuber indicum complex in southwest China. Internal transcribed spacer (ITS) and simple sequence repeat (SSR) markers were used in the study. Phylogeography and population genetics analyses were combined to detect 31 wild populations of the T. indicum complex. Two distinct lineages, Tuber cf. indicum and Tuber cf. himalayense, were identified in the T...
February 12, 2018: Fungal Genetics and Biology: FG & B
Gianguglielmo Zehender, Alessia Lai, Carla Veo, Annalisa Bergna, Massimo Ciccozzi, Massimo Galli
Variola virus (VARV), the causative agent of smallpox, is an exclusively human virus belonging to the genus Orthopoxvirus, which includes many other viral species covering a wide range of mammal hosts, such as vaccinia, cowpox, camelpox, taterapox, ectromelia and monkeypox virus. The tempo and mode of evolution of Orthopoxviruses were reconstructed using a Bayesian phylodynamic framework by analysing 80 hemagglutinin sequences retrieved from public databases. Bayesian phylogeography was used to estimate their putative ancestral hosts...
February 15, 2018: Journal of Medical Virology
Seo-Jin Lee, Mu-Yeong Lee, Liang-Kong Lin, Y Kirk Lin, Yuchun Li, E-Hyun Shin, Sang-Hoon Han, Mi-Sook Min, Hang Lee, Kyung Seok Kim
Many peninsulas in the temperate zone played an important role as refugia of various flora and fauna, and the southern Korean Peninsula also served as a refugium for many small mammals in East Asia during the Pleistocene. The Asian lesser white-toothed shrew, Crocidura shantungensis, is a widely distributed species in East Asia, and is an appropriate model organism for exploring the role of the Korean Peninsula as a refugium of small mammals. Here, we investigated phylogenetic relationships and genetic diversity based on the entire sequence of the mitochondrial cytochrome b gene (1140 bp)...
February 13, 2018: Genetica
Shuang Tian, Yixuan Kou, Zhirong Zhang, Lin Yuan, Derong Li, Jordi López-Pujol, Dengmei Fan, Zhiyong Zhang
BACKGROUND: Mountains have not only provided refuge for species, but also offered dispersal corridors during the Neogene and Quaternary global climate changes. Compared with a plethora of studies on the refuge role of China's mountain ranges, their dispersal corridor role has received little attention in plant phylogeographic studies. Using phylogeographic data of Eomecon chionantha Hance (Papaveraceae), this study explicitly tested whether the Nanling Mountains, which spans from west to east for more than 1000 km in subtropical China, could have functioned as a dispersal corridor during the late Quaternary in addition to a glacial refugium...
February 9, 2018: BMC Evolutionary Biology
Anita Küpper, Harish K Manmathan, Darci Giacomini, Eric L Patterson, William B McCloskey, Todd A Gaines
Palmer amaranth (Amaranthus palmeri) is a major weed in United States cotton and soybean production systems. Originally native to the Southwest, the species has spread throughout the country. In 2004 a population of A. palmeri was identified with resistance to glyphosate, a herbicide heavily relied on in modern no-tillage and transgenic glyphosate-resistant (GR) crop systems. This project aims to determine the degree of genetic relatedness among eight different populations of GR and glyphosate-susceptible (GS) A...
2018: Frontiers in Plant Science
Jacobo Reyes-Velasco, Joseph D Manthey, Yann Bourgeois, Xenia Freilich, Stéphane Boissinot
Understanding the diversification of biological lineages is central to evolutionary studies. To properly study the process of speciation, it is necessary to link micro-evolutionary studies with macro-evolutionary mechanisms. Micro-evolutionary studies require proper sampling across a taxon's range to adequately infer genetic diversity. Here we use the grass frogs of the genus Ptychadena from the Ethiopian highlands as a model to study the process of lineage diversification in this unique biodiversity hotspot...
2018: PloS One
Yu-Min Ju, Kui-Ching Hsu, Jin-Quan Yang, Jui-Hsien Wu, Shan Li, Wei-Kuang Wang, Fang Ding, Jun Li, Hung-Du Lin
Mitochondrial DNA cytochrome b sequences (1141 bp) in 229 specimens of Acrossocheilus paradoxus from 26 populations were identified as four lineages. The pairwise genetic distances among these four lineages ranged from 1.57 to 2.37% (mean= 2.00%). Statistical dispersal-vicariance analysis suggests that the ancestral populations were distributed over mainland China and Northern and Western Taiwan. Approximate Bayesian computation approaches show that the three lineages in Taiwan originated from the lineage in mainland China through three colonization routes during two glaciations...
January 31, 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
Casper-Emil T Pedersen, Anders Albrechtsen, Paul D Etter, Eric A Johnson, Ludovic Orlando, Lounes Chikhi, Hans R Siegismund, Rasmus Heller
The plains zebra (Equus quagga) is an ecologically important species of the African savannah. It is also one of the most numerous and widely distributed ungulates, and six subspecies have been described based on morphological variation. However, the within-species evolutionary processes have been difficult to resolve due to its high mobility and a lack of consensus regarding the population structure. We obtained genome-wide DNA polymorphism data from more than 167,000 loci for 59 plains zebras from across the species range, encompassing all recognized extant subspecies, as well as three mountain zebras (Equus zebra) and three Grevy's zebras (Equus grevyi)...
January 22, 2018: Nature Ecology & Evolution
M Ruffley, M L Smith, A Espíndola, B C Carstens, J Sullivan, D C Tank
Model selection approaches in phylogeography have allowed researchers to evaluate the support for competing demographic histories, which provides a mode of inference and a measure of uncertainty in understanding climatic and spatial influences on intraspecific diversity. Here, to rank all models in the comparison set, and determine what proportion of the total support the top-ranked model garners, we conduct model selection using two analytical approaches -allele frequency-based, implemented in fastsimcoal2, and gene tree-based, implemented in PHRAPL...
January 15, 2018: Molecular Ecology
Mei-Na Wang, Lei Duan, Qi Qiao, Zheng-Feng Wang, Elizabeth A Zimmer, Zhong-Chao Li, Hong-Feng Chen
Bretschneidera sinensis, a class-I protected wild plant in China, is a relic of the ancient Tertiary tropical flora endemic to Asia. However, little is known about its genetics and phylogeography. To elucidate the current phylogeographic patterns and infer the historical population dynamics of B. sinensis, and to make recommendations for its conservation, three non-coding regions of chloroplast DNA (trnQ-rps16, rps8-rps11, and trnT-trnL) were amplified and sequenced across 256 individuals from 23 populations of B...
2018: PloS One
Sebastián Poljak, Alejandro M Ferreiro, Marina B Chiappero, Julieta Sánchez, Magalí Gabrielli, Marta S Lizarralde
Little is known about phylogeography of armadillo species native to southern South America. In this study we describe the phylogeography of the screaming hairy armadillo Chaetophractus vellerosus, discuss previous hypothesis about the origin of its disjunct distribution and propose an alternative one, based on novel information on genetic variability. Variation of partial sequences of mitochondrial DNA Control Region (CR) from 73 individuals from 23 localities were analyzed to carry out a phylogeographic analysis using neutrality tests, mismatch distribution, median-joining (MJ) network and paleontological records...
2018: PloS One
Tiago Menezes, Maria M Romeiras, Miguel M de Sequeira, Mónica Moura
Macaronesia has long been recognized as a natural model for studying evolutionary processes in plant diversification. Several studies have attempted to focus on single lineages, and few have covered the diversification of a family across all the archipelagos. We used a comprehensive sample to clarify the phylogenetic relationships and the biogeographic history of the Macaronesian Campanulaceae. Hypotheses related to the colonization of these archipelagos will be used to examine the diversification patterns of different lineages...
January 2018: Ecology and Evolution
Thomas Lenormand, Odrade Nougué, Roula Jabbour-Zahab, Fabien Arnaud, Laurent Dezileau, Luis-Miguel Chevin, Marta I Sánchez
Resurrection ecology (RE) is a very powerful approach to address a wide range of question in ecology and evolution. This approach rests on using appropriate model systems, and only few are known to be available. In this study, we show that Artemia has multiple attractive features (short generation time, cyst bank and collections, well-documented phylogeography, and ecology) for a good RE model. We show in detail with a case study how cysts can be recovered from sediments to document the history and dynamics of a biological invasion...
January 2018: Evolutionary Applications
Jing Li, Yibo Luo, Lingling Xu
Premise of the study: To investigate genetic diversity and structure, microsatellite markers were developed and characterized for Cypripedium tibeticum, an endangered orchid species, and their utility tested in two relatives: C. flavum and C. bardolphianum. Methods and Results: Candidate microsatellite loci were isolated based on next-generation sequencing. We identified 20 polymorphic loci with di- or trinucleotide repeats in three populations of C. tibeticum. Genotyping results showed the total number of alleles per locus varied from two to 21, and the observed and expected heterozygosity ranged from 0...
December 2017: Applications in Plant Sciences
Vanderly Andrade-Souza, Janisete G Silva, Neusa Hamada
High morphological homogeneity and cryptic speciation may cause the diversity within Simuliidae to be underestimated. Recent molecular studies on population genetics and phylogeography have contributed to reveal which factors influenced the diversity within this group. This study aimed at examining the genetic diversity of Simulium hirtipupa Lutz, 1910 in populations from the biomes Caatinga, Cerrado, and Atlantic Forest. In this study, we carried out phylogeographic and population genetic analyses using a fragment of the mitochondrial gene COI...
2017: PloS One
Аida Daugaliyeva, Akhmetzhan Sultanov, Bekbolat Usserbayev, Sholpan Baramova, Paola Modesto, Akmaral Adambayeva, Pier Luigi Acutis, Simone Peletto
Currently, although the prevalence of brucellosis in Kazakhstan remains high, there are limited data available on the genetic diversity of circulating Brucella strains. Here, MLVA was employed to genotype a panel of 102 Brucella isolates collected from eight Kazakh regions and neighboring countries (Russia, Kyrgyzstan) during the period 1935-2017. MLVA-11 analysis classified 64 B. abortus strains into genotypes 72, 82, 331, 71, 341 and 69, while one genotype was novel, having no correspondence within the MLVA international database...
December 23, 2017: Infection, Genetics and Evolution
Manuel Ruiz-García, Ángela Cerón, Sebastián Sánchez-Castillo, Pilar Rueda-Zozaya, Myreya Pinedo-Castro, Gustavo Gutierrez-Espeleta, Joseph Mark Shostell
We analyzed 156 specimens of diverse howler monkey taxa (Alouatta; Atelidae, Primates) for different mitochondrial genes (5,567 base pairs), with special emphasis on A. palliata and related taxa. Our results showed no relevant differences among individuals of different putative taxa, A. p. palliata, A. p. aequatorialis, A. coibensis coibensis, and A. c. trabeata. We found no spatial differences in genetic structure of A. p. palliata throughout Costa Rica, Nicaragua, and Honduras. A. p. mexicana (genetic distance: 1...
December 21, 2017: Folia Primatologica; International Journal of Primatology
Richard G J Hodel, Shichao Chen, Adam C Payton, Stuart F McDaniel, Pamela Soltis, Douglas E Soltis
The widespread adoption of RAD-Seq data in phylogeography means genealogical relationships previously evaluated using relatively few genetic markers can now be addressed with thousands of loci. One challenge, however, is that RAD-Seq generates complete genotypes for only a small subset of loci or individuals. Simulations indicate that loci with missing data can produce biased estimates of key population genetic parameters, although the influence of such biases in empirical studies is not well understood. Here we compare microsatellite data (8 loci) and RAD-Seq data (six datasets ranging from 239 to 25,198 loci) from red mangroves (Rhizophora mangle) in Florida to evaluate how different levels of data filtering influence phylogeographic inferences...
December 14, 2017: Scientific Reports
Jeffrey L Weinell, Aaron M Bauer
A systematic study of the Trachylepis varia complex was conducted using mitochondrial and nuclear DNA markers for individuals sampled across the species range. The taxonomic history of T. varia has been complicated and its broad geographic distribution and considerable phenotypic variation has made taxonomic revision difficult, leading earlier taxonomists to suggest that T. varia is a species complex. We used maximum likelihood and Bayesian inference to estimate gene trees and a multilocus time-tree, respectively, and we used these trees to identify the major clades (putative species) within T...
December 9, 2017: Molecular Phylogenetics and Evolution
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