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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
#1
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
#2
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
#3
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
#4
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
https://www.readbyqxmd.com/read/28426818/alternative-glacial-interglacial-refugia-demographic-hypotheses-tested-on-cephalocereus-columna-trajani-cactaceae-in-the-intertropical-mexican-drylands
#5
Amelia Cornejo-Romero, Carlos Fabián Vargas-Mendoza, Gustavo F Aguilar-Martínez, Javier Medina-Sánchez, Beatriz Rendón-Aguilar, Pedro Luis Valverde, Jose Alejandro Zavala-Hurtado, Alejandra Serrato, Sombra Rivas-Arancibia, Marco Aurelio Pérez-Hernández, Gerardo López-Ortega, Cecilia Jiménez-Sierra
Historic demography changes of plant species adapted to New World arid environments could be consistent with either the Glacial Refugium Hypothesis (GRH), which posits that populations contracted to refuges during the cold-dry glacial and expanded in warm-humid interglacial periods, or with the Interglacial Refugium Hypothesis (IRH), which suggests that populations contracted during interglacials and expanded in glacial times. These contrasting hypotheses are developed in the present study for the giant columnar cactus Cephalocereus columna-trajani in the intertropical Mexican drylands where the effects of Late Quaternary climatic changes on phylogeography of cacti remain largely unknown...
2017: PloS One
https://www.readbyqxmd.com/read/28422966/taming-the-late-quaternary-phylogeography-of-the-eurasiatic-wild-ass-through-ancient-and-modern-dna
#6
E Andrew Bennett, Sophie Champlot, Joris Peters, Benjamin S Arbuckle, Silvia Guimaraes, Mélanie Pruvost, Shirli Bar-David, Simon J M Davis, Mathieu Gautier, Petra Kaczensky, Ralph Kuehn, Marjan Mashkour, Arturo Morales-Muñiz, Erich Pucher, Jean-François Tournepiche, Hans-Peter Uerpmann, Adrian Bălăşescu, Mietje Germonpré, Can Y Gündem, Mahmoud-Reza Hemami, Pierre-Elie Moullé, Aliye Ötzan, Margarete Uerpmann, Chris Walzer, Thierry Grange, Eva-Maria Geigl
Taxonomic over-splitting of extinct or endangered taxa, due to an incomplete knowledge of both skeletal morphological variability and the geographical ranges of past populations, continues to confuse the link between isolated extant populations and their ancestors. This is particularly problematic with the genus Equus. To more reliably determine the evolution and phylogeographic history of the endangered Asiatic wild ass, we studied the genetic diversity and inter-relationships of both extinct and extant populations over the last 100,000 years, including samples throughout its previous range from Western Europe to Southwest and East Asia...
2017: PloS One
https://www.readbyqxmd.com/read/28417603/squamate-conserved-loci-sqcl-a-unified-set-of-conserved-loci-for-phylogenomics-and-population-genetics-of-squamate-reptiles
#7
Sonal Singhal, Maggie Grundler, Guarino Colli, Daniel L Rabosky
The identification of conserved loci across genomes, along with advances in target capture methods and high-throughput sequencing, has helped spur a phylogenomics revolution by enabling researchers to gather large numbers of homologous loci across clades of interest with minimal upfront investment in locus design. Target capture for vertebrate animals is currently dominated by two approaches - anchored hybrid enrichment (AHE) and ultraconserved elements (UCE) - and both approaches have proven useful for addressing questions in phylogenomics, phylogeography, and population genomics...
April 18, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28411209/phylogeography-of-the-wild-and-cultivated-stimulant-plant-qat-catha-edulis-celastraceae-in-areas-of-historical-cultivation
#8
Luke R Tembrock, Mark P Simmons, Christopher M Richards, Patrick A Reeves, Ann Reilley, Manuel A Curto, Harald Meimberg, Grace Ngugi, Sebsebe Demissew, Abdul Wali Al Khulaidi, Mansoor Al-Thobhani, Sheron Simpson, Daniel M Varisco
PREMISE OF THE STUDY: Qat (Catha edulis, Celastraceae) is a woody plant species cultivated for its stimulant alkaloids. Qat is important to the economy and culture in large regions of Ethiopia, Kenya, and Yemen. Despite the importance of this species, the wild origins and dispersal of cultivars have only been described in often contradictory historical documents. We examined the wild origins, human-mediated dispersal, and genetic divergence of cultivated qat compared to wild qat. METHODS: We sampled 17 SSR markers and 1561 wild and cultivated individuals across the historical areas of qat cultivation...
April 14, 2017: American Journal of Botany
https://www.readbyqxmd.com/read/28411160/life-on-the-rocks-multilocus-phylogeography-of-rock-hyrax-procavia-capensis-from-southern-africa
#9
K Amanda Maswanganye, Michael J Cunningham, Nigel C Bennett, Christian T Chimimba, Paulette Bloomer
Understanding the role of geography and climatic cycles in determining patterns of biodiversity is important in comparative and evolutionary biology and conservation. We studied the phylogeographic pattern and historical demography of a rock-dwelling small mammal species from southern Africa, the rock hyrax Procavia capensis. Using a multilocus coalescent approach, we assessed the influence of strong habitat dependence and fluctuating regional climates on genetic diversity. We sequenced a mitochondrial gene (cytochrome b) and two nuclear introns (AP5, PRKC1) supplemented with microsatellite genotyping, in order to assess evolutionary processes over multiple temporal scales...
April 11, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28407107/phylogeography-of-sophora-moorcroftiana-supports-wu-s-hypothesis-on-the-origin-of-tibetan-alpine-flora
#10
Shanmei Cheng, Qiong La, Fan Lu, Takahiro Yonezawa, Ganqiang Yin, Zhiping Song, Yuguo Wang, Ji Yang, Wenju Zhang
Wu hypothesized that the Tibetan flora originated mostly from the paleotropical Tertiary flora in the Hengduan Mountains by adapting to the cold and arid environments associated with the strong uplift of the Qinghai-Tibet Plateau (QTP). Here, we combine the phylogeographic history of Sophora moorcroftiana with that of S. davidii to explore the speciation of S. moorcroftiana to test this hypothesis. We collected 151 individuals from 17 populations and sequenced two chloroplast fragments and the internal transcribed spacer of rDNA...
April 12, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/28406905/a-latitudinal-phylogeographic-diversity-gradient-in-birds
#11
Brian Tilston Smith, Glenn F Seeholzer, Michael G Harvey, Andrés M Cuervo, Robb T Brumfield
High tropical species diversity is often attributed to evolutionary dynamics over long timescales. It is possible, however, that latitudinal variation in diversification begins when divergence occurs within species. Phylogeographic data capture this initial stage of diversification in which populations become geographically isolated and begin to differentiate genetically. There is limited understanding of the broader implications of intraspecific diversification because comparative analyses have focused on species inhabiting and evolving in restricted regions and environments...
April 2017: PLoS Biology
https://www.readbyqxmd.com/read/28404508/model-based-analyses-reveal-insular-population-diversification-and-cryptic-frog-species-in-the-ischnocnema-parva-complex-in-the-atlantic-forest-of-brazil
#12
Marcelo Gehara, Adriane Barth, Eliana Faria de Oliveira, Marco Antonio Costa, Célio Fernando Baptista Haddad, Miguel Vences
The Atlantic Forest (AF) of Brazil has long been recognized as a biodiversity conservation hotspot. Despite decades of studies the species inventory of this biome continues to increase with the discovery of cryptic diversity and the description of new species. Different diversification mechanisms have been proposed to explain the diversity in the region, including models of forest dynamics, barriers to gene flow and dispersal. Also, sea level change is thought to have influenced coastal diversification and isolated populations on continental islands...
April 9, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28399302/genetic-diversity-and-phylogenetic-relationships-of-cytochrome-c-oxidase-subunit-i-in-cimex-hemipterus-hemiptera-cimicidae-populations-in-malaysia
#13
Siti Nor Ain Seri Masran, Abdul Hafiz Ab Majid
The tropical bed bug is scientifically recognized as a significant public health problem. While there is an increased awareness about their resurgence by medical and life science committees, efficient bed bug management still remains unresolved. The solution may soon arise, as information about bed bugs' infestation dynamics and systematics are becoming more distinguishable. Recent developments in studies about bed bugs are based on molecular intervention by determining their genetic variation and phylogeography...
February 8, 2017: Journal of Medical Entomology
https://www.readbyqxmd.com/read/28386433/historical-gene-flow-constraints-in-a-northeastern-atlantic-fish-phylogeography-of-the-ballan-wrasse-labrus-bergylta-across-its-distribution-range
#14
Frederico Almada, Sara M Francisco, Cristina S Lima, Richard FitzGerald, Luca Mirimin, David Villegas-Ríos, Fran Saborido-Rey, Pedro Afonso, Telmo Morato, Sérgio Bexiga, Joana I Robalo
The distribution and demographic patterns of marine organisms in the north Atlantic were largely shaped by climatic changes during the Pleistocene, when recurrent glacial maxima forced them to move south or to survive in northern peri-glacial refugia. These patterns were also influenced by biological and ecological factors intrinsic to each species, namely their dispersion ability. The ballan wrasse (Labrus bergylta), the largest labrid fish along Europe's continental margins, is a target for fisheries and aquaculture industry...
February 2017: Royal Society Open Science
https://www.readbyqxmd.com/read/28385604/the-niche-and-phylogeography-of-a-passerine-reveal-the-history-of-biological-diversification-between-the-andean-and-the-atlantic-forests
#15
Natalia Trujillo-Arias, Gisele Dantas, Enrique Arbeláez-Cortés, Kazuya Naoki, Maria I Gómez, Fabricio R Santos, Cristina Y Miyaki, Alexandre Aleixo, Pablo L Tubaro, Gustavo S Cabanne
The Atlantic Forest is separated from the Andean tropical forest by dry and open vegetation biomes (Chaco and Cerrado). Despite this isolation, both rainforests share closely related lineages, which suggest a past connection. This connection could have been important for forest taxa evolution. In this study, we used the Saffron-billed Sparrow (Arremon flavirostris) as a model to evaluate whether the Andean and the Atlantic forests act as a refugia system, as well as to test for a history of biogeographic connection between them...
April 3, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28380021/phylogeography-of-y-chromosome-haplogroup-o3a2b2-n6-reveals-patrilineal-traces-of-austronesian-populations-on-the-eastern-coastal-regions-of-asia
#16
Lan-Hai Wei, Shi Yan, Yik-Ying Teo, Yun-Zhi Huang, Ling-Xiang Wang, Ge Yu, Woei-Yuh Saw, Rick Twee-Hee Ong, Yan Lu, Chao Zhang, Shu-Hua Xu, Li Jin, Hui Li
Austronesian diffusion is considered one of the greatest dispersals in human history; it led to the peopling of an extremely vast region, ranging from Madagascar in the Indian Ocean to Easter Island in Remote Oceania. The Y-chromosome haplogroup O3a2b*-P164(xM134), a predominant paternal lineage of Austronesian populations, is found at high frequencies in Polynesian populations. However, the internal phylogeny of this haplogroup remains poorly investigated. In this study, we analyzed -seventeen Y-chromosome sequences of haplogroup O3a2b*-P164(xM134) and generated a revised phylogenetic tree of this lineage based on 310 non-private Y-chromosome polymorphisms...
2017: PloS One
https://www.readbyqxmd.com/read/28369338/origin-and-evolution-of-the-kiwifruit-canker-pandemic
#17
Honour C McCann, Li Li, Yifei Liu, Dawei Li, Hui Pan, Caihong Zhong, Erik H A Rikkerink, Matthew D Templeton, Christina Straub, Elena Colombi, Paul B Rainey, Hongwen Huang
Recurring epidemics of kiwifruit (Actinidia spp.) bleeding canker disease are caused by Pseudomonas syringae pv. actinidiae (Psa). In order to strengthen understanding of population structure, phylogeography, and evolutionary dynamics, we isolated Pseudomonas from cultivated and wild kiwifruit across six provinces in China. Based on the analysis of 80 sequenced Psa genomes, we show that China is the origin of the pandemic lineage but that strain diversity in China is confined to just a single clade. In contrast, Korea and Japan harbor strains from multiple clades...
April 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28348869/nasp-an-accurate-rapid-method-for-the-identification-of-snps-in-wgs-datasets-that-supports-flexible-input-and-output-formats
#18
Jason W Sahl, Darrin Lemmer, Jason Travis, James M Schupp, John D Gillece, Maliha Aziz, Elizabeth M Driebe, Kevin P Drees, Nathan D Hicks, Charles Hall Davis Williamson, Crystal M Hepp, David Earl Smith, Chandler Roe, David M Engelthaler, David M Wagner, Paul Keim
Whole-genome sequencing (WGS) of bacterial isolates has become standard practice in many laboratories. Applications for WGS analysis include phylogeography and molecular epidemiology, using single nucleotide polymorphisms (SNPs) as the unit of evolution. NASP was developed as a reproducible method that scales well with the hundreds to thousands of WGS data typically used in comparative genomics applications. In this study, we demonstrate how NASP compares with other tools in the analysis of two real bacterial genomics datasets and one simulated dataset...
August 2016: Microbial Genomics
https://www.readbyqxmd.com/read/28348833/microreact-visualizing-and-sharing-data-for-genomic-epidemiology-and-phylogeography
#19
Silvia Argimón, Khalil Abudahab, Richard J E Goater, Artemij Fedosejev, Jyothish Bhai, Corinna Glasner, Edward J Feil, Matthew T G Holden, Corin A Yeats, Hajo Grundmann, Brian G Spratt, David M Aanensen
Visualization is frequently used to aid our interpretation of complex datasets. Within microbial genomics, visualizing the relationships between multiple genomes as a tree provides a framework onto which associated data (geographical, temporal, phenotypic and epidemiological) are added to generate hypotheses and to explore the dynamics of the system under investigation. Selected static images are then used within publications to highlight the key findings to a wider audience. However, these images are a very inadequate way of exploring and interpreting the richness of the data...
November 2016: Microbial Genomics
https://www.readbyqxmd.com/read/28347888/on-the-importance-of-geographic-and-taxonomic-sampling-in-phylogeography-a-reevaluation-of-diversification-and-species-limits-in-a-neotropical-thrush-aves-turdidae
#20
Jorge Enrique Avendaño, Enrique Arbeláez-Cortés, Carlos Daniel Cadena
Phylogeographic studies seeking to describe biogeographic patterns, infer evolutionary processes, and revise species-level classification should properly characterize the distribution ranges of study species, and thoroughly sample genetic variation across taxa and geography. This is particularly necessary for widely distributed organisms occurring in complex landscapes, such as the Neotropical region. Here, we clarify the geographic range and revisit the phylogeography of the Black-billed Thrush (Turdus ignobilis), a common passerine bird from lowland tropical South America, whose evolutionary relationships and species limits were recently evaluated employing phylogeographic analyses based on partial knowledge of its distribution and incomplete sampling of populations...
March 24, 2017: Molecular Phylogenetics and Evolution
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