MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

Tamura, Koichiro; Stecher, Glen; Peterson, Daniel S.; Filipski, Alan; Kumar, Sudhir

doi:10.1093/molbev/mst197

Cited by 38,876 publications

(26,212 citation statements)

References 11 publications

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“…Briefly, the ortholog sequences were aligned with Clustal Omega v1.2.0 (Sievers et al., 2011) and concatenated gap‐free with Gblocks v0.91 (Castresana, 2000). The tree was constructed using neighbor‐joining method (Saitou & Nei, 1987) in Mega 6.06 (Tamura, Stecher, Peterson, Filipski & Kumar, 2013) and calibrated using the estimates of divergence time in the literature. The Drosophila expression phylogram was based on a distance matrix of 1 minus Spearman correlation coefficient and constructed by neighbor‐joining method using R package “ape” (Paradis, Claude & Strimmer, 2004).…”

Section: Methodsmentioning

confidence: 99%

Comparative transcriptomics across 14 Drosophila species reveals signatures of longevity

Avanesov

Porter

et al. 2018

Aging Cell

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SummaryLifespan varies dramatically among species, but the biological basis is not well understood. Previous studies in model organisms revealed the importance of nutrient sensing, mTOR, NAD/sirtuins, and insulin/IGF1 signaling in lifespan control. By studying life‐history traits and transcriptomes of 14 Drosophila species differing more than sixfold in lifespan, we explored expression divergence and identified genes and processes that correlate with longevity. These longevity signatures suggested that longer‐lived flies upregulate fatty acid metabolism, downregulate neuronal system development and activin signaling, and alter dynamics of RNA splicing. Interestingly, these gene expression patterns resembled those of flies under dietary restriction and several other lifespan‐extending interventions, although on the individual gene level, there was no significant overlap with genes previously reported to have lifespan‐extension effects. We experimentally tested the lifespan regulation potential of several candidate genes and found no consistent effects, suggesting that individual genes generally do not explain the observed longevity patterns. Instead, it appears that lifespan regulation across species is modulated by complex relationships at the system level represented by global gene expression.

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Section: Methodsmentioning

confidence: 99%

Comparative transcriptomics across 14 Drosophila species reveals signatures of longevity

Avanesov

Porter

et al. 2018

Aging Cell

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“…Nucleotide sequences of human H3N2 (from 2007 to 2013) and pandemic H1N1 viruses (from 2009 to 2013) from Central America and the Caribbean were downloaded from the EpiFlu database of the Global Initiative on Sharing All Influenza Data (the search included sequences also available in GenBank, in addition to those only available in EpiFlu) (GISAID, http://platform.gisaid.org, Table S1). Phylogenetic analyses were performed in MEGA 6.0 23. Sequences were manually trimmed and final coding sequences were aligned with MUSCLE for codons.…”

Section: Methodsmentioning

confidence: 99%

Origin, distribution, and potential risk factors associated with influenza A virus in swine in two production systems in Guatemala

Gonzalez‐Reiche

Ramírez

Müller

et al. 2017

Influenza Resp Viruses

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BackgroundGuatemala is the country with the largest swine production in Central America; however, evidence of influenza A virus (IAV) in pigs has not been clearly delineated.ObjectivesIn this study, we analyzed the presence and spatial distribution of IAV in commercial and backyard swine populations.MethodsSamples from two nationwide surveys conducted in 2010 and 2011 were tested using virological (rRT‐PCR and virus isolation) and serological (ELISA and hemagglutination inhibition) assays to detect IAV.ResultsInfluenza A virus was detected in 15.7% of the sampled pigs (30.6% of herds) in 2010 and in 11.7% (24.2% of herds) in 2011. The percentage of seropositive pigs was 10.6% (16.1% of herds) and 1.4% (3.1% of herds) for each year, respectively. Three pandemic H1N1 and one seasonal human‐like H3N2 viruses were isolated. Antibodies against viruses from different genetic clusters were detected. No reassortant strains with swine viruses were detected. The H3N2 virus was closely related to human viruses that circulated in Central America in 2010, distinct to the most recent human seasonal vaccine lineages. Spatial clusters of rRT‐PCR positive herds were detected each year by scan statistics.ConclusionsOur results demonstrate circulation of IAV throughout Guatemala and identify commercial farms, animal health status, and age as potential risk factors associated with IAV infection and exposure. Detection of human‐origin viruses in pigs suggests a role for humans in the molecular epidemiology of IAV in swine in Guatemala and evidences gaps in local animal and human surveillance.

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“…A phylogenetic tree based on maximum‐parsimony (MP) assumptions was also generated with the same dataset. ML and MP phylogenetic trees were created in MEGA6 (Tamura, Stecher, Peterson, Filipski, & Kumar, 2013). The final MP tree is a consensus of the three most equally parsimonious trees, and the final ML tree is the tree with the highest supported nodes under the maximum‐likelihood framework.…”

Section: Methodsmentioning

confidence: 99%

Insight into the population structure of hardhead silverside,Atherinomorus stipes(Teleostei: Atherinidae), in Belize and the Florida Keys usingnd2

Nash

Kraczkowski

Chernoff

2017

Ecology and Evolution

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Little is known about the natural history, biology, and population genetic structure of the Hardhead Silverside, Atherinomorus stipes, a small schooling fish found around islands throughout the Caribbean. Our field observations of A. stipes in the cays of Belize and the Florida Keys found that populations tend to be in close association with the shoreline in mangrove habitats. Due to this potential island‐based population structuring, A. stipes represents an ideal system to examine questions about gene flow and isolation by distance at different geographic scales. For this study, the mitochondrial gene nd2 was amplified from 394 individuals collected from seven different Belizean Cays (N = 175) and eight different Floridian Keys (N = 219). Results show surprisingly high haplotype diversity both within and between island‐groups, as well as a high prevalence of unique haplotypes within each island population. The results are consistent with models that require gene flow among populations as well as in situ evolution of rare haplotypes. There was no evidence for an isolation by distance model. The nd2 gene tree consists of two well‐supported monophyletic groups: a Belizean‐type clade and a Floridian‐type clade, indicating potential species‐level differentiation.

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MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

Cited by 38,876 publications

References 11 publications

Comparative transcriptomics across 14 Drosophila species reveals signatures of longevity

Comparative transcriptomics across 14 Drosophila species reveals signatures of longevity

Origin, distribution, and potential risk factors associated with influenza A virus in swine in two production systems in Guatemala

Insight into the population structure of hardhead silverside,Atherinomorus stipes(Teleostei: Atherinidae), in Belize and the Florida Keys usingnd2

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