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Miller, Mark A.; Pfeiffer, Wayne; Schwartz, Terri

doi:10.1145/2016741.2016785

Cited by 389 publications

(156 citation statements)

References 22 publications

(18 reference statements)

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“…Colony CSM1323 was excluded, as it happened to be infected with Spiroplasma; see Results for details. We then inferred a maximum likelihood phylogeny of the most common OTUs and their GenBank relatives using the RAxML (45) on the CIPRES web portal (46). We included the largest clusters that cumulatively accounted for 90% of read numbers generated by 454 sequencing and also the largest clusters that accounted for 90% of sequences generated through cloning.…”

Section: Methodsmentioning

confidence: 99%

Surveying the Microbiome of Ants: Comparing 454 Pyrosequencing with Traditional Methods To Uncover Bacterial Diversity

Kautz

Rubin

Russell

et al. 2013

Appl Environ Microbiol

112

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We are only beginning to understand the depth and breadth of microbial associations across the eukaryotic tree of life. Reliably assessing bacterial diversity is a key challenge, and next-generation sequencing approaches are facilitating this endeavor. In this study, we used 16S rRNA amplicon pyrosequencing to survey microbial diversity in ants. We compared 454 libraries with Sanger-sequenced clone libraries as well as cultivation of live bacteria. Pyrosequencing yielded 95,656 bacterial 16S rRNA reads from 19 samples derived from four colonies of one ant species. The most dominant bacterial orders in the microbiome of the turtle ant Cephalotes varians were Rhizobiales, Burkholderiales, Opitutales, Xanthomonadales, and Campylobacterales, as revealed through both 454 sequencing and cloning. Even after stringent quality filtering, pyrosequencing recovered 445 microbe operational taxonomic units (OTUs) not detected with traditional techniques. In comparing bacterial communities associated with specific tissues, we found that gut tissues had significantly higher diversity than nongut tissues, and many of the OTUs identified from these groups clustered within ant-specific lineages, indicating a deep coevolutionary history of Cephalotes ants and their associated microbes. These lineages likely function as nutritional symbionts. One of four ant colonies investigated was infected with a Spiroplasma sp. (order Entomoplasmatales), a potential ant pathogen. Our work shows that the microbiome associated with Cephalotes varians is dominated by a few dozen bacterial lineages and that 454 sequencing is a cost-efficient tool to screen ant symbiont diversity.

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Section: Methodsmentioning

confidence: 99%

Surveying the Microbiome of Ants: Comparing 454 Pyrosequencing with Traditional Methods To Uncover Bacterial Diversity

Kautz

Rubin

Russell

et al. 2013

Appl Environ Microbiol

112

View full text Add to dashboard Cite

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“…1.2 (ref. 31), via the CIPRES web portal 32 , for 5 Â 10 6 generations, sampling parameters every 100 generations and a burn-in of 5 Â 10 4 . A chronogram was generated using a PATHd8 (ref.…”

Section: Methodsmentioning

confidence: 99%

Fine-scale niche structure of Neotropical forests reflects a legacy of the Great American Biotic Interchange

et al. 2013

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The tendency of species to retain their ancestral niches may link processes that determine community assembly with biogeographic histories that span geological time scales. Biogeographic history is likely to have had a particularly strong impact on Neotropical forests because of the influence of the Great American Biotic Interchange, which followed emergence of a land connection between North and South America B3 Ma. Here we examine the community structure, ancestral niches and ancestral distributions of the related, hyperdiverse woody plant genera Psychotria and Palicourea (Rubiaceae) in Panama. We find that 49% of the variation in hydraulic traits, a strong determinant of community structure, is explained by species' origins in climatically distinct biogeographic regions. Niche evolution models for a regional sample of 152 species indicate that ancestral climatic niches are associated with species' habitat distributions, and hence local community structure and composition, even millions of years after dispersal into new geographic regions.

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“…GenBlock v0.91b (Castresana 2000) was used to eliminate ambiguously aligned positions, with the following parameter settings: minimum number of sequences for a conserved position = 21, minimum number of sequences for a flank position = 21, maximum number of contiguous non-conserved positions = 5, minimum block size = 3 bp, and gaps allowed within selected blocks in half of the sequences. Maximum likelihood (ML) phylogenetic tree inference was performed using RAxML HPC2 v. 8.2 (Stamatakis 2014) on the CIPRES Science Gateway (Miller et al 2009). The ML analyses was performed using a mixedmodel with two partitions, ITS1 + ITS2 and 5.8S.…”

Section: Phylogenetic Analysismentioning

confidence: 99%