How Many Bootstrap Replicates Are Necessary?

Pattengale, Nicholas D.; Alipour, Masoud; Bininda‐Emonds, Olaf R. P.; Moret, Bernard M. E.; Stamatakis, Alexandros

doi:10.1007/978-3-642-02008-7_13

Cited by 441 publications

(405 citation statements)

References 29 publications

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“…The parametric bootstrap method was applied to obtain the confidence intervals. A large enough replicate sample size of 10 4 was chosen to run the parametric bootstrap method (Pattengale et al 2009). …”

Section: Discussionmentioning

confidence: 99%

Urban impacts on air temperature and precipitation over The Netherlands

Golroudbary¹,

Zeng²,

Mannaerts³

et al. 2018

Clim. Res.

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The detection of changes in the weather of urban areas is an important issue for understanding the impact of weather on human lives. Five years of basic weather observations (2011−2015) from automatic and amateur networks across The Netherlands were used to investigate the urban effects on meteorological parameters with a focus on temperature (e.g. urban heat island [UHI]) and precipitation. Representative stations were selected based on metadata and a set of criteria for data quality control. An hourly analysis indicates that UHIs are a nocturnal phenomenon in The Netherlands and are more prominent after sunset, when they exceed 2°C. A seasonal analysis shows that UHIs occur in all seasons during the year, with the most significant UHI occurring in the summer. Furthermore, the differences in the precipitation of urban and rural areas were shown to be greatest after sunrise during the day. The maximum hourly UHI and hourly precipitation distributions were analyzed using a generalized extreme value model. The occurrences of maximum precipitation are likely to be more frequent at urban stations than at the nearby rural stations. Additionally, the distinct seasonal cycle of precipitation that is dependent on the UHI demonstrates that the maximum UHI and precipitation occurred in the summer. Our results indicate that the UHI and precipitation enhancements in Dutch urban residential areas, as obtained from the data of weather amateurs, are in agreement with the results presented in the literature, and that 7% more precipitation occurs in cities than in rural areas.

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Section: Discussionmentioning

confidence: 99%

Urban impacts on air temperature and precipitation over The Netherlands

Golroudbary¹,

Zeng²,

Mannaerts³

et al. 2018

Clim. Res.

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show abstract

“…We performed a full tree inference under the general-time-reversible model allowing for site-specific rate variation and partition-wise optimised substitution rates coupled with a fast bootstrapping, where the number of necessary bootstrap replicates was determined by the extended majority rule consensus bootstop criterion (Pattengale et al 2009). To test for potential sampling or missing data bias – a number of Loranthaceae genera are only incompletely known for the five gene regions (File S3) – a gene-jackknifing procedure was applied, using a restricted data set with no missing gene region (full results included in the OSM; summarised in File S1).…”

Section: Methodsmentioning

confidence: 99%

Evolution of pollen morphology in Loranthaceae

Grímsson

Grimm

Zetter

2017

Grana

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Earlier studies indicate a strong correlation of pollen morphology and ultrastructure with taxonomy in Loranthaceae. Using high-resolution light microscopy and scanning electron microscopy imaging of the same pollen grains, we document pollen types of 35 genera including 15 studied for the first time. Using a molecular phylogenetic framework based on currently available sequence data with good genus-coverage, we reconstruct trends in the evolution of Loranthaceae pollen and pinpoint traits of high diagnostic value, partly confirming earlier intuitive hypotheses based on morphological observations. We find that pollen morphology in Loranthaceae is strongly linked to phylogenetic relationships. Some pollen types are diagnostic for discrete genera or evolutionary lineages, opening the avenue to recruit dispersed fossil pollen as age constraints for dated phylogenies and as independent data for testing biogeographic scenarios; so far based exclusively on modern-day data. Correspondences and discrepancies between palynological and molecular data and current taxonomic/systematic concepts are identified and suggestions made for future palynological and molecular investigations of Loranthaceae.

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“…We applied our method to the datasets we used in an earlier study of bootstrapping methods [13] and available at http://lcbb.epfl.ch/BS.tar.bz2. There are 10 datasets of single-gene and multi-gene DNA sequences, with anywhere from 125 to 994 taxa.…”

Section: Results On Biological Datamentioning

confidence: 99%

Uncovering Hidden Phylogenetic Consensus

Pattengale

Swenson

Moret³

2010

Lecture Notes in Computer Science

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Abstract. Many of the steps in phylogenetic reconstruction can be confounded by "rogue" taxa, taxa that cannot be placed with assurance anywhere within the tree-whose location within the tree, in fact, varies with almost any choice of algorithm or parameters. Phylogenetic consensus methods, in particular, are known to suffer from this problem. In this paper we provide a novel framework in which to define and identify rogue taxa. In this framework, we formulate a bicriterion optimization problem that models the net increase in useful information present in the consensus tree when certain taxa are removed from the input data. We also provide an effective greedy heuristic to identify a subset of rogue taxa and use it in a series of experiments, using both pathological examples described in the literature and a collection of large biological datasets. As the presence of rogue taxa in a set of bootstrap replicates can lead to deceivingly poor support values, we propose a procedure to recompute support values in light of the rogue taxa identified by our algorithm; applying this procedure to our biological datasets caused a large number of edges to change from "unsupported" to "supported" status, indicating that many existing phylogenies should be recomputed and reevaluated to reduce any inaccuracies introduced by rogue taxa.

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How Many Bootstrap Replicates Are Necessary?

Cited by 441 publications

References 29 publications

Urban impacts on air temperature and precipitation over The Netherlands

Urban impacts on air temperature and precipitation over The Netherlands

Evolution of pollen morphology in Loranthaceae

Uncovering Hidden Phylogenetic Consensus

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