rfishbase: exploring, manipulating and visualizing FishBase data from R

Boettiger, Carl; Lang, Duncan Temple; Wainwright, Peter C.

doi:10.1111/j.1095-8649.2012.03464.x

Cited by 308 publications

(249 citation statements)

References 15 publications

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“…The second list is based on the percentage of extant species that are 'reef associated' according to FishBase (Froese and Pauly 2013), which includes fishes living on or near any shallow water, consolidated and wave-resistant structure. For each family, we calculated the percentage of extant species living on reefs using FishBase, accessed through functions in the R package rfishbase (Boettiger et al 2012). These percentages were then used to calibrate a binomial distribution for every family from which we sampled 100 times.…”

Section: Identifying Clusters Of Reef Families and Their History Of Rmentioning

confidence: 99%

Phylogenetic insights into the history and diversification of fishes on reefs

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Claverie²,

Near

et al. 2015

Coral Reefs

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Studies of the phylogenetic history of fishes on reefs and the impact of reefs on fish diversification have, to date, been limited to relatively small clades. We take advantage of a recent multi-locus, time-calibrated phylogeny of acanthomorph fishes and a broad-scale morphological dataset of body shape in reef acanthomorphs to explore the history and diversification of fish on reefs at the family level. We find that no reef family exhibits exceptional species diversity for their stem age and some, such as Aulostomidae, Zanclidae, Menidae, and Triodontidae may in fact be species poor. The inferred history of reef colonization is highly dependent on how a reef family is defined; one classification scheme raises the possibility that most modern acanthomorph families originated on reefs. We find that most reef families occupy surprisingly distinct regions of morphospace and yet, some of the most diverse reef families occupy central and highly overlapping positions within the body shape morphospace. To the extent that proximity in morphospace reflects ecological similarity, these results imply that most reef fish families have diversified in adaptive zones away from other families. In contrast, a few of the most successful (e.g., Labridae and Pomacentridae) have achieved dominance while potentially facing stronger interactions with other lineages. Finally, we find no relationship between species diversity and body shape diversity. Assuming neither are diversity dependent, this result suggests that morphological and ecological diversification within families of reef fish may not be linked to the accumulation of species. Time-calibrated phylogenies provide the means for generating a greater understanding of the macroevolutionary processes influencing reef fish diversification, but we are currently limited by the lack of robust crown-group ages for many reef fish families.

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Section: Identifying Clusters Of Reef Families and Their History Of Rmentioning

confidence: 99%

Phylogenetic insights into the history and diversification of fishes on reefs

Price

Claverie²,

Near

et al. 2015

Coral Reefs

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“…In addition to packages for phylogenetic and comparative analyses, a growing number of R packages allow users to query and access data from the web [e.g. rFISHBASE (Boettiger, Lang & Wainwright 2012), rAvis (Varela et al 2014) and paleobioDB (Varela et al 2015)], such that data associated with taxa in a given phylogeny can be obtained directly in R.…”

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confidence: 99%

rotl: an R package to interact with the Open Tree of Life data

2016

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Summary1. While phylogenies have been getting easier to build, it has been difficult to reuse, combine and synthesize the information they provide because published trees are often only available as image files, and taxonomic information is not standardized across studies. 2. The Open Tree of Life (OTL) project addresses these issues by providing a digital tree that encompasses all organisms, built by combining taxonomic information and published phylogenies. The project also provides tools and services to query and download parts of this synthetic tree, as well as the source data used to build it. Here, we present rotl, an R package to search and download data from the Open Tree of Life directly in R. 3. rotl uses common data structures allowing researchers to take advantage of the rich set of tools and methods that are available in R to manipulate, analyse and visualize phylogenies. Here, and in the vignettes accompanying the package, we demonstrate how rotl can be used with other R packages to analyse biodiversity data. 4. As phylogenies are being used in a growing number of applications, rotl facilitates access to phylogenetic data and allows their integration with statistical methods and data sources available in R.Key-words: comparative methods, macroevolution, Open Tree of Life, phylogenetics Advances in sequencing and computing technologies have lead to a revolution in systematic biology. The ability to routinely generate molecular data sets from any extant organism has allowed researchers to resolve long-standing taxonomic disputes and estimate phylogenies for previously understudied groups. In parallel, the ease with which phylogenies can be estimated has spurred the development of new phylogenetic comparative methods. These methods allow researchers to explore fundamental questions about the origin of biodiversity including the evolution of morphological and ecological traits, the spatiotemporal variation in speciation rates, or both (O'Meara 2012;Pennell & Harmon 2013).Ideally, the ever increasing number of published phylogenies would contribute to a synthesis of phylogenetic knowledge, ultimately leading to a better understanding of the history of life while at the same time providing high-quality phylogenetic information for use in comparative analyses. However, in practice, synthesizing phylogenetic data is a difficult task. Phylogenetic information is largely scattered, often only available as image files within publications, and the lack of standardization to store and represent phylogenetic data makes it difficult for researchers to access, synthesize and integrate this information into their own research (Stoltzfus et al. 2012;Drew et al. 2013;Magee, May & Moore 2014; but see Cranston et al. 2014 for suggestions of best practices).The Open Tree of Life (OTL) project aims at assembling and synthesizing our current understanding of phylogenetic relationships across all organisms on Earth while providing tools and services that facilitate access to this information (Hinchliff et al. 2015). OTL ...

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“…Availability and quality of trait data varied between vertebrate group, each requiring special handling. Fish: Standard, fork, and total lengths were extracted from Fishbase using RFishbase (Boettiger et al 2012). For each fish clade, we used an allometric regression to convert all taxa to the most frequently observed length type (Gaygusuz et al 2006).…”

Section: Vertebrate Datasetmentioning

confidence: 99%

Punctuated evolution shaped modern vertebrate diversity

Landis

Schraiber

2017

Preprint

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The relative importance of different modes of evolution in shaping phenotypic diversity remains a hotly debated question. Fossil data suggest that stasis may be a common mode of evolution, while modern data suggest very fast rates of evolution. One way to reconcile these observations is to imagine that evolution is punctuated, rather than gradual, on geological time scales. To test this hypothesis, we developed a novel maximum likelihood framework for fitting Lévy processes to comparative morphological data. This class of stochastic processes includes both a gradual and punctuated component. We found that a plurality of modern vertebrate clades examined are best fit by punctuated processes over models of gradual change, gradual stasis, and adaptive radiation. When we compare our results to theoretical expectations of the rate and speed of regime shifts for models that detail fitness landscape dynamics, we find that our quantitative results are broadly compatible with both microevolutionary models and with observations from the fossil record.A key debate in evolutionary biology centers around the seeming contradictions regarding the tempo and mode of evolution as seen in fossil data compared to ecological data. Fossil data often support models of stasis, in which little evolutionary change is seen within lineages over long timescales (Hunt 2007;Estes and Arnold 2007), while ecological data show that rapid bursts of evolution are not only possible, but potentially common (Reznick et al. 1997;Herrel et al. 2008;Brown and Brown 2013;Cresko et al. 2004). At face value, these observations seem to contradict one another, an observation known as the "paradox of stasis" (Hansen and Houle 2004). These observations are often reconciled through a descriptive model of punctuated evolution, entailing stasis interrupted by pulses of rapid change, as famously articulated by Simpson (Simpson 1944;1953).On macroevolutionary timescales, pulses of rapid change are expected to look roughly instantaneous. Only recently have statistical methods grown sophisticated enough to model punctuated evolution as a stochastic process, with advances showing that punctuation is detectable in some fossil time series (Hunt et al. 2015) and between pairs of living and extinct taxa (Uyeda et al. 2011).While these studies establish the existence of punctuated evolution, it is still unknown whether the evolutionary mode is common or rare. How many clades in the Tree of Life were shaped by abrupt pulses of rapid evolution? If these evolutionary pulses are common, then that should inform our expectations about how traits evolved for clades that left no fossils, and the potential for vulnerable species to adapt rapidly to climate change (Quintero and Wiens 2013). To this end, phylogenetic models-models of trait evolution that account for the shared ancestry of species-have played a vital role in measuring the relative support of competing Simpsonian modes of evolution.A pioneering meta-analysis (Harmon et al. 2010a) fitted a collection of phylogen...

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rfishbase: exploring, manipulating and visualizing FishBase data from R

Cited by 308 publications

References 15 publications

Phylogenetic insights into the history and diversification of fishes on reefs

Phylogenetic insights into the history and diversification of fishes on reefs

rotl: an R package to interact with the Open Tree of Life data

Punctuated evolution shaped modern vertebrate diversity

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