paleobioDB: an R package for downloading, visualizing and processing data from the Paleobiology Database

Varela, Sara; González-Hernández, Javier; Sgarbi, Luciano Fabris; Marshall, Charles R.; Uhen, Mark D.; Peters, Shanan E.; McClennen, Michael

doi:10.1111/ecog.01154

Cited by 36 publications

(30 citation statements)

References 24 publications

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“…Fossil records extrapolated from the Paleobiology Database are indicated with colored points (red: Miocene, blue: Pliocene, green: Pleistocene). The map was created using ‘paleobioDB’ package in R version 3.5.1 (Varela et al, ). Abbreviations are provided in Figure…”

Section: Discussionmentioning

confidence: 99%

“…The extensive catalogue of taxon‐specific GWS fossils featured in the online and open access Paleobiology Database (https://paleobiodb.org/#/), and its associated R package ‘paleobioDB’ (Varela et al, ), was used to create a distribution and stratigraphic map of global GWS fossils. The downloaded database was filtered manually to avoid the use of homonym extinct taxa and dubious records.…”

Section: Methodsmentioning

confidence: 99%

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Pliocene colonization of the Mediterranean by Great White Shark inferred from fossil records, historical jaws, phylogeographic and divergence time analyses

Leone

Puncher

Ferretti

et al. 2020

Journal of Biogeography

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Aim: Determine the evolutionary origin of the heretofore poorly characterized contemporary Great White Shark (GWS; Carcharodon carcharias) of the Mediterranean Sea, using phylogenetic and dispersal vicariance analyses to trace back its global palaeo-migration pattern. Location: Mediterranean Sea.Taxon: Carcharodon carcharias. Methods:We have built the largest mitochondrial DNA control region (CR) sequence dataset for the Mediterranean GWS from referenced historical jaws spanning the 19th and 20th centuries. Mediterranean and global GWS CR sequences were analysed Handling Editor: Michelle Gaither for genetic diversity, phylogenetic relationships and divergence time. A Bayes factor approach was used to assess two scenarios of GWS lineage divergence and emergence of the Mediterranean GWS line using fossil records and palaeo-geographical events for calibration of the molecular clock. Results: The results confirmed a closer evolutionary relationship between Mediterranean GWS and populations from Australia-New Zealand and the North-eastern Pacific coast rather than populations from South African and North-western Atlantic. The Mediterranean GWS lineage showed the lowest genetic diversity at the global level, indicating its recent evolutionary origin. An evaluation of various divergence scenarios determined the Mediterranean GWS lineage most likely appeared some 3.23 million years ago by way dispersal/vicariance from Australian/Pacific palaeo-populations. Main conclusion: Based on the fossil records, phylogeographic patterns and divergence time, we revealed that the Mediterranean GWS population originated in the Pliocene following the Messinian Salinity Crisis. Colonization of the Mediterranean by GWS likely occurred via an eastward palaeo-migration of Australian/eastern Pacific elements through the Central American Seaway, before the complete closure of the Isthmus of Panama. This Pliocene origin scenario contrasts with a previously proposed scenario in which Australian GWS colonized the Mediterranean via antipodean northward migration resulting from navigational errors from South Africa during Quaternary climatic oscillations.

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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Pliocene colonization of the Mediterranean by Great White Shark inferred from fossil records, historical jaws, phylogeographic and divergence time analyses

Leone

Puncher

Ferretti

et al. 2020

Journal of Biogeography

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“…Then, we downloaded all available fossil occurrences of these taxa from the Paleobiology Database (http://paleobiodb.org/; accessed March 2019) using the package paleobioDB (Varela et al . ). Because our objective was to assess the completeness of the fossil record of living taxa in the last 5 million years, we limited our search to the Neogene and the Quaternary.…”

Section: Methodsmentioning

confidence: 97%

The impact of the Pull of the Recent on extant elasmobranchs

Pimiento

Benton

2020

Palaeontology

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Modern elasmobranchs have a long evolutionary history and an abundant fossil record that consists mainly of teeth. Many fossil taxa have living representatives. However, the representation of extant taxa in the fossil record is unknown. To begin to understand the geological history of extant elasmobranchs, we here assess the quality of their fossil record. We do so by assessing the Pull of the Recent (POR). The POR can bias the fossil record because the rather complete record of living taxa allows palaeontologists to identify fossil members of the modern clades and to bridge time bins where fossils are absent. We assessed the impact of the POR by quantifying the proportion of extant elasmobranchs that have a fossil record, but do not occur in the last 5 million years (Pliocene and Pleistocene). We found that the POR does not affect orders and families, but it does affect 24% of elasmobranch genera. Within the different elasmobranch orders, the Lamniformes display the most complete generic fossil record, with no impact of the POR. Although modest, the impact of the POR in extant elasmobranch genera is higher than that found in other taxa. Overall, the geological history of elasmobranchs contradicts the usual assumption that the fossil record becomes worse backwards in time. This is the case across geographical regions and tooth size, further suggesting that sampling intensity and outcrop availability might explain the POR effect on sharks and rays.

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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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paleobioDB: an R package for downloading, visualizing and processing data from the Paleobiology Database

Cited by 36 publications

References 24 publications

Pliocene colonization of the Mediterranean by Great White Shark inferred from fossil records, historical jaws, phylogeographic and divergence time analyses

Pliocene colonization of the Mediterranean by Great White Shark inferred from fossil records, historical jaws, phylogeographic and divergence time analyses

The impact of the Pull of the Recent on extant elasmobranchs

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

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