The impact of shifts in marine biodiversity hotspots on patterns of range evolution: Evidence from the Holocentridae (squirrelfishes and soldierfishes)

Dornburg, Alex; Moore, Jon A.; Beaulieu, Jeremy M.; Eytan, Ron I.; Near, Thomas J.

doi:10.1111/evo.12562

Cited by 41 publications

(33 citation statements)

References 119 publications

(188 reference statements)

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“…This high species diversity (or the presence of a “basal” taxon) does not mean that this is the center of origin of teleost fishes or even that it is a fixed center of diversity. As noted by Dornburg, Moore, Beaulieu, Eytan, and Near (), Thacker (), and others, the center of diversity of teleosts, as measured in numbers of species, has shifted through time with openings and closures of the succession of Tethyan oceans (Metcalfe, , ). Patterns described here are for clades regardless of the numbers of species in each.…”

Section: Discussionmentioning

confidence: 92%

The shape of biogeography: Endemism, maps, and classification of fish distributions in the western Pacific

Parenti

2019

Journal of Biogeography

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Aim The aim of this study is to describe and illustrate with maps the distribution and shape of biotic areas of endemism of fish clades in the western Pacific, including East Asia and Australasia. This study also depicts the allopatric or sympatric distributions of major subclades and makes general statements about the shared history among the areas using information provided by the shape of the distributions, phylogeny, and geology. This study also tests the hypothesis that Australasia is a locus of survival or differentiation for inferred “basal” subclades of global taxa. Location Western Pacific. Taxa Teleost fishes. Methods Clades are mapped to illustrate the shape of their distribution and to infer the shared relationships among distribution, phylogeny, and geology. Phylogenetic hypotheses for groups of taxa are converted into area cladograms which are used to summarize area relationships. This information is compared with that from other clades, ecology, and geology, to make general statements about the biogeographical history of the fish biota. Results The distribution of each clade has an identifiable shape. The “basal” subclades of many widespread teleost fish taxa are endemic to the western Pacific, including East Asia and Australasia; hence, this is the inferred location of a principal vicariant event for each clade. The “basal” subclade and its sister clade may be allopatric and represent remnants of general distributional patterns. The distribution of a clade, including its geography and its relationship with a geographical or geological feature, conveys historical information about the clade and the area in which it evolved: its area of endemism. These features repeat in unrelated or distantly related taxa in the biota indicating a shared history. Main conclusions The western Pacific including East Asia and Australasia is a locus of survival or differentiation, the site of the principal breaks in the distribution, for an array of teleost clades. It is not their center of origin. Biology and geology should be integrated in biogeographical analyses. Modern distributions reflect remnants of once more widespread distributions. When biogeography acknowledges the connections and correlations between geology and biology, it implements a guiding principle of the work of Alexander von Humboldt.

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Section: Discussionmentioning

confidence: 92%

The shape of biogeography: Endemism, maps, and classification of fish distributions in the western Pacific

Parenti

2019

Journal of Biogeography

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“…Concomitant with our results, Jokiel and Martinelli () ascribed the high diversity of coral reefs to a net dispersal of taxa caused by prevailing currents toward tropical latitudes, which may occur via ‘bridge species’ or isolated deep‐water colonies (Roberts et al , Jablonski et al ). Moreover, this hypothesis has not only been put forward for stony corals but also for reef associated organisms such as the ember parrotfish, the yellow tang, the tropical sea cucumber and the holocentrid fishes (Eble et al , Fitzpatrick et al , Skillings et al , Dornburg et al ).…”

Section: Discussionmentioning

confidence: 99%

Evolutionary dispersal drives the latitudinal diversity gradient of stony corals

2015

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Early View (EV): 1-EV that show large distributional changes over time (Jablonski et al. 2006, Roy andGoldberg 2007). In marine bivalves, for instance, more than half of the genera that originated in the tropics have extend their geographic range towards higher latitudes, evidence used by Jablonski et al. (2006) to suggest an ' out of the tropics ' (OTT) dynamic. Linking evolutionary and ecological processes through a spatially explicit approach, this model pose that ' taxa preferentially originate in the tropics and expand toward the poles but without losing their tropical presence ' . Although the OTT model was tested in marine organisms, phylogenetic information on terrestrial clades also confi rmed these predictions over the tropical conservatism hypothesis (Jansson et al. 2013). In fact, dynamic model simulations of range shifts and diversifi cation processes have shown that extratropical regions may act not only as a macroevolutionary sink but as a dispersal source as well (Goldberg et al. 2005, Arita and V á zquez-Dom í nguez 2008). Either way, results consistently indicate that speciation and extinction cannot fully explain the canonical LDG, thus it seems quite likely that historical dispersion plays a central role in the current distribution of taxa (Goldberg et al. 2005, Jablonski et al. 2006, Roy and Goldberg 2007, Arita and V á zquezDom í nguez 2008, Escarguel et al. 2008, Soria-Carrasco and Castresana 2012.

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“…To facilitate faster throughput, parallel processing is supported using the foreach software package [24]. PhyInformR can be downloaded along with an in depth user guide and example phylogenies [25–27] from github: https://github.com/carolinafishes/PhyInformR. As an input, PhyInformR uses site rates estimated from software such as Hyphy [28] and user tree topologies to rapidly enable quantification of PI across datasets or user defined dataset partitions.…”

Section: Methodsmentioning

confidence: 99%

PhyInformR: phylogenetic experimental design and phylogenomic data exploration in R

et al. 2016

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BackgroundAnalyses of phylogenetic informativeness represent an important step in screening potential or existing datasets for their proclivity toward convergent or parallel evolution of molecular sites. However, while new theory has been developed from which to predict the utility of sequence data, adoption of these advances have been stymied by a lack of software enabling application of advances in theory, especially for large next-generation sequence data sets. Moreover, there are no theoretical barriers to application of the phylogenetic informativeness or the calculation of quartet internode resolution probabilities in a Bayesian setting that more robustly accounts for uncertainty, yet there is no software with which a computationally intensive Bayesian approach to experimental design could be implemented.ResultsWe introduce PhyInformR, an open source software package that performs rapid calculation of phylogenetic information content using the latest advances in phylogenetic informativeness based theory. These advances include modifications that incorporate uneven branch lengths and any model of nucleotide substitution to provide assessments of the phylogenetic utility of any given dataset or dataset partition. PhyInformR provides new tools for data visualization and routines optimized for rapid statistical calculations, including approaches making use of Bayesian posterior distributions and parallel processing. By implementing the computation on user hardware, PhyInformR increases the potential power users can apply toward screening datasets for phylogenetic/genomic information content by orders of magnitude.ConclusionsPhyInformR provides a means to implement diverse substitution models and specify uneven branch lengths for phylogenetic informativeness or calculations providing quartet based probabilities of resolution, produce novel visualizations, and facilitate analyses of next-generation sequence datasets while incorporating phylogenetic uncertainty through the use parallel processing. As an open source program, PhyInformR is fully customizable and expandable, thereby allowing for advanced methodologies to be readily integrated into local bioinformatics pipelines.Software is available through CRAN and a package containing the software, a detailed manual, and additional sample data is also provided freely through github: https://github.com/carolinafishes/PhyInformR.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-016-0837-3) contains supplementary material, which is available to authorized users.

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The impact of shifts in marine biodiversity hotspots on patterns of range evolution: Evidence from the Holocentridae (squirrelfishes and soldierfishes)

Cited by 41 publications

References 119 publications

The shape of biogeography: Endemism, maps, and classification of fish distributions in the western Pacific

The shape of biogeography: Endemism, maps, and classification of fish distributions in the western Pacific

Evolutionary dispersal drives the latitudinal diversity gradient of stony corals

PhyInformR: phylogenetic experimental design and phylogenomic data exploration in R

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