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Published May 21, 2019 | Version v1
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Data from: The molecular biogeography of the Indo-Pacific: testing hypotheses with multispecies genetic patterns

Creators

  • 1. California State University, Monterey Bay
  • 2. University of Queensland
  • 3. Texas A&M University Corpus Christi Corpus Christi Texas*
  • 4. Massey University
  • 5. Deakin University
  • 6. University of Leeds
  • 7. University of California Los Angeles
  • 8. James Cook University
  • 9. Curtin University
  • 10. Florida Institute of Technology
  • 11. University of Southern Mississippi
  • 12. Vrije Universiteit Brussel
  • 13. Smithsonian Tropical Research Institute
  • 14. National Sun Yat-sen University
  • 15. Louisiana State University
  • 16. Bogor Agricultural University
  • 17. University of Hawaii at Manoa
  • 18. University of Central Florida

Description

Aim: To test hypothesized biogeographic partitions of the tropical Indo-Pacific Ocean with phylogeographic data from 56 taxa, and to evaluate the strength and nature of barriers emerging from this test. Location: The Indo-Pacific Ocean. Time Period: Pliocene through the Holocene. Major Taxa Studied: 56 marine species. Methods: We tested eight biogeographic hypotheses for partitioning of the Indo-Pacific using a novel modification to analysis of molecular variance. Putative barriers to gene flow emerging from this analysis were evaluated for pairwise ΦST, and these ΦST distributions were compared to distributions from randomized datasets and simple coalescent simulations of vicariance arising from the Last Glacial Maximum. We then weighed the relative contribution of distance vs. environmental or geographical barriers to pairwise ΦST with a distance-based redundancy analysis (dbRDA). Results: We observed a diversity of outcomes, although the majority of species fit a few broad biogeographic regions. Repeated coalescent simulation of a simple vicariance model yielded a wide distribution of pairwise ΦST that was very similar to empirical distributions observed across five putative barriers to gene flow. Three of these barriers had median ΦST that were significantly larger than random expectation. Only 21 of 52 species analyzed with dbRDA rejected the null model. Among these, 15 had overwater distance as a significant predictor of pairwise ΦST, while 11 were significant for geographical or environmental barriers other than distance. Main Conclusions: Although there is support for three previously described barriers, phylogeographic discordance in the Indo-Pacific oceans indicates incongruity between processes shaping the distributions of diversity at the species and population levels. Among the many possible causes of this incongruity, genetic drift provides the most compelling explanation: given massive effective population sizes of Indo-Pacific species, even hard vicariance for tens of thousands of years can yield ΦST values that range from 0 to nearly 0.5.

Notes

Indo-Pacific mtDNA database 2019_01_08
This is the full database that we used in the paper. Sequence data are contained in the "sequence" field, and are aligned within each species. The bioregion that each sample fell into under the various regionalizations are in columns named for that regionalization. Most other columns are self explanatory, or are defined as part of DarwinCore: https://dwc.tdwg.org/terms/. All of these data and metadata are also available in GeOMe -https://geome-db.org
indo_pacific_mtDNA_database_2019_01_08.csv
IPDB_UPPER-OverWater_LOWER-Euclidean
These are the overwater and Euclidean distances that were calculated for dbRDA analysis. Methods can be found in the readme file.

Funding provided by: National Science Foundation
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000001
Award Number: DEB-1457848

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Additional details

Related works

Is cited by
10.1111/geb.12905 (DOI)