PFR2: a curated database of planktonic foraminifera 18S ribosomal DNA as a resource for studies of plankton ecology, biogeography and evolution

  title={PFR2: a curated database of planktonic foraminifera 18S ribosomal DNA as a resource for studies of plankton ecology, biogeography and evolution},
  author={Raphael Morard and Kate F. Darling and Fr{\'e}d{\'e}ric Mah{\'e} and St{\'e}phane Audic and Yurika Ujii{\'e} and Agnes K. M. Weiner and Aurore Andr{\'e} and Heidi A. Seears and Christopher M. Wade and Fr{\'e}d{\'e}ric Quill{\'e}v{\'e}r{\'e} and Christophe J. Douady and Gilles Escarguel and Thibault Garidel‐Thoron and Michael Siccha and Michal Ku{\vc}era and Colomban de Vargas},
  journal={Molecular Ecology Resources},
Planktonic foraminifera (Rhizaria) are ubiquitous marine pelagic protists producing calcareous shells with conspicuous morphology. They play an important role in the marine carbon cycle, and their exceptional fossil record serves as the basis for biochronostratigraphy and past climate reconstructions. A major worldwide sampling effort over the last two decades has resulted in the establishment of multiple large collections of cryopreserved individual planktonic foraminifera samples. Thousands… 

Surface ocean metabarcoding confirms limited diversity in planktonic foraminifera but reveals unknown hyper-abundant lineages

This work targets planktonic foraminifera, a group of protists whose known morphological diversity is limited, taxonomically resolved and linked to ribosomal DNA barcodes, and identifies 69 genetic types belonging to 41 morphotaxa in the metabarcoding dataset.

dinoref: A curated dinoflagellate (Dinophyceae) reference database for the 18S rRNA gene

An updated 18S rRNA reference database of dinoflagellates: dinoref is provided, providing an opportunity to test the level of taxonomic resolution of different 18S barcode markers based on a large number of sequences and species.

Taxonomic review of living planktonic foraminifera

Abstract. Applications of fossil shells of planktonic foraminifera to decipher past environmental change and plankton evolution require a robust operational taxonomy. In this respect, extant

Planktonic foraminifera genomic variations reflect paleoceanographic changes in the Arctic: evidence from sedimentary ancient DNA

This study correlated the distribution of ribosomal amplicon sequence variants (ASVs) with paleoceanographic changes by analyzing the high-throughput sequence data assigned to Neogloboquadrina pachyderma in a 140,000-year-old sediment core from the Arctic Ocean.

A new sequence data set of SSU rRNA gene for Scleractinia and its phylogenetic and ecological applications

A time‐calibrated phylogeny of Scleractinia is provided, and mutation rate heterogeneity is demonstrated across main lineages, and the V4 and V9 regions seem to be promising barcode loci because variation at commonly used barcode primer binding sites was extremely low, while their levels of divergence allowed families and genera to be distinguished.

First report of mitochondrial COI in foraminifera and implications for DNA barcoding

The first mitochondrial cytochrome c oxidase subunit 1 (COI) gene sequences (“barcodes”) of Foraminifera are presented and species delimitation with ASAP and ABGD algorithms showed that foraminiferal species can be identified based on COI barcodes.

Unassigned diversity of planktonic foraminifera from environmental sequencing revealed as known but neglected species

Most of the modern diversity in planktonic foraminifera has been taxonomically captured, but the role of the small and neglected taxa has be severely underestimated.

Mitochondrial cytochrome c oxidase subunit I (COI) metabarcoding of Foraminifera communities using taxon-specific primers

Foraminifera are a species-rich phylum of rhizarian protists that are highly abundant in most marine environments. Molecular methods such as metabarcoding have revealed a high, yet undescribed

Metabarcoding Insights Into the Trophic Behavior and Identity of Intertidal Benthic Foraminifera

The application of metabarcoding is proposed as a tool for the elucidation of the in situ feeding behavior of benthic foraminifera, while also allowing the correct taxonomic assignment of the feeder, using the V9 region of the 18S (small subunit; SSU) rRNA gene.

Planktonic foraminifera-derived environmental DNA extracted from abyssal sediments preserves patterns of plankton macroecology

Re-analyze foraminiferal-specific metabarcodes from 31 deep-sea sediment samples, which were shown to contain a small fraction of sequences from planktonic foraminifera, to assess the process controlling the transport and deposition of eDNA onto the sediment and the extent to which it preserves the features of past oceanic biota remains unknown.



Planktic foraminiferal molecular evolution and their polyphyletic origins from benthic taxa

Molecular evidence of cryptic speciation in planktonic foraminifers and their relation to oceanic provinces.

The genetic data reveal the presence of three cryptic species, whose distribution is clearly correlated to hydrographic provinces, and particularly to sea-surface total chlorophyll a concentration, and suggest that a considerable part of the diversity among planktonic foraminifers has been overlooked in morphological taxonomies.

Phylogeny and Rates of Molecular Evolution of Planktonic Foraminifera: SSU rDNA Sequences Compared to the Fossil Record

Differences in absolute rates of evolution at all taxonomic levels in planktonic foraminifera are revealed and their effect on phylogenetic reconstructions is demonstrated.

Cryptic species of planktonic foraminifera: their effect on palaeoceanographic reconstructions

  • M. KučeraK. Darling
  • Environmental Science, Geography
    Philosophical Transactions of the Royal Society of London. Series A: Mathematical, Physical and Engineering Sciences
  • 2002
This study indicates that genetic diversity among planktonic foraminifera may become more of a gift than malaise to palaeoproxies, and if it becomes possible to distinguish these genetic types in the fossil record, the accuracy of proxies based on planktono-based species will indeed substantially increase.

The genetic diversity of planktic foraminifera and the global distribution of ribosomal RNA genotypes

Phylogeography of the Tropical Planktonic Foraminifera Lineage Globigerinella Reveals Isolation Inconsistent with Passive Dispersal by Ocean Currents

This work uses a database of 387 single-specimen sequences of the SSU rDNA of the planktonic foraminifera Globigerinella as a model to assess the biogeographic and phylogenetic distributions of cryptic diversity in marine microplankton on a global scale and observes an uneven allocation of cryptic Diversity among the phylogenetic lineages.

Worldwide Genotyping in the Planktonic Foraminifer Globoconella inflata: Implications for Life History and Paleoceanography

Biometric measurements from plankton tows north and south of the Antarctic Subpolar Front indicate that Types I and II display slight but significant differences in shell morphology, which may allow recognition of the G. inflata pseudo-cryptic species back into the fossil record, which in turn may contribute to monitor past movements of the Antarctica Subpolars Front during the middle and late Pleistocene.

SSU rDNA Divergence in Planktonic Foraminifera: Molecular Taxonomy and Biogeographic Implications

A molecular taxonomy that ranks 49 genetic types of planktonic foraminifera as genuine (pseudo)cryptic species is provided, synthesizing geographic, ecological and morphological differentiations that can occur among the genuine ( Pseudo) cryptic species.