Widespread intra-specific genetic homogeneity of coastal Antarctic benthic foraminifera

Majewski, Wojciech; Bowser, Samuel S.; Pawłowski, Jan

doi:10.1007/s00300-015-1765-1

Cited by 13 publications

(4 citation statements)

References 66 publications

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“…However, despite the sequencing of a limited number of genomes and transcriptomes 29 – 31 and few phylogenetic studies using nuclear markers 32 – 34 , only one genetic marker, the nuclear 18S rRNA, is commonly available and used for molecular work on Foraminifera 18 – 20 , 23 , 25 , 28 , 61 , 62 . As Foraminifera can show high levels of intragenomic variability in this marker and highly variable rates of evolution are found in some genera and families, species identification and phylogenetic placement can be challenging 21 , 26 , 27 , 63 . Although approaches for molecularly identifying species and species groups based on 18S rRNA have been developed 15 , intragenomic polymorphisms in this marker can hamper inference of ecological and evolutionary patterns.…”

Section: Discussionmentioning

confidence: 99%

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

Macher

Wideman

Girard

et al. 2021

Sci Rep

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Foraminifera are a species-rich phylum of rhizarian protists that are highly abundant in many marine environments and play a major role in global carbon cycling. Species recognition in Foraminifera is mainly based on morphological characters and nuclear 18S ribosomal RNA barcoding. The 18S rRNA contains variable sequence regions that allow for the identification of most foraminiferal species. Still, some species show limited variability, while others contain high levels of intragenomic polymorphisms, thereby complicating species identification. The use of additional, easily obtainable molecular markers other than 18S rRNA will enable more detailed investigation of evolutionary history, population genetics and speciation in Foraminifera. Here we present the first mitochondrial cytochrome c oxidase subunit 1 (COI) gene sequences (“barcodes”) of Foraminifera. We applied shotgun sequencing to single foraminiferal specimens, assembled COI, and developed primers that allow amplification of COI in a wide range of foraminiferal species. We obtained COI sequences of 49 specimens from 17 species from the orders Rotaliida and Miliolida. Phylogenetic analysis showed that the COI tree is largely congruent with previously published 18S rRNA phylogenies. Furthermore, species delimitation with ASAP and ABGD algorithms showed that foraminiferal species can be identified based on COI barcodes.

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Section: Discussionmentioning

confidence: 99%

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

Macher

Wideman

Girard

et al. 2021

Sci Rep

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“…The presence of high intra-genomic variability in some of the studied species may also be the results of cryptic speciation. Cryptic species in benthic and planktonic foraminifera have been identified multiple times (e.g., Holzmann, 2002, 2009;Majewski et al, 2015;Morard et al, 2016). Morard et al (2016) developed an integrative molecular taxonomic system for community metabarcoding in order to identify biological species and cryptic diversity in planktonic foraminifera.…”

Section: High Molecular Diversity In Large Benthic Foraminiferamentioning

confidence: 99%

Mitochondrial Cytochrome Oxidase Subunit 1: A Promising Molecular Marker for Species Identification in Foraminifera

et al. 2022

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Traditional morphological methods for species identification are highly time consuming, especially for small organisms, such as Foraminifera, a group of shell-building microbial eukaryotes. To analyze large amounts of samples more efficiently, species identification methods have extended to molecular tools in the last few decades. Although a wide range of phyla have good markers available, for Foraminifera only one hypervariable marker from the ribosomal region (18S) is widely used. Recently a new mitochondrial marker cytochrome oxidase subunit 1 (COI) has been sequenced. Here we investigate whether this marker has a higher potential for species identification compared to the ribosomal marker. We explore the genetic variability of both the 18S and COI markers in 22 benthic foraminiferal morphospecies (orders Miliolida and Rotaliida). Using single-cell DNA, the genetic variability within specimens (intra) and between specimens (inter) of each species was assessed using next-generation sequencing. Amplification success rate was twice as high for COI (151/200 specimens) than for 18S (73/200 specimens). The COI marker showed greatly decreased intra- and inter-specimen variability compared to 18S in six out of seven selected species. The 18S phylogenetic reconstruction fails to adequately cluster multiple species together in contrast to COI. Additionally, the COI marker helped recognize misclassified specimens difficult to morphologically identify to the species level. Integrative taxonomy, combining morphological and molecular characteristics, provides a robust picture of the foraminiferal species diversity. Finally, we suggest the use of a set of sequences (two or more) to describe species showing intra-genomic variability additionally to using multiple markers. Our findings highlight the potential of the newly discovered mitochondrial marker for molecular species identification and metabarcoding purposes.

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“…Tentatively, we assume that all the lenticular Cassidulina described from numerous locations around Antarctica indeed represent a single species. This assumption is based on the molecular population structures of many other Antarctic foraminifera, showing single, widely distributed species (Majda et al, 2018; Majewski et al, 2015). Moreover, most genetically investigated Antarctic foraminifera from shallow‐water settings exhibit genetic divergence between morphologically similar sister genotypes from the Antarctic continental shelf and from the Northern Hemisphere polar regions (Pawlowski et al, 2008) and/or just north of Drake Passage (Majda et al, 2018).…”

Section: Discussionmentioning

confidence: 99%

Foraminiferal Patterns in Deglacial Sediment in the Western Ross Sea, Antarctica: Life Near Grounding Lines

Majewski

Prothro

Simkins

et al. 2020

Paleoceanog and Paleoclimatol

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Improved multibeam swath bathymetry allows targeted coring of glacial landforms aiming at improving our understanding of sedimentary facies that developed in glacimarine settings during the post-Last Glacial Maximum (LGM) deglaciation. Coupled with radiocarbon dates, we explore foraminiferal records from 18 sediment cores from the western Ross Sea largely from sites near paleo-grounding lines. We investigate post-LGM foraminiferal assemblages from glacimarine environments, including those proximal and more distal to paleo-grounding lines, including environments influenced by subglacial meltwater outflow and further removed from direct glacial influence and subject to different oceanographic conditions. Agglutinated benthic foraminiferal assemblages dominate open marine facies deposited under the presence of High Salinity Shelf Water and significant primary production, while calcareous foraminiferal assemblages characterize grounding line-proximal settings, some of which were potentially influenced by Modified Circumpolar Deep Water. Rapid deposition of meltwater plume deposits inhibited and, in some cases, significantly altered foraminifera abundance and diversity. Broadly in the Ross Sea, it appears that the high bathymetric gradient of grounding zone wedges is a key factor promoting rich benthic foraminiferal communities in habitats proximal to grounding lines. Therefore, we demonstrate that paleo-grounding line settings may archive high quality in situ foraminiferal data, which is imperative for paleoenvironmental and geochemical studies on glaciated continental margins worldwide.

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Widespread intra-specific genetic homogeneity of coastal Antarctic benthic foraminifera

Cited by 13 publications

References 66 publications

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

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

Mitochondrial Cytochrome Oxidase Subunit 1: A Promising Molecular Marker for Species Identification in Foraminifera

Foraminiferal Patterns in Deglacial Sediment in the Western Ross Sea, Antarctica: Life Near Grounding Lines

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