Coiling directions in the planktonic foraminifer Pulleniatina: A complex eco-evolutionary dynamic spanning millions of years

Planktonic foraminifera are heterotrophic sexually reproducing marine protists with an exceptionally complete fossil record that provides unique insights into long-term patterns and processes of evolution. Populations often exhibit strong biases towards either right (dextral) or left (sinistral) shells. Deep-sea sediment cores spanning millions of years reveal that some species show large and often rapid fluctuations in their dominant coiling direction through time. This is useful for biostratigraphic correlation but further work is required to understand the population dynamical processes that drive these fluctuations. Here we address the case of coiling fluctuations in the planktonic foraminifer genus Pulleniatina based on new high-resolution counts from two recently recovered sediment cores from either side of the Indonesian through-flow in the tropical west Pacific and Indian Oceans (International Ocean Discovery Program Sites U1486 and U1483). We use single-specimen stable isotope analyses to show that dextral and sinistral shells from the same sediment samples can show significant differences in both carbon and oxygen isotopes, implying a degree of ecological separation between populations. In one case we detect a significant difference in size between dextral and sinistral specimens. We suggest that major fluctuations in coiling ratio are caused by cryptic populations replacing one another in competitive sweeps, a mode of evolution that is more often associated with asexual organisms than with the classical ‘biological species concept’.

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Early diagenetic overprint in Caribbean sediment cores and its effect on the geochemical composition of planktonic foraminifera

Biogeosciences ◽

10.5194/bg-4-957-2007 ◽

2007 ◽

Vol 4 (6) ◽

pp. 957-973 ◽

Cited By ~ 27

Author(s):

M. Regenberg ◽

D. Nürnberg ◽

J. Schönfeld ◽

G.-J. Reichart

Keyword(s):

Planktonic Foraminifera ◽

Sediment Cores ◽

Time Interval ◽

Tropical Atlantic ◽

Carbonate Platforms ◽

Geochemical Composition ◽

Deep Sea Sediment ◽

Pelagic Environment ◽

Magnesium Calcite ◽

High Magnesium Calcite

Abstract. Early diagenetic features are noticed in the vicinity of carbonate platforms. Planktonic foraminifera of two tropical Atlantic deep-sea sediment cores show the strict relation between micro-scale euhydral crystallites of inorganic precipitates, higher oxygen isotope values and Mg/Ca ratios, and lower Sr/Ca ratios than expected for their pelagic environment in the time interval of ~100 000–550 000 calendar years before present. Laser ablation Mg/Ca (Sr/Ca) of crystallite-bearing foraminiferal chamber walls revealed 4–6 times elevated (2–3 times depleted) ratios, when ablating the diagenetic overgrowth. Crystalline overgrowth in proportion of 10–20% are estimated to cause the observed geochemical alteration. The extent of foraminiferal Mg/Ca alteration, moreover, seems to be controlled by the composition of the bulk sediment, especially the content of high-magnesium calcite. Anomalous ratios of >6 mmol/mol only occur, when high-magnesium calcite has dissolved within the sediment. The older parts (back to ~800 kyrs) of the records are characterized by similar trends of Mg/Ca and Sr/Ca. We discuss possible scenarios to accommodate the obtained geochemical information.

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A flexible pipeline combining clustering and correction tools for prokaryotic and eukaryotic metabarcoding

10.1101/717355 ◽

2019 ◽

Cited By ~ 5

Author(s):

Miriam I. Brandt ◽

Blandine Trouche ◽

Laure Quintric ◽

Patrick Wincker ◽

Julie Poulain ◽

...

Keyword(s):

Clustering Algorithm ◽

Sequence Similarity ◽

Alpha Diversity ◽

Biological Species ◽

Biological Species Concept ◽

Ribosomal Database Project ◽

Taxonomic Assignment ◽

Deep Sea Sediment ◽

Biodiversity Inventories ◽

Identity Threshold

ABSTRACTEnvironmental metabarcoding is an increasingly popular tool for studying biodiversity in marine and terrestrial biomes. With sequencing costs decreasing, multiple-marker metabarcoding, spanning several branches of the tree of life, is becoming more accessible. However, bioinformatic approaches need to adjust to the diversity of taxonomic compartments targeted as well as to each barcode gene specificities. We built and tested a pipeline based on Illumina read correction with DADA2 allowing analyzing metabarcoding data from prokaryotic (16S) and eukaryotic (18S, COI) life compartments. We implemented the option to cluster Amplicon Sequence Variants (ASVs) into Operational Taxonomic Units (OTUs) with swarm v2, a network-based clustering algorithm, and to further curate the ASVs/OTUs based on sequence similarity and co-occurrence rates using a recently developed algorithm, LULU. Finally, flexible taxonomic assignment was implemented via Ribosomal Database Project (RDP) Bayesian classifier and BLAST. We validate this pipeline with ribosomal and mitochondrial markers using eukaryotic mock communities and 42 deep-sea sediment samples. The results show that ASVs, reflecting genetic diversity, may not be appropriate for alpha diversity estimation of organisms fitting the biological species concept. The results underline the advantages of clustering and LULU-curation for producing more reliable metazoan biodiversity inventories, and show that LULU is an effective tool for filtering metazoan molecular clusters, although the minimum identity threshold applied to co-occurring OTUs has to be increased for 18S. The comparison of BLAST and the RDP Classifier underlined the potential of the latter to deliver very good assignments, but highlighted the need for a concerted effort to build comprehensive, ecosystem-specific, databases adapted to the studied communities.

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Early diagenetic overprint in Caribbean sediment cores and its effect on the geochemical composition of planktonic foraminifera

Biogeosciences Discussions ◽

10.5194/bgd-4-2179-2007 ◽

2007 ◽

Vol 4 (4) ◽

pp. 2179-2213 ◽

Cited By ~ 1

Author(s):

M. Regenberg ◽

D. Nürnberg ◽

J. Schönfeld ◽

G.-J. Reichart

Keyword(s):

Planktonic Foraminifera ◽

Sediment Cores ◽

Time Interval ◽

Tropical Atlantic ◽

Carbonate Platforms ◽

Geochemical Composition ◽

Deep Sea Sediment ◽

Pelagic Environment ◽

Magnesium Calcite ◽

High Magnesium Calcite

Abstract. Early diagenetic features are noticed in the vicinity of carbonate platforms. Planktonic foraminifera of two tropical Atlantic deep-sea sediment cores show the strict relation between micro-scale euhydral crystallites of inorganic precipitates, higher oxygen isotope values and Mg/Ca ratios, and lower Sr/Ca ratios than expected for their pelagic environment in the time interval of ~100 000–550 000 calendar years before present. Laser ablation Mg/Ca (Sr/Ca) of crystallite-bearing foraminiferal chamber walls revealed 4–6 times elevated (2–3 times depleted) ratios, when ablating the diagenetic overgrowth. Crystalline overgrowth in proportions of 10–20% are estimated to cause the observed geochemical alteration. The extent of foraminiferal Mg/Ca alteration, moreover, seems to be controlled by the composition of the bulk sediment, especially the content of high-magnesium calcite. Anomalous ratios of >6 mmol/mol only occur, when high-magnesium calcite has dissolved within the sediment. The older parts (back to ~800 kyrs) of the records are characterized by similar trends of Mg/Ca and Sr/Ca. We discuss possible scenarios to accommodate the obtained geochemical information.

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A geographic test of species selection using planktonic foraminifera during the Cretaceous/Paleogene mass extinction

Paleobiology ◽

10.1666/10010.1 ◽

2011 ◽

Vol 37 (3) ◽

pp. 426-437 ◽

Cited By ~ 10

Author(s):

Matthew G. Powell ◽

Johnryan MacGregor

Keyword(s):

Mass Extinction ◽

Planktonic Foraminifera ◽

Sediment Cores ◽

Species Level ◽

Species Selection ◽

Extinction Rate ◽

Deep Sea Sediment ◽

Geographic Ranges ◽

Level Of Selection ◽

Very High

Species selection has received a great deal of theoretical attention but it has rarely been empirically tested. It is important to determine the level of selection that operated during a particular extinction event because it can help distinguish between traits that were actually responsible for extinction and those that were merely correlated with it. Here, we present a test that can help distinguish between organismal and species-level selection, which we demonstrate using the high-resolution fossil record of planktonic foraminifera species recorded in deep-sea sediment cores. Our test examines the fate of survivors and victims during the Cretaceous/Paleogene (K/Pg) mass extinction within single geographic regions, where all individuals experience the same selection pressures. Selection at the organismal level implies that individual members of surviving species are more fit than those of victimized species, and therefore should be more likely to survive in affected areas; conversely, selection at the species level implies individuals will suffer equally within an affected area. We find that survivors of the mass extinction suffered very high extirpation rates in cores where the overall extinction rate was high, indicating that individual members of the surviving species were generally no more fit than individual members of extinct species. Rather, these species were able to survive because they possessed advantageous species-level traits, such as larger geographic ranges and greater abundances than victimized species. This geographic pattern of extirpation suggests that selection operated at the species, rather than organismal, level during the K/Pg mass extinction of planktonic foraminifera.

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Disruption of the Atlantic Meridional Circulation during Deglacial Climates Inferred from Planktonic Foraminiferal Shell Weights

Journal of Marine Science and Engineering ◽

10.3390/jmse9050519 ◽

2021 ◽

Vol 9 (5) ◽

pp. 519

Author(s):

Stergios D. Zarkogiannis

Keyword(s):

Atlantic Ocean ◽

Meridional Circulation ◽

Order Approximation ◽

Planktonic Foraminifera ◽

Sediment Cores ◽

Meridional Overturning Circulation ◽

Density Structure ◽

Last Interglacial ◽

Shell Weight ◽

The North

Changes in the density structure of the upper oceanic water masses are an important forcing of changes in the Atlantic Meridional Overturning Circulation (AMOC), which is believed to widely affect Earth’s climate. However, very little is known about past changes in the density structure of the Atlantic Ocean, despite being extensively studied. The physical controls on planktonic foraminifera calcification are explored here, to obtain a first-order approximation of the horizontal density gradient in the eastern Atlantic during the last 200,000 years. Published records of Globigerina bulloides shells from the North and Tropical eastern Atlantic were complemented by the analysis of a South Atlantic core. The masses of the same species shells from three different dissolution assessed sediment cores along the eastern Atlantic Ocean were converted to seawater density values using a calibration equation. Foraminifera, as planktonic organisms, are subject to the physical properties of the seawater and thus their shells are sensitive to buoyancy forcing through surface temperature and salinity perturbations. By using planktonic foraminifera shell weight as an upper ocean density proxy, two intervals of convergence of the shell masses are identified during cold intervals of the last two deglaciations that may be interpreted as weak ocean density gradients, indicating nearly or completely eliminated meridional circulation, while interhemispheric Atlantic density differences appear to alleviate with the onset of the last interglacial. The results confirm the significance of variations in the density of Atlantic surface waters for meridional circulation changes.

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Discriminating arboviral species

Journal of General Virology ◽

10.1099/jgv.0.001572 ◽

2021 ◽

Vol 102 (4) ◽

Author(s):

Yiyuan Li ◽

Angela C. O’Donnell ◽

Howard Ochman

Keyword(s):

Evolutionary History ◽

Viral Vectors ◽

Species Concept ◽

International Committee ◽

Biological Species ◽

Biological Species Concept ◽

Substantial Variation ◽

Artificial Boundaries ◽

Human Infections

Mosquito-borne arboviruses, including a diverse array of alphaviruses and flaviviruses, lead to hundreds of millions of human infections each year. Current methods for species-level classification of arboviruses adhere to guidelines prescribed by the International Committee on Taxonomy of Viruses (ICTV), and generally apply a polyphasic approach that might include information about viral vectors, hosts, geographical distribution, antigenicity, levels of DNA similarity, disease association and/or ecological characteristics. However, there is substantial variation in the criteria used to define viral species, which can lead to the establishment of artificial boundaries between species and inconsistencies when inferring their relatedness, variation and evolutionary history. In this study, we apply a single, uniform principle – that underlying the Biological Species Concept (BSC) – to define biological species of arboviruses based on recombination between genomes. Given that few recombination events have been documented in arboviruses, we investigate the incidence of recombination within and among major arboviral groups using an approach based on the ratio of homoplastic sites (recombinant alleles) to non-homoplastic sites (vertically transmitted alleles). This approach supports many ICTV-designations but also recognizes several cases in which a named species comprises multiple biological species. These findings demonstrate that this metric may be applied to all lifeforms, including viruses, and lead to more consistent and accurate delineation of viral species.

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Not just a peep: The evolution of calling in Pseudacris crucifer

Inquiry@Queen's Undergraduate Research Conference Proceedings ◽

10.24908/iqurcp.10032 ◽

2018 ◽

Author(s):

Amanda Cicchino

Keyword(s):

Reproductive Isolation ◽

Full Range ◽

Mate Recognition ◽

Preliminary Evidence ◽

Biological Species ◽

Biological Species Concept ◽

Incipient Species ◽

Pseudacris Crucifer ◽

Full Analysis ◽

American Frog

Reproductive isolation is the hallmark of speciation as defined by the biological species concept. A species that is evolving towards reproductive isolation, but has not reached full isolation, is defined as an incipient species. One mechanism used by incipient species to further drive speciation is the use of mate recognition signals. The spring peeper, Pseudacris crucifer, is a North American frog that can be classified as an incipient species, as previous studies have found 6 distinct mitochondrial lineages within its range. Spring peepers use vocal signals for mate recognition and exhibit a female choice mating system where the males call to attract females. This study investigates the evolution of calling in spring peepers. Using calls from each lineage across the full range of spring peepers, I analyzed 11 different characteristics to determine whether the calls were different, and if so, which characteristics are being selected for. Preliminary evidence suggests that the calls between the lineages are distinct and that certain characteristics of the call are more heavily selected for than others. Full analysis on the data has not been completed at this time. This study will expand the understanding of the evolution of spring peepers, as well as offer insight into the role of mating systems on reproductive isolation.

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Quantifying sea surface temperature ranges of the Arabian Sea for the past 20 000 years

Climate of the Past ◽

10.5194/cp-7-1337-2011 ◽

2011 ◽

Vol 7 (4) ◽

pp. 1337-1349 ◽

Cited By ~ 37

Author(s):

G. M. Ganssen ◽

F. J. C. Peeters ◽

B. Metcalfe ◽

P. Anand ◽

S. J. A. Jung ◽

...

Keyword(s):

Arabian Sea ◽

Isotope Composition ◽

Planktonic Foraminifera ◽

Sediment Cores ◽

Maximum Temperature ◽

Physical Parameters ◽

Seasonal Temperature ◽

Mean Values ◽

The Past ◽

Temperature Ranges

Abstract. The oxygen isotopic composition of planktonic foraminifera tests is one of the widest used geochemical tools to reconstruct past changes of physical parameters of the upper ocean. It is common practice to analyze multiple individuals from a mono-specific population and assume that the outcome reflects a mean value of the environmental conditions during calcification of the analyzed individuals. Here we present the oxygen isotope composition of individual specimens of the surface-dwelling species Globigerinoides ruber and Globigerina bulloides from sediment cores in the Western Arabian Sea off Somalia, inferred as indicators of past seasonal ranges in temperature. Combining the δ18O measurements of individual specimens to obtain temperature ranges with Mg/Ca based mean calcification temperatures allows us to reconstruct temperature extrema. Our results indicate that over the past 20 kyr the seasonal temperature range has fluctuated from its present value of 16 °C to mean values of 13 °C and 11 °C for the Holocene and LGM, respectively. The data for the LGM suggest that the maximum temperature was lower, whilst minimum temperature remained approximately constant. The rather minor variability in lowest summer temperatures during the LGM suggests roughly constant summer monsoon intensity, while upwelling-induced productivity was lowered.

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Identification and correlation of distal tephra layers in deep-sea sediment cores, Scotia Sea, Antarctica

Annals of Glaciology ◽

10.3189/1998aog27-1-285-289 ◽

1998 ◽

Vol 27 ◽

pp. 285-289 ◽

Cited By ~ 21

Author(s):

S. G. Moreton ◽

J. L. Smellie

Keyword(s):

Deep Sea ◽

Volcanic Ash ◽

Sediment Cores ◽

Quaternary Deposits ◽

Deep Sea Sediment ◽

Scotia Sea ◽

Ash Layer ◽

Tephra Layers ◽

Major Oxide ◽

Water Depths

Quaternary deposits in six sediment cores from the Scotia Sea, Antarctica, were examined for the presence of volcanic ash layers. The cores were recovered from water depths of 3369-4025 m. Altogether, 23 ash layers were found, 18 of which have been investigated by electron-probe microanalysis. Deception Island is identified as the source of all the ash layers analyzed. The upper ash layer in each core can be correlated across all six cores, over a distance of -100 km, on the basis of its unusual bimodal composition, major oxide geochemistry and stratigraphie position. Two other ash layers can also be correlated between several of the cores.

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