Manuel Weinkauf

Phylogeography of the tropical planktonic foraminifera lineage Globigerinella reveals isolation inconsistent with passive dispersal by ocean currents

Morphologically defined species of marine plankton often harbor a considerable level of cryptic diversity. Since many morphospecies show cosmopolitan distribution, an understanding of biogeographic and evolutionary processes at the level of genetic diversity requires global sampling. We use 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. Our data confirm the existence of multiple, well isolated genetic lineages. An analysis of their abundance and distribution indicates that our sampling is likely to approximate the actual total diversity. Unexpectedly, we observe an uneven allocation of cryptic diversity among the phylogenetic lineages. We show that this pattern is neither an artifact of sampling intensity nor a function of lineage age. Instead, we argue that it reflects an ongoing speciation process in one of the three major lineages. Surprisingly, four of the six genetic types in the hyperdiverse lineage are biogeographically restricted to the Indopacific. Their mutual co-occurrence and their hierarchical phylogenetic structure provide no evidence for an origin through sudden habitat fragmentation and their limitation to the Indopacific challenges the view of a global gene flow within the warm-water provinces. This phenomenon shows that passive dispersal is not sufficient to describe the distribution of plankton diversity. Rather, these organisms show differentiated distribution patterns shaped by species interactions and reflecting phylogenetic contingency with unique histories of diversification rates.

Seasonal Variation in Shell Calcification of Planktonic Foraminifera in the NE Atlantic Reveals Species-Specific Response to Temperature, Productivity, and Optimum Growth Conditions.

Using shells collected from a sediment trap series in the Madeira Basin, we investigate the effects of seasonal variation of temperature, productivity, and optimum growth conditions on calcification in three species of planktonic Foraminifera. The series covers an entire seasonal cycle and reflects conditions at the edge of the distribution of the studied species, manifesting more suitable growth conditions during different parts of the year. The seasonal variation in seawater carbonate saturation at the studied site is negligible compared to other oceanic regions, allowing us to assess the effect of parameters other than carbonate saturation. Shell calcification is quantified using weight and size of individual shells. The size–weight scaling within each species is robust against changes in environmental parameters, but differs among species. An analysis of the variation in calcification intensity (size-normalized weight) reveals species-specific response patterns. In Globigerinoides ruber (white) and Globigerinoides elongatus, calcification intensity is correlated with temperature (positive) and productivity (negative), whilst in Globigerina bulloides no environmental forcing is observed. The size–weight scaling, calcification intensity, and response of calcification intensity to environmental change differed between G. ruber (white) and G. elongatus, implying that patterns extracted from pooled analyses of these species may reflect their changing proportions in the samples. Using shell flux as a measure of optimum growth conditions, we observe significant positive correlation with calcification intensity in G. elongatus, but negative correlation in G. bulloides. The lack of a consistent response of calcification intensity to optimum growth conditions is mirrored by the results of shell size analyses. We conclude that calcification intensity in planktonic Foraminifera is affected by factors other than carbonate saturation. These factors include temperature, productivity, and optimum growth conditions, but the strength and sign of the relationships differ among species, potentially complicating interpretations of calcification data from the fossil record.

Disruptive selection and bet-hedging in planktonic Foraminifera: shell morphology as predictor of extinctions

Extinction is a remarkably difficult phenomenon to study under natural conditions. This is because the outcome of stress exposure and associated fitness reduction is not known until the extinction occurs and it remains unclear whether there is any phenotypic reaction of the exposed population that can be used to predict its fate. Here we take advantage of the fossil record, where the ecological outcome of stress exposure is known. Specifically, we analyze shell morphology of planktonic Foraminifera in sediment samples from the Mediterranean, during an interval preceding local extinctions. In two species representing different plankton habitats, we observe shifts in trait state and decrease in variance in association with non-terminal stress, indicating stabilizing selection. At terminal stress levels, immediately before extinction, we observe increased growth asymmetry and trait variance, indicating disruptive selection and bet-hedging. The pre-extinction populations of both species show a combination of trait states and trait variance distinct from all populations exposed to non-terminal levels of stress. This finding indicates that the phenotypic history of a population may allow the detection of threshold levels of stress, likely to lead to extinction. It is thus an alternative to population dynamics in studying and monitoring natural population ecology.

Methodology for single-cell genetic analysis of planktonic foraminifera for studies of protist diversity and evolution

Single-cell genetic analysis is an essential method to investigate the biodiversity and evolutionary ecology of marine protists. In protist groups that do not reproduce under laboratory conditions, this approach provides the only means to directly associate molecular sequences with cell morphology. The resulting unambiguous taxonomic identification of the DNA sequences is a prerequisite for barcoding and analyses of environmental metagenomic data. Extensive single-cell genetic studies have been carried out on planktonic foraminifera over the past 20 years to elucidate their phylogeny, cryptic diversity, biogeography and the relationship between genetic and morphological variability. In the course of these investigations, it has become evident that genetic analysis at the individual specimen level is confronted by innumerable challenges ranging from the negligible amount of DNA present in the single cell to the substantial amount of DNA contamination introduced by endosymbionts or food particles. Consequently, a range of methods has been developed and applied throughout the years for the genetic analysis of planktonic foraminifera in order to enhance DNA amplification success rates. Yet, the description of these methods in the literature rarely occurred with equivalent levels of detail and the different approaches have never been compared in terms of their efficiency and reproducibility. Here, aiming at a standardization of methods, we provide a comprehensive review of all methods that have been employed for the single-cell genetic analysis of planktonic foraminifera. We compile data on success rates of DNA amplification and use these to evaluate the effects of key parameters associated with the methods of sample collection, storage and extraction of single-cell DNA. We show that the chosen methods influence the success rates of single-cell genetic studies, but the differences between them are not sufficient to hinder comparisons between studies carried out by different methods. The review thus not only provides a comprehensive reference with guidelines for future genetic studies on foraminifera, but it also establishes an important benchmark for investigations using existing single-cell datasets. The methods are widely applicable and the review may help to establish similar standard principles for their utilization in other protist groups.

Pacman profiling: a simple procedure to identify stratigraphic outliers in high-density deep-sea microfossil data

Abstract The deep-sea microfossil record is characterized by an extraordinarily high density and abundance of fossil specimens, and by a very high degree of spatial and temporal continuity of sedimentation. This record provides a unique opportunity to study evolution at the species level for entire clades of organisms. Compilations of deep-sea microfossil species occurrences are, however, affected by reworking of material, age model errors, and taxonomic uncertainties, all of which combine to displace a small fraction of the recorded occurrence data both forward and backwards in time, extending total stratigraphic ranges for taxa. These data outliers introduce substantial errors into both biostratigraphic and evolutionary analyses of species occurrences over time. We propose a simple method—Pacman—to identify and remove outliers from such data, and to identify problematic samples or sections from which the outlier data have derived. The method consists of, for a large group of species, compiling species occurrences by time and marking as outliers calibrated fractions of the youngest and oldest occurrence data for each species. A subset of biostratigraphic marker species whose ranges have been previously documented is used to calibrate the fraction of occurrences to mark as outliers. These outlier occurrences are compiled for samples, and profiles of outlier frequency are made from the sections used to compile the data; the profiles can then identify samples and sections with problematic data caused, for example, by taxonomic errors, incorrect age models, or reworking of sediment. These samples/sections can then be targeted for re-study.

Testing the applicability of a benthic foraminiferal-based transfer function for the reconstruction of paleowater depth changes in Rhodes (Greece) during the early Pleistocene

We present paleo-water depth reconstructions for the Pefka E section deposited on the island of Rhodes (Greece) during the early Pleistocene. For these reconstructions, a transfer function (TF) using modern benthic foraminifera surface samples from the Adriatic and Western Mediterranean Seas has been developed. The TF model gives an overall predictive accuracy of ~50 m over a water depth range of ~1200 m. Two separate TF models for shallower and deeper water depth ranges indicate a good predictive accuracy of 9 m for shallower water depths (0–200 m) but far less accuracy of 130 m for deeper water depths (200–1200 m) due to uneven sampling along the water depth gradient. To test the robustness of the TF, we randomly selected modern samples to develop random TFs, showing that the model is robust for water depths between 20 and 850 m while greater water depths are underestimated. We applied the TF to the Pefka E fossil data set. The goodness-of-fit statistics showed that most fossil samples have a poor to extremely poor fit to water depth. We interpret this as a consequence of a lack of modern analogues for the fossil samples and removed all samples with extremely poor fit. To test the robustness and significance of the reconstructions, we compared them to reconstructions from an alternative TF model based on the modern analogue technique and applied the randomization TF test. We found our estimates to be robust and significant at the 95% confidence level, but we also observed that our estimates are strongly overprinted by orbital, precession-driven changes in paleo-productivity and corrected our estimates by filtering out the precession-related component. We compared our corrected record to reconstructions based on a modified plankton/benthos (P/B) ratio, excluding infaunal species, and to stable oxygen isotope data from the same section, as well as to paleo-water depth estimates for the Lindos Bay Formation of other sediment sections of Rhodes. These comparisons indicate that our orbital-corrected reconstructions are reasonable and reflect major tectonic movements of Rhodes during the early Pleistocene.

Grasping the shape of belemnoid arm hooks : a quantitative approach

Abstract. Chitinous arm hooks (onychites) of belemnoid coleoid cephalopods are widely distributed in Mesozoic sediments. Due to their relative abundance and variable morphology compared with the single, bullet-shaped, belemnite rostrum, arm hooks came into the focus of micropaleontologists as a promising index fossil group for the Jurassic—Cretaceous rock record and have been the target of functional, ecological, and phylogenetic interpretations in the past. Based on three well-preserved arm crowns of the Toarcian diplobelid Chondroteuthis wunnenbergi, we analyzed the shape of a total of 87micro-hooks. The arm crown of Chondroteuthis is unique in having uniserial rather than biserial hooks. The first application of elliptic Fourier shape analysis to the arm weapons of belemnoid coleoids allows for the distinction of four micro-hook morphotypes and the quantification of shape variation within these morphotypes. Based on the best-preserved arm crown, we reconstructed the distribution of morphotypes within the arm crown and along a single arm. Our quantitative data support former observations that smaller hookswere found close to the mouth and at the most distal arm parts, while the largest hooks were found in the central part of the arm crown. Furthermore, we found a distinct arm differentiation, as not every arm was equipped with the same hook morphotype. Here, we report the functional specialization of the belemnoid arm crown for the first time and speculate about the potential function of the four morphotypes based on comparisons with modern cephalopods. Our analyses suggest a highly adapted functional morphology and intra-individual distribution of belemnoid hooks serving distinct purposes mainly during prey capture.

The Effect of Size Fraction in Analyses of Benthic Foraminiferal Assemblages: A Case Study Comparing Assemblages From the >125 and >150 μm Size Fractions

Benthic Foraminifera assemblages are employed for past environmental reconstructions, as well as for biomonitoring studies in recent environments. Despite their established status for such applications, and existing protocols for sample treatment, not all studies using benthic Foraminifera employ the same methodology. For instance, there is no broad practical consensus whether to use the >125 µm or >150 µm size fraction for benthic foraminiferal assemblage analyses. Here, we use early Pleistocene material from the Pefka E section on the Island of Rhodes (Greece), which has been counted in both size fractions, to investigate whether a 25 µm difference in the counted fraction is already sufficient to have an impact on ecological studies. We analysed the influence of the difference in size fraction on studies of biodiversity as well as multivariate assemblage analyses of the sample material. We found that for both types of studies, the general trends remain the same regardless of the chosen size fraction, but in detail significant differences emerge which are not consistently distributed between samples. Studies which require a high degree of precision can thus not compare results from analyses that used different size fractions, and the inconsistent distribution of differences makes it impossible to develop corrections for this issue. We therefore advocate the consistent use of the >125 µm size fraction for benthic foraminiferal studies in the future.

Evaluating morphospace discontinuity within the Globigerinoides ruber-elongatus plexus, and the potential for a consistent fossil classification scheme

Geochemical analysis of fossil foraminifera is a routine approach to paleoceaneanographic reconstruction. Certain stable isotopes and minor elements substituted into the CaCO3 lattice during calcification vary at predictable rates in response to changes in ambient seawater such as temperature, glacial ice volume, salinity, water column structure, or productivity. Such rates vary, as shell development is influenced by species-specific offsets in isotopic fractionation during growth. Above all, paleo-reconstruction necessarily assumes the foraminifera assessed represent uniform species, incorporating seawater chemistry consistently through time. Interpretation of parameters that caused chemical or morphological changes in fossil shells is then extrapolated from living analogues. As foraminiferal species differ evolutionarily, and in physiological response to local environmental influences, their shape and chemistry is unsurprisingly diverse. The greater the extent of morphological plasticity, the more vulnerable the species is to biased or erroneous interpretation. A prime example is the Globigerinoides ruber-elongatus plexus. G. ruber (d’Orbigny 1839) is a common planktonic foraminifer used in studies of the upper mixed layer of low-latitude oceans since the Miocene. Taxonomic revisions since 1839 resulted in the inclusion of numerous transitional morphologies now known to be unique biological species. At least two of these (G. ruber & G. elongatus) substitute isotopes dissimilarly. Whether these morphospecies ought to be separated when used as a paleo-proxy – and how – is cause for consideration. Various criteria exist to differentiate morphologies, but their efficacy has not been tested quantitatively and they yield inconsistent geochemical data in different ocean basins. Here, we present morphometric and stable isotope analyses of coretop and downcore G. ruber and G. elongatus from the Atlantic and Pacific, identified using only three criteria: 1) final chamber compression, and 2) asymmetry, and 3) aperture compression. Manual classification, superimposed on objective measurements of shell morphology, allows us to assess to what degree classification reflects morphospace discontinuity, how reliable it is, and what implications this may have for paleoceanographic research.

Community- and population-level response of marine plankton to stress exposure: learning from the past

The effects of stress exposure in marine plankton are difficult to assess directly, because it is hard to replicate realistic conditions in laboratory experiments and because the physiological changes and adaptations in response to stress exposure occur over times scales that cannot be covered by direct observations. A viable alternative is provided by studies of marine microfossils. Census counts of microfossil assemblages allow reconstructions of community-level changes, whilst biometric studies provide information on the reaction of populations to different levels of stress