Phylogenetic Relationships and Evolutionary Patterns of the Order Collodaria (Radiolaria)

Collodaria are the only group of Radiolaria that has a colonial lifestyle. This group is potentially the most important plankton in the oligotrophic ocean because of its large biomass and the high primary productivity associated with the numerous symbionts inside a cell or colony. The evolution of Collodaria could thus be related to the changes in paleo-productivity that have affected organic carbon fixation in the oligotrophic ocean. However, the fossil record of Collodaria is insufficient to trace their abundance through geological time, because most collodarians do not have silicified shells. Recently, molecular phylogeny based on nuclear small sub-unit ribosomal DNA (SSU rDNA) confirmed Collodaria to be one of five orders of Radiolaria, though the relationship among collodarians is still unresolved because of inadequate taxonomic sampling. Our phylogenetic analysis has revealed four novel collodarian sequences, on the basis of which collodarians can be divided into four clades that correspond to taxonomic grouping at the family level: Thalassicollidae, Collozoidae, Collosphaeridae, and Collophidae. Comparison of the results of our phylogenetic analyses with the morphological characteristics of each collodarian family suggests that the first ancestral collodarians had a solitary lifestyle and left no silica deposits. The timing of events estimated from molecular divergence calculations indicates that naked collodarian lineages first appeared around 45.6 million years (Ma) ago, coincident with the diversification of diatoms in the pelagic oceans. Colonial collodarians appeared after the formation of the present ocean circulation system and the development of oligotrophic conditions in the equatorial Pacific (ca. 33.4 Ma ago). The divergence of colonial collodarians probably caused a shift in the efficiency of primary production during this period

Evolution of a Planktonic Foraminifer during Environmental Changes in the Tropical Oceans.

Ecological adaptation to environmental changes is a strong driver of evolution, enabling speciation of pelagic plankton in the open ocean without the presence of effective physical barriers to gene flow. The tropical ocean environment, which plays an important role in shaping marine biodiversity, has drastically and frequently changed since the Pliocene. Nevertheless, the evolutionary history of tropical pelagic plankton has been poorly understood, as phylogeographic investigations are still in the developing state and paleontological approaches are insufficient to obtain a sequential record from the deep-sea sediments. The planktonic foraminifer Pulleniatina obliquiloculata is widely distributed in the tropical area throughout the world's oceans, and its phylogeography is well established. It is thus one of the best candidates to examine how past environmental changes may have shifted the spatial distribution and affected the diversification of tropical pelagic plankton. Such an examination requires the divergence history of the planktonic foraminifers, yet the gene marker (partial small subunit (SSU) rDNA) previously used for phylogeographic studies was not powerful enough to achieve a high accuracy in estimating the divergence times. The present study focuses on improving the precision of divergence time estimates for the splits between sibling species (genetic types) of planktonic foraminifers by increasing the number of genes as well as the number of nucleotide bases used for molecular clock estimates. We have amplified the entire coding regions of two ribosomal RNA genes (SSU rDNA and large subunit (LSU) rDNA) of three genetic types of P. obliquiloculata and two closely related species for the first time and applied them to the Bayesian relaxed clock method. The comparison of the credible intervals of the four datasets consisting either of sequences of the partial SSU rDNA, the complete SSU rDNA, LSU rDNA, or a combination of both genes (SSU+LSU) clearly demonstrated that the two-gene dataset improved the accuracy of divergence time estimates. The P. obliquiloculata lineage diverged twice, first at the end of the Pliocene (3.1 Ma) and again in the middle Pleistocene (1.4 Ma). Both timings coincided with the environmental changes, which indirectly involved geographic separation of populations. The habitat of P. obliquiloculata was expanded toward the higher latitudinal zones during the stable warm periods and subsequently placed on the steep environmental gradients following the global cooling. Different environmental conditions in the stable warm tropics and unstable higher latitudes may have triggered ecological divergence among the populations, leading to adaptive differentiation and eventually speciation. A comprehensive analysis of divergence time estimates combined with phylogeography enabled us to reveal the evolutionary history of the pelagic plankton and to find the potential paleoenvironmental events, which could have changed their biogeography and ecology

Advanced approach to analyzing calcareous protists for present and past pelagic ecology: Comprehensive analysis of 3D-morphology, stable isotopes, and genes of planktic foraminifers.

Marine protists play an important role in oceanic ecosystems and biogeochemical cycles. However, the difficulties in culturing pelagic protists indicate that their ecology and behavior remain poorly understood; phylogeographic studies based on single-cell genetic analyses have often shown that they are highly divergent at the biological species level, with variable geographic distributions. This indicates that their ecology could be complex. On the other hand, the biomineral (calcareous) shells of planktic foraminifers are widely used in geochemical analyses to estimate marine paleoenvironmental characteristics (i.e., temperature), because the shell chemical composition reflects ambient seawater conditions. Among the pelagic protists, planktic foraminifers are ideal study candidates to develop a combined approach of genetic, morphological, and geochemical methods, thus reflecting environmental and ecological characteristics. The present study precisely tested whether the DNA extraction process physically and chemically affects the shells of the planktic foraminifer Globigerinoides ruber. We used a nondestructive method for analyzing physical changes (micro-focus X-ray computed tomography (MXCT) scanning) to compare specimens at the pre- and post-DNA extraction stages. Our results demonstrate that DNA extraction has no significant effect on shell density and thickness. We measured stable carbon and oxygen isotopes on the shell of each individual in a negative control or one of two DNA-extracted groups and detected no significant differences in isotopic values among the three groups. Moreover, we evaluated isotopic variations at the biological species level with regard to their ecological characteristics such as depth habitat, life stages, and symbionts. Thus, our examination of the physiochemical effects on biomineral shells through DNA extraction shows that morphological and isotopic analyses of foraminifers can be combined with genetic analysis. These analytical methods are applicable to other shell-forming protists and microorganisms. In this study, we developed a powerful analytical tool for use in ecological and environmental studies of modern and past oceans

Uncovering sibling species in Radiolaria: Evidence for ecological partitioning in a marine planktonic protist

Phylogeography of unicellular plankton, as representative pelagic organisms, is fundamental to understanding their evolution in the ocean. Historically, these microplankton were believed to have cosmopolitan distributions achieved through passive transport and little potential for speciation because of a lack of geographic barriers in the oceans. Recent phylogeographic studies of these microplankton, however, have often revealed high diversity and fine-scale geographic distributions. These apparent contradictions may result from poor knowledge of the spatial distributions of pelagic microplankton in the water column. More information about both geographic and vertical distributions of pelagic populations could reveal the dispersal pathways, gene flow, and resulting diversifications in the open ocean. Here we demonstrate that two genetic types of the radiolarian morphospecies Spongotrochus glacialis with morphological differences are vertically segregated into the upper and lower surface waters within the pycnocline of the North Pacific Subtropical Water. This vertically separated distribution of two sister species is associated with distinct ecological partitioning. These two species could survive on different food resources from their respective environments: one in oligotrophic surface waters by using nutrients from symbionts, and the other at greater depths by depending on both heterotrophic and symbiotic nutrition. Moreover, molecular divergence-time estimates suggest that the two species diverged during the period of oligotrophic surface-water development in the Pacific Ocean. Our findings suggest that genetic isolation in the vertical dimension occurs through ecological partitioning even in the absence of physical barriers in the pelagic oceans

Bayesian phylogeny of the SSU + LSU rDNA sequences obtained from <i>P</i>. <i>obliquiloculata</i> and two outgroup species.

<p>Bayesian posterior probability (PP) and bootstrap values (BV) are shown at each node. The nodes used for divergence time estimations are named in enclosed boxes. Grey and white circles indicate high posterior PPs and BVs (PP/BV = 1.00/100 and PP/BP = 1.00/99, respectively).</p

Upper (maximum) and Lower (minimum) constraints of the basal nodes used for estimating divergence dates.

<p>Upper (maximum) and Lower (minimum) constraints of the basal nodes used for estimating divergence dates.</p

Geographic distribution of the three genetic types of <i>P</i>. <i>obliquiloculata</i>.

<p>Pie chart shows the frequencies of three genetic types at each sampling site based on the previous studies [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0148847#pone.0148847.ref005" target="_blank">5</a>,<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0148847#pone.0148847.ref028" target="_blank">28</a>]. The small and large circles indicate the locations where only one or more specimens were collected. The asterisks show the locations, where the samples were obtained for the present study. The genetic types of <i>P</i>. <i>obliquiloculata</i> specimens from Seears et al. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0148847#pone.0148847.ref028" target="_blank">28</a>] were identified based on the alignment of the partial SSU rDNA sequences with all existing data of Ujiié et al. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0148847#pone.0148847.ref005" target="_blank">5</a>]. Grey areas on the map show the ranges of water temperatures between 20–25, 25–28, and >28°C. The temperature data were obtained from the World Ocean Atlas 2005 [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0148847#pone.0148847.ref029" target="_blank">29</a>]. The map is drawn by using the Ocean Data View [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0148847#pone.0148847.ref030" target="_blank">30</a>].</p

List of divergence times estimated by using the four datasets: partial SSU, LSU, SSU, and SSU + LSU, with four different fossil calibration sets.

<p>List of divergence times estimated by using the four datasets: partial SSU, LSU, SSU, and SSU + LSU, with four different fossil calibration sets.</p

Location of the primers used to amplify and sequence the SSU rDNA and LSU rDNA.

<p>The names and orientations of the primers correspond to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0148847#pone.0148847.t001" target="_blank">Table 1</a>. The primers used for PCR amplification are shown by key arrows.</p

Evolution of the North Pacific Subtropical Gyre during the past 190 kyr through the interaction of the Kuroshio Current with the surface and intermediate waters

International audienceThe North Pacific Subtropical Gyre (NPSG) has two important functions, i.e., one in ocean heat transfer and another as a driving force for circulation of the surface and intermediate waters on the basin scale. In the present study, we describe records of the vertical thermal structures and distributions of water masses in the upper ocean of the subtropical northwest (NW) Pacific for the past 190 kyr, using two sediment cores collected from the Kuroshio Current area in the East China Sea and the NPSG area. During the two glacial periods, the Kuroshio Current was weakened owing to changes in ocean-atmosphere circulation and eustasy. The differences in the Mg/Ca-derived temperatures between surface and thermocline waters show the changes of depth and temperature (warming) of thermocline during glacial periods. Conversely, the planktonic foraminiferal assemblages demonstrate that the indicator of the intermediate water from the central area of the NPSG increased synchronously with thermocline warming during marine isotope stage (MIS) 6. These results suggest that warm intermediate water strongly affected the changes in the water-column structure of the subtropical NW Pacific during MIS 6. However, during MIS 2, cold water had precedence over intermediate water probably owing to the southward shift of the subtropical front associated with the reduced transport of the Kuroshio Current. Thus, the NPSG has evolved differently during the two glacial periods (MIS 2 and MIS 6) through interactions between the Kuroshio Current, surface water, and intermediate water