Evidence of cryptic and pseudocryptic speciation in the Paracalanus parvus species complex (Crustacea, Copepoda, Calanoida), supplementary material

Introduction Many marine planktonic crustaceans such as copepods have been considered as widespread organisms. However, the growing evidence for cryptic and pseudo-cryptic speciation has emphasized the need of re-evaluating the status of copepod species complexes in molecular and morphological studies to get a clearer picture about pelagic marine species as evolutionary units and their distributions. This study analyses the molecular diversity of the ecologically important Paracalanus parvus species complex. Its seven currently recognized species are abundant and also often dominant in marine coastal regions worldwide from temperate to tropical oceans. Results COI and Cytochrome b sequences of 160 specimens of the Paracalanus parvus complex from all oceans were obtained. Furthermore, 42 COI sequences from GenBank were added for the genetic analyses. Thirteen distinct molecular operational taxonomic units (MOTU) and two single sequences were revealed with cladistic analyses (Maximum Likelihood, Bayesian Inference), of which seven were identical with results from species delimitation methods (barcode gaps, ABDG, GMYC, Rosenberg's P(AB)). In total, 10 to 12 putative species were detected and could be placed in three categories: (1) temperate geographically isolated, (2) warm-temperate to tropical wider spread and (3) circumglobal warm-water species. Conclusions The present study provides evidence of cryptic or pseudocryptic speciation in the Paracalanus parvus complex. One major insight is that the species Paracalanus parvus s.s. is not panmictic, but may be restricted in its distribution to the northeastern Atlantic.

Ground beetle (Carabidae) abundance data from north-eastern Australian rainforest, between June 2008 - January 2010, using pitfall traps

Understanding how the environment influences patterns of diversity is vital for effective conservation management, especially in a changing global climate. While assemblage structure and species richness patterns are often correlated with current environmental factors, historical influences may also be considerable, especially for taxa with poor dispersal abilities. Mountain-top regions throughout tropical rainforests can act as important refugia for taxa characterised by low dispersal capacities such as flightless ground beetles (Carabidae), an ecologically significant predatory group. We surveyed flightless ground beetles along elevational gradients in five different subregions within the Australian Wet Tropics World Heritage Area to investigate (1) whether the diversity and composition of flightless ground beetles are elevationally stratified, and, if so, (2) what environmental factors (other than elevation per se) are associated with these patterns. Generalised linear models and model averaging techniques were used to relate patterns of diversity to environmental factors. Unlike most taxonomic groups, flightless ground beetles increased in species richness and abundance with elevation. Additionally, each subregion consisted of distinct assemblages containing a high level of regional endemic species. Species richness was most strongly positively associated with the historical climatic conditions and negatively associated with severity of recent disturbance (treefalls) and current climatic conditions. Assemblage composition was associated with latitude and current and historical climatic conditions. Our results suggest that distributional patterns of flightless ground beetles are not only likely to be associated with factors that change with elevation (current climatic conditions), but also factors that are independent of elevation (recent disturbance and historical climatic conditions). Variation in historical vegetation stability explained both species richness and assemblage composition patterns, probably reflecting the significance of upland refugia at a geographic time scale. These findings are important for conservation management as upland habitats are under threat from climate change.

Planktonic foraminiferal oxygen isotopes of ODP Site 143-865 samples

Cool tropical sea surface temperatures (SSTs) are reported for warm Paleogene greenhouse climates based on the d18O of planktonic foraminiferal tests. These results are difficult to reconcile with models of greenhouse gas-forced climate. It has been suggested that this "cool tropics paradox" arises from postdepositional alteration of foraminiferal calcite, yielding erroneously high d18O values. Recrystallization of foraminiferal tests is cryptic and difficult to quantify, and the compilation of robust d18O records from moderately altered material remains challenging. Scanning electron microscopy of planktonic foraminiferal chamber-wall cross sections reveals that the basal area of muricae, pustular outgrowths on the chamber walls of species belonging to the genus Morozovella, contain no mural pores and may be less susceptible to postdepositional alteration. We analyzed the d18O in muricae bases of morozovellids from the central Pacific (Ocean Drilling Program Site 865) by ion microprobe using 10 ?m pits with an analytical reproducibility of ±0.34 per mil (2 standard deviations). In situ measurements of d18O in these domains yield consistently lower values than those published for conventional multispecimen analyses. Assuming that the original d18O is largely preserved in the basal areas of muricae, this new d18O record indicates Early Paleogene (~49-56 Ma) tropical SSTs in the central Pacific were 4°-8°C higher than inferred from the previously published d18O record and that SSTs reached at least ~33°C during the Paleocene-Eocene thermal maximum. This study demonstrates the utility of ion microprobe analysis for generating more reliable paleoclimate records from moderately altered foraminiferal tests preserved in deep-sea sediments.

(Table S2) Cell concentrations of individual and combined Alexandrium spp. and phylogenetic groups as obtained by qPCR assay and Utermöhl counts, as well as particulate PSP toxin concentrations from discrete water depths

Molecular methods provide promising tools for routine detection and quantification of toxic microalgae in plankton samples. To this end, novel TaqMan minor groove binding probes and primers targeting the small (SSU) or large (LSU) ribosomal subunit (rRNA) were developed for two species of the marine dinoflagellate genus Alexandrium (A. minutum, A. tamutum) and for three groups/ribotypes of the A. tamarense species complex: Group I/North American (NA), Group II/Mediterranean (ME) and Group III/Western European (WE). Primers and probes for real-time quantitative PCR (qPCR) were species-specific and highly efficient when tested in qPCR assays for cross-validation with pure DNA from cultured Alexandrium strains. Suitability of the qPCR assays as molecular tools for the detection and estimation of relative cell abundances of Alexandrium species and groups was evaluated from samples of natural plankton assemblages along the Scottish east coast. The results were compared with inverted microscope cell counts (Utermöhl technique) of Alexandrium spp. and associated paralytic shellfish poisoning (PSP) toxin concentrations. The qPCR assays indicated that A. tamarense (Group I) and A. tamutum were the most abundant Alexandrium taxa and both were highly positively correlated with PSP toxin content of plankton samples. Cells of A. tamarense (Group III) were present at nearly all stations but in low abundance. Alexandrium minutum and A. tamarense (Group II) cells were not detected in any of the samples, thereby arguing for their absence from the specific North Sea region, at least at the time of the survey. The sympatric occurrence of A. tamarense Group I and Group III gives further support to the hypothesis that the groups/ribotypes of the A. tamarense species complex are cryptic species rather than variants belonging to the same species.

The Fohsella chronocline in middle Miocene sediments from the Ontong Java Plateau, Pacific Ocean

Micropaleontologists have traditionally recognized the mid-Miocene Fohsella lineage as a flagship for phyletic gradualism within the planktic foraminifera. However, study of a deep-sea record from the western equatorial Pacific (ODP Site 806) reveals that coiling ratios within this clade suddenly (<5 kyr) shift after a prolonged, ancestral state of near randomness (~50%) to a transient phase (13.42-13.43 Ma) of dextral dominance (~75%) immediately following the first common occurrence of keeled fohsellids. This brief period of dextral dominance was abruptly (<5 kyr) succeeded by an irreversible change to sinistral dominance (~96%). Fohsellid abundances decline markedly through the interval in which the sinistral preference is established. The shift to sinistrality (13.42 Ma) predated the deepening of fohsellid depth ecology by ~240-488 kyr, indicating that these two events were unrelated. This view is supported by a lack of delta 18O evidence for depth-habitat differences between the two chiral forms, which refutes the notion that sinistral fohsellids were "pre-adapted" for ensuing hydrographic change because they occupied a deeper depth habitat than their dextral counterparts. Planktic foraminiferal assemblages become strongly oligotrophic in character through the interval in which the fohsellid delta 18O increase is recorded, indicating that the migration to deeper depths was fostered by an expansion of the mixed layer in the western equatorial Pacific. Salient aspects of this brief, but conspicuous faunal change are a marked increase in the abundance of symbiont-bearing globigerinoidids, a concomitant collapse of local Jenkinsella mayeri/siakensis populations, and reduced fohsellid abundances. The rapid and permanent nature of the Fohsella sinistral shift provides a distinct, unequivocal datum that may prove useful for correlating mid-Miocene sections throughout the Caribbean Sea and tropical regions in the western sectors of the Pacific and Atlantic. The coiling ratio changes that occurred during the evolution of the Fohsella chronocline probably reflect changing population dynamics between cryptic genotypes with different coiling preferences.

Mineral composition and major element oxides of gabbros from ODP Hole 179-1105A, southwest Indian Ridge

Hole 1105A penetrated 158 m of gabbros at a site offset 1.3 km east-northeast from Hole 735B on the Atlantis Bank near the Atlantis II Fracture Zone. A total of 118 m of dominantly medium- to coarse-grained intercalated Fe-Ti oxide gabbro and olivine gabbro was recovered from Hole 1105A that shows many petrographic features similar to those recovered from the upper part of Hole 735B. The main rock types are distinguished based on the constituent cumulus phases, with the most primitive gabbros consisting of olivine, plagioclase, and clinopyroxene. The inferred crystallization order is subsequently Fe-Ti oxides (ilmenite and titanomagnetite), followed by orthopyroxene, then apatite, and finally biotite. Orthopyroxene appears to replace olivine in a narrow middle interval. The magmatic evolution is likewise reflected in the mineral compositions. Plagioclase varies from An66 to An28. Olivine varies from Fo78 to Fo35. The gap in olivine crystallization occurs between Fo46 and Fo40 and coincides approximately with the appearance of orthopyroxene (~En50). The clinopyroxenes show large compositional variation in Mg/(Mg + Fe total) from 0.84 to 0.51. The nonquadrilateral cations of clinopyroxene similarly show large variations with Ti increasing for the olivine gabbros and decreasing for the Fe-Ti oxide gabbros with the decrease in Mg/(Mg + Fe total). The apatites are mainly flourapatites. The compositional variation in the gabbros is interpreted as a comagmatic suite resulting from fractional crystallization. Pyroxene geothermometry suggests equilibration temperatures from 1100°C and below. The coexisting Fe-Ti oxide minerals indicate subsolidus equilibration temperatures from 900°C for olivine gabbros to 700°C for the most evolved apatite-bearing gabbros. The cryptic variation in the olivine gabbros defines two or three lenses, 40 to 60 m thick, each characterized by a distinct convex zoning with a lower segment indicating upward reverse fractionation, a central maximum, and an upper segment showing normal fractionation. The Fe-Ti oxide gabbros show cryptic variations independent of the host olivine gabbros and reveal a systematic upward normal fractionation trend transgressing host olivine gabbro boundaries. Forward fractional crystallization modeling, using a likely parental magma composition from the Atlantis II Fracture Zone (MgO = 7.2 wt%; Mg/[Mg + Fe2+] = 0.62), closely matches the compositions of coexisting olivine, plagioclase, and clinopyroxene. This modeling suggests cosaturation of olivine, plagioclase, and clinopyroxene from 1155°C and the addition of Fe-Ti oxides from 1100°C. The liquid line of descent initially shows increasing FeO with moderately increasing SiO2. After saturation of Fe-Ti oxides, the liquid strongly decreases in FeO and TiO2 and increases in SiO2, reaching dacitic compositions at ~10% liquid remaining. The calculations indicate that formation of olivine gabbros can be accounted for by <65% fractionation and that only the residual 35% liquid was saturated in Fe-Ti oxides. The modeling of the solid fractionation products shows that both the olivine gabbro and the Fe-Ti oxide gabbros contain very small amounts of trapped liquid (<5%). The implications are that the gabbros represent crystal mush that originated in a recharging and tapping subaxial chamber. Compaction and upward melt migration in the crystal mush appear to have been terminated with relatively large amounts of interstitial liquid remaining in the upper parts of the cumulate mush. This termination may have been caused by tectonic disturbances, uplift, and associated withdrawal of magma into the subaxial dike and sill system. Prolonged compaction and cooling of the trapped melt in the mush formed small differentiated bodies and lenses by pressure release migration and crystallization along syntectonic channels. This resulted in differentiation products along lateral and vertical channelways in the host gabbro that vary from olivine gabbro, to Fe-Ti oxide gabbro, gabbronorite, and apatite gabbros and show large compositional variations independent of the host olivine gabbros.

Geochemical composition of gabbroic rocks from ODP Hole 179-1105A, southwest Indian Ridge

Oxide-free olivine gabbro and gabbro, and oxide olivine gabbro and gabbro make up the bulk of the gabbroic suite recovered from Ocean Drilling Program (ODP) Leg 179 Hole 1105A, which lies 1.2 km away from Hole 735B on the eastern transverse ridge of the Atlantis II Fracture Zone, Southwest Indian Ridge. The rocks recovered during Leg 179 show striking similarities to rocks recovered from the uppermost 500 m of Hole 735B during ODP Leg 118. The rocks of the Atlantis platform were likely unroofed as part of the footwall block of a large detachment fault on the inside corner of the intersection of the Southwest Indian Ridge and the Atlantis II Transform at ~11.5 Ma. We analyzed the lithologic, geochemical, and structural stratigraphy of the section. Downhole lithologic variation allowed division of the core into 141 lithologic intervals and 4 main units subdivided on the basis of predominance of oxide gabbroic vs. oxide-free gabbroic rocks. Detailed analyses of whole-rock chemistry, mineral chemistry, microstructure, and modes of 147 samples are presented and clearly show that the gabbroic rocks are of cumulate origin. These studies also indicate that geochemistry results correlate well with downhole magnetic susceptibility and Formation MicroScanner (FMS) resistivity measurements and images. FMS images show rocks with a well-layered structure and significant numbers of mappable layer contacts or compositional contrasts. Downhole cryptic mineral and whole-rock chemical variations depict both "normal" and inverse fine-scale variations on a scale of 10 m to <2 m with significant compositional variation over a short distance within the 143-m section sampled. A Mg# shift in whole-rock or Fo contents of olivine of as much as 20-30 units over a few meters of section is not atypical of the extreme variation in downhole plots. The products of the earliest stages of basaltic differentiation are not represented by any cumulates, as the maximum Fo content was Fo78. Similarly, the extent of fractionation represented by the gabbroic rocks and scarce granophyres in the section is much greater than that represented in the Atlantis II basalts. The abundance of oxide gabbros is similar to that in Hole 735B, Unit IV, which is tentatively correlated as a similar unit or facies with the oxide gabbroic units of Hole 1105A. Oxide phases are generally present in the most fractionated gabbroic rocks and lacking in more primitive gabbroic rocks, and there is a definite progression of oxide abundance as, for example, the Mg# of clinopyroxene falls below 73-75. Coprecipitation of oxide at such early Mg#s cannot be modeled by perfect fractional crystallization. In situ boundary layer fractionation may offer a more plausible explanation for the complex juxtaposition of oxide- and nonoxide-bearing more primitive gabbroic rocks. The geochemical signal may, in part, be disrupted by the presence of mylonitic shear zones, which strike east-west and dip both to the south and north, but predominantly to the south away from the northern rift valley where they formed. Downhole deformation textures indicate increasing average strain and crystal-plastic deformation in units that contain oxides. Oxide-rich zones may represent zones of rheologic weakness in the cumulate section along which mylonitic and foliated gabbroic shear zones nucleate in the solid state at high temperature, or the oxide may be a symptom of former melt-rich zones and hypersolidus flow, as predicted during study of Hole 735B.

Impact of thermal stress on evolutionary trajectories of pathogen resistance in three-spined stickleback (Gasterosteus aculeatus), supplementary material

Background: Pathogens are a major regulatory force for host populations, especially under stressful conditions. Elevated temperatures may enhance the development of pathogens, increase the number of transmission stages, and can negatively influence host susceptibility depending on host thermal tolerance. As a net result, this can lead to a higher prevalence of epidemics during summer months. These conditions also apply to marine ecosystems, where possible ecological impacts and the population-specific potential for evolutionary responses to changing environments and increasing disease prevalence are, however, less known. Therefore, we investigated the influence of thermal stress on the evolutionary trajectories of disease resistance in three marine populations of three-spined sticklebacks Gasterosteus aculeatus by combining the effects of elevated temperature and infection with a bacterial strain of Vibrio sp. using a common garden experiment. Results: We found that thermal stress had an impact on fish weight and especially on survival after infection after only short periods of thermal acclimation. Environmental stress reduced genetic differentiation (QST) between populations by releasing cryptic within-population variation. While life history traits displayed positive genetic correlations across environments with relatively weak genotype by environment interactions (GxE), environmental stress led to negative genetic correlations across environments in pathogen resistance. This reversal of genetic effects governing resistance is probably attributable to changing environment-dependent virulence mechanisms of the pathogen interacting differently with host genotypes, i.e. GPathogenxGHostxE or (GPathogenxE)x(GHostxE) interactions, rather than to pure host genetic effects, i.e. GHostxE interactions. Conclusion: To cope with climatic changes and the associated increase in pathogen virulence, host species require wide thermal tolerances and pathogen-resistant genotypes. The higher resistance we found for some families at elevated temperatures showed that there is evolutionary potential for resistance to Vibrio sp. in both thermal environments. The negative genetic correlation of pathogen resistance between thermal environments, on the other hand, indicates that adaptation to current conditions can be a weak predictor for performance in changing environments. The observed feedback on selective gradients exerted on life history traits may exacerbate this effect, as it can also modify the response to selection for other vital components of fitness.

Epiphytic orchid diversity found on trees and shrubs in coffee cultivated Afromontane rainforest, SW Ethiopia

The moist evergreen Afromontane forest of SW Ethiopia has become extremely fragmented and most remnants are intensively managed for cultivation of coffee (Coffea arabica). We investigated the distributions of epiphytic orchids in shade trees and their understory in forests with contrasting management intensity to determine biodiversity losses associated with coffee cultivation and to determine the capacity of coffee shrubs to act as refugia for orchid species. We studied epiphytic orchids in managed forests and natural forests and recorded orchid diversity and abundance in different tree zones of 339 trees and in the understory. Coffee management was associated with a downward shift of orchid species as orchid species were occurring in significantly lower tree zones in managed forest. The number of shrubs in the understory of managed forest was not higher than in natural forests, yet orchid abundance was higher in the understory of managed forests. Local extinctions of epiphytic orchids and species losses in the outer tree zones (a contraction of habitat) in managed forests are most likely driven by losses of large, complex-structured climax trees, and changes in microclimate, respectively. Coffee shrubs and their shade trees in managed forests are shown here to be a suitable habitat for only a limited set of orchid species. As farmers continue to convert natural forest into managed forest for coffee cultivation, further losses of habitat quality and collateral declines in regional epiphytic orchid diversity can be expected. Therefore, the conservation of epiphytic orchid diversity, as well as other components of diversity of the coffee forests, must primarily rely on avoiding coffee management intensification in the remaining natural forest. Convincing farmers to keep forest-climax trees in their coffee forest and to tolerate orchids on their coffee shrubs may also contribute to a more favorable conservation status of orchids in Ethiopian coffee agroecosystems.

Processed data from CTD casts and fluorospectrometer measurements from the SONNE SO226/3 cruise track

The Sonne transit cruise SO226-3 DipFIP took place from March 4th (Wellington, New Zealand) to March 28th (Kaohsiung, Taiwan) in 2013. CTD data for 16 stations along the cruise track were recorded using the onboard a SEABIRD SBE 9 plus CTD down to depth of 800m. Obtained hydrographic data were binned to 1 m intervals with the available SBE software. Obvious outliers in the readings of the oxygen sensor close to the sea surface have been manually removed. Fluorospectrometer (bbe Moldaenke) pigment data measured for 24 depth intervals are available for 10 stations. Measurements were conducted in the shipboard laboratory on water samples from the CTD rosette. Data are averages of a least 30 readings per sample.

Experiment: Physiological responses of the calcifying rhodophyte, Corallina officinalis (L.), to future CO2 levels

Future atmospheric CO2 levels will most likely have complex consequences for marine organisms, particulary photosynthetic calcifying organisms. Corallina officinalis L. is an erect calcifying macroalga found in the inter- and subtidal regions of temperate rocky coastlines and provides important substrate and refugia for marine meiofauna. The main goal of the current study was to determine the physiological responses of C. officinalis to increased CO2 concentrations expected to occur within the next century and beyond. Our results show that growth and production of inorganic material decreased under high CO2 levels, while carbonic anhydrase activity was stimulated and negatively correlated to algal inorganic content. Photosynthetic efficiency based on oxygen evolution was also negatively affected by increased CO2. The results of this study indicate that C. officinalis may become less competitive under future CO2 levels, which could result in structural changes in future temperate intertidal communities.

Effect of ocean acidification and pH fluctuations on the growth and development of coralline algal recruits, and an associated benthic algal assemblage

Coralline algae are susceptible to the changes in the seawater carbonate system associated with ocean acidification (OA). However, the coastal environments in which corallines grow are subject to large daily pH fluctuations which may affect their responses to OA. Here, we followed the growth and development of the juvenile coralline alga Arthrocardia corymbosa, which had recruited into experimental conditions during a prior experiment, using a novel OA laboratory culture system to simulate the pH fluctuations observed within a kelp forest. Microscopic life history stages are considered more susceptible to environmental stress than adult stages; we compared the responses of newly recruited A. corymbosa to static and fluctuating seawater pH with those of their field-collected parents. Recruits were cultivated for 16 weeks under static pH 8.05 and 7.65, representing ambient and 4*preindustrial pCO2 concentrations, respectively, and two fluctuating pH treatments of daily (daytime pH = 8.45, night-time pH = 7.65) and daily (daytime pH = 8.05, night-time pH = 7.25). Positive growth rates of new recruits were recorded in all treatments, and were highest under static pH 8.05 and lowest under fluctuating pH 7.65. This pattern was similar to the adults' response, except that adults had zero growth under fluctuating pH 7.65. The % dry weight of MgCO3 in calcite of the juveniles was reduced from 10% at pH 8.05 to 8% at pH 7.65, but there was no effect of pH fluctuation. A wide range of fleshy macroalgae and at least 6 species of benthic diatoms recruited across all experimental treatments, from cryptic spores associated with the adult A. corymbosa. There was no effect of experimental treatment on the growth of the benthic diatoms. On the community level, pH-sensitive species may survive lower pH in the presence of diatoms and fleshy macroalgae, whose high metabolic activity may raise the pH of the local microhabitat.