Coastal plankton communities under elevated CO2: community barcoding results, link to data files in FASTA format

The acidification of the oceans could potentially alter marine plankton communities with consequences for ecosystem functioning. While several studies have investigated effects of ocean acidifications on communities using traditional methods, few have used genetic analyses. Here, we use community barcoding to assess the impact of ocean acidification on the composition of a coastal plankton community in a large scale, in situ, long-term mesocosm experiment. High-throughput sequencing resulted in the identification of a wide range of planktonic taxa (Alveolata, Cryptophyta, Haptophyceae, Fungi, Metazoa, Hydrozoa, Rhizaria, Straminipila, Chlorophyta). Analyses based on predicted operational taxonomical units as well as taxonomical compositions revealed no differences between communities in high CO2 mesocosms (~760 µatm) and those exposed to present day CO2 conditions. Observed shifts in the planktonic community composition were mainly related to seasonal changes in temperature and nutrients.

(Table S1) Molecular analyses and morphological comparisons of deep-sea clams

Large vesicomyid clams are common inhabitants of sulphidic deep-sea habitats such as hydrothermal vents, hydrocarbon seeps and whale-falls. Yet, the species- and genus-level taxonomy of these diverse clams has been unstable due to insufficiencies in sampling and absence of detailed taxonomic studies that would consistently compare molecular and morphological characters. To clarify uncertainties about species-level assignments, we examined DNA sequences from mitochondrial cytochrome-c-oxidase subunit I (COI) in conjunction with morphological characters. New and published COI sequences were used to create a molecular database for 44 unique evolutionary lineages corresponding to species. Overall, the congruence between molecular and morphological characters was good. Several discrepancies due to synonymous species designations were recognized, and acceptable species names were rectified with published COI sequences in cases where morphological specimens were available. We identified seven species with trans-Pacific distributions, and two species with Indo-Pacific distributions. Presently, 27 species have only been documented from one region, which might reflect limited ranges, or insufficient geographical sampling. Vesicomyids exhibit the greatest species diversity along the northwest Pacific ridge systems and in the eastern Pacific, along the western America margin, where depth zonation typically results in segregation of closely related species. The broad distributions of several vesicomyid species suggest that their required chemosynthetic habitats might be more common than previously recognized and occur along most continental margins.

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.

Sedimentology, biogeochemistry stable isotopes, pollen, plant macrofossils, and diatoms from two sediments cores from the northern Yukon permafrost peatlands (Canada)

Ice-wedge polygon (IWP) mires in the Arctic and Subarctic are extremely vulnerable to climatic and environmental change. We present the results of a multidisciplinary paleoenvironmental study on IWPs in the northern Yukon, Canada. High-resolution laboratory analyses were carried out on a permafrost core and the overlying seasonally thawed (active) layer, from a low-centered IWP located in a drained lake basin on Herschel Island. In relation to 14 Accelerator Mass Spectrometry (AMS) radiocarbon dates spanning the last 5000 years, we report sedimentary data including grain size distribution and biogeochemical parameters (organic carbon, nitrogen, C/N ratio, d13C), stable water isotopes (d18O, dD), as well as fossil pollen, plant macrofossil and diatom assemblages. Three sediment units (SUs) correspond to the main stages of deposition (1) in a thermokarst lake (SU1: 4950 to 3950 cal yrs BP), (2) during transition from lacustrine to palustrine conditions after lake drainage (SU2: 3950 to 3120 cal yrs BP), and (3) in palustrine conditions in the IWP field that developed after drainage (SU3: 3120 cal yrs BP to AD 2012). The lacustrine phase (pre 3950 cal yrs BP) is characterized by planktonic-benthic and pioneer diatoms species indicating circumneutral waters, and very few plant macrofossils. The pollen record has captured a regional signal of relatively stable vegetation composition and climate for the lacustrine stage of the record until 3950 cal yrs BP. Palustrine conditions with benthic and acidophilic species characterize the peaty shallow-water environments of the low-centered IWP. The transition from lacustrine to palustrine conditions was accompanied by acidification and rapid revegetation of the lake bottom within about 100 years. Since the palustrine phase we consider the pollen record as a local vegetation proxy dominated by the plant communities growing in the IWP. Ice-wedge cracking in water-saturated sediments started immediately after lake drainage at about 3950 cal yrs BP and led to the formation of an IWP mire. Permafrost aggradation through downward closed-system freezing of the lake talik is indicated by the stable water isotope record. The originally submerged IWP center underwent gradual drying during the past 2000 years. This study highlights the sensitivity of permafrost landscapes to climate and environmental change throughout the Holocene.

Availability of sequences of aquatic and terrestrial taxa in genetic databases (GenBank and BOLD - the Barcode of Life Database) in 2010, 2012 and 2016

Correct species identifications are of tremendous importance for invasion ecology, as mistakes could lead to misdirecting limited resources against harmless species or inaction against problematic ones. DNA barcoding is becoming a promising and reliable tool for species identifications, however the efficacy of such molecular taxonomy depends on gene region(s) that provide a unique sequence to differentiate among species and on availability of reference sequences in existing genetic databases. Here, we assembled a list of aquatic and terrestrial non-indigenous species (NIS) and checked two leading genetic databases for corresponding sequences of six genome regions used for DNA barcoding. The genetic databases were checked in 2010, 2012, and 2016. All four aquatic kingdoms (Animalia, Chromista, Plantae and Protozoa) were initially equally represented in the genetic databases, with 64, 65, 69, and 61% of NIS included, respectively. Sequences for terrestrial NIS were present at rates of 58 and 78% for Animalia and Plantae, respectively. Six years later, the number of sequences for aquatic NIS increased to 75, 75, 74, and 63% respectively, while those for terrestrial NIS increased to 74 and 88% respectively. Genetic databases are marginally better populated with sequences of terrestrial NIS of plants compared to aquatic NIS and terrestrial NIS of animals. The rate at which sequences are added to databases is not equal among taxa. Though some groups of NIS are not detectable at all based on available data - mostly aquatic ones - encouragingly, current availability of sequences of taxa with environmental and/or economic impact is relatively good and continues to increase with time.

Pollen record and age determinations of a profile at Cape Mamontov Klyk, Siberia

Non-glaciated Arctic lowlands in north-east Siberia were subjected to extensive landscape and environmental changes during the Late Quaternary. Coastal cliffs along the Arctic shelf seas expose terrestrial archives containing numerous palaeoenvironmental indicators (e.g., pollen, plant macro-fossils and mammal fossils) preserved in the permafrost. The presented sedimentological (grain size, magnetic susceptibility and biogeochemical parameters), cryolithological, geochronological (radiocarbon, accelerator mass spectrometry and infrared-stimulated luminescence), heavy mineral and palaeoecological records from Cape Mamontov Klyk record the environmental dynamics of an Arctic shelf lowland east of the Taymyr Peninsula, and thus, near the eastern edge of the Eurasian ice sheet, over the last 60 Ky. This region is also considered to be the westernmost part of Beringia, the non-glaciated landmass that lay between the Eurasian and the Laurentian ice caps during the Late Pleistocene. Several units and subunits of sand deposits, peat-sand alternations, ice-rich palaeocryosol sequences (Ice Complex) and peaty fillings of thermokarst depressions and valleys were presented. The recorded proxy data sets reflect cold stadial climate conditions between 60 and 50 Kya, moderate inderstadial conditions between 50 and 25 Kya and cold stadial conditions from 25 to 15 Kya. The Late Pleistocene to Holocene transition, including the Allerød warm period, the early to middle Holocene thermal optimum and the late Holocene cooling, are also recorded. Three phases of landscape dynamic (fluvial/alluvial, irregular slope run-off and thermokarst) were presented in a schematic model, and were subsequently correlated with the supraregional environmental history between the Early Weichselian and the Holocene.

Palynological and stratigraphic record from Löddigsee in Mecklenburg-Vorpommern, Germany

A Late Pleistocene and Holocene sediment core from the nowadays terrestrialised portion of the Löddigsee in Southern Mecklenburg, Germany was palynologically investigated. The lake is situated in the rarely investigated Young moraine area at the transition from the Weichselian to the Saalian glaciation. The high-resolution pollen diagram contributes to the establishment of the north-eastern German Late Pleistocene pollen stratigraphy. The vegetation distribution pattern after the end of the Weichselian is in good agreement with other studies from North-eastern Germany, but also has its own characteristics. The Holocene vegetation development reveals features from the north-eastern and north-western German lowlands. A special focus was laid on the environmental history of the two settlements on an island within the lake (Late Neolithic and Younger Slavic period), which were preserved under moist conditions. Both settlements were constructed during a period of low lake level. Although there is evidence of agriculture in the area during the respective periods, the two island settlements seem to have served other purposes.

Sampling information, length measurements, DNA alignments, models and phylogenetics trees for Oithona similis s.l.

Traditionally, many small-sized copepod species are considered to be widespread, bipolar or cosmopolitan. However, these large-scale distribution patterns need to be re-examined in view of increasing evidence of cryptic and pseudo-cryptic speciation in pelagic copepods. Here, we present a phylogeographic study of Oithona similis s.l. populations from the Arctic Ocean, the Southern Ocean and its northern boundaries, the North Atlantic and the Mediterrranean Sea. O. similis s.l. is considered as one of the most abundant species in temperate to polar oceans and acts as an important link in the trophic network between the microbial loop and higher trophic levels such as fish larvae. Two gene fragments were analysed: the mitochondrial cytochrome oxidase c subunit I (COI), and the nuclear ribosomal 28S genetic marker. Seven distinct, geographically delimitated, mitochondrial lineages could be identified, with divergences among the lineages ranging from 8 to 24 %, thus representing most likely cryptic or pseudocryptic species within O. similis s.l. Four lineages were identified within or close to the borders of the Southern Ocean, one lineage in the Arctic Ocean and two lineages in the temperate Northern hemisphere. Surprisingly the Arctic lineage was more closely related to lineages from the Southern hemisphere than to the other lineages from the Northern hemisphere, suggesting that geographic proximity is a rather poor predictor of how closely related the clades are on a genetic level. Molecular clock application revealed that the evolutionary history of O. similis s.l. is possibly closely associated with the reorganization of the ocean circulation in the mid Miocene and may be an example of allopatric speciation in the pelagic zone.