Contemporary genetic, historical genetic and morphological data sets for the Yellow-tufted Honeyeater Lichenostomus melanops

Understanding the evolutionary history of threatened populations can improve their conservation management. Re-establishment of past but recent gene flow could re-invigorate threatened populations and replenish genetic diversity, necessary for population persistence. One of the four nominal subspecies of the common yellow-tufted honeyeater, Lichenostomus melanops cassidix, is critically endangered despite substantial conservation efforts over 55 years. Using a combination of morphometric, genetic and modelling approaches we tested for its evolutionary distinctiveness and conservation merit. We confirmed that cassidix has at least one morphometric distinction. It also differs genetically from the other subspecies in allele frequencies but not phylogenetically, implying that its evolution was recent. Modelling historical distribution supported the lack of vicariance and suggested a possibility of gene flow among subspecies at least since the late Pleistocene. Multi-locus coalescent analyses indicated that cassidix diverged from its common ancestor with neighbouring subspecies gippslandicus sometime from the mid-Pleistocene to the Holocene, and that it has the smallest historical effective population size of all subspecies. It appears that cassidix diverged from its ancestor with gippslandicus through a combination of drift and local selection. From patterns of genetic subdivision on two spatial scales and morphological variation we concluded that cassidix, gippslandicus and (melanops + meltoni) are diagnosable as subspecies. Low genetic diversity and effective population size of cassidix may translate to low genetic fitness and evolutionary potential, thus managed gene flow from gippslandicus is recommended for its recovery.

Population genetic and dispersal modeling data for Bathymodiolus mussels from the Mid-Atlantic Ridge

The zip folder comprises a text file and a gzipped tar archive. 1) The text file contains individual genotype data for 90 SNPs, 9 microsatellites and the mitochondrial ND4 gene that were determined in deep-sea hydrothermal vent mussels from the Mid-Atlantic Ridge (genus Bathymodiolus). Mussel specimens are grouped according to the population (pop)/location from which they have been sampled (first column). The remaining columns contain the respective allele/haplotype codes for the different genetic loci (names in the header line). The data file is in CONVERT format and can be directly transformed into different input files for population genetic statistics. 2) The tar archive contains NetCDF files with larval dispersal probabilities for simulated annual larval releases between 1998 and 2007. For each simulated vent location (Menez Gwen, Lucky Strike, Rainbow, Vent 1-10) two NetCDF files are given, one for an assumed pelagic larval duration of 1 year and the other one for an assumed pelagic larval duration of 6 months (6m).

Data compilation on the biological response to ocean acidification: environmental and experimental context of data sets and related literature

The exponential growth of studies on the biological response to ocean acidification over the last few decades has generated a large amount of data. To facilitate data comparison, a data compilation hosted at the data publisher PANGAEA was initiated in 2008 and is updated on a regular basis (doi:10.1594/PANGAEA.149999). By January 2015, a total of 581 data sets (over 4 000 000 data points) from 539 papers had been archived. Here we present the developments of this data compilation five years since its first description by Nisumaa et al. (2010). Most of study sites from which data archived are still in the Northern Hemisphere and the number of archived data from studies from the Southern Hemisphere and polar oceans are still relatively low. Data from 60 studies that investigated the response of a mix of organisms or natural communities were all added after 2010, indicating a welcomed shift from the study of individual organisms to communities and ecosystems. The initial imbalance of considerably more data archived on calcification and primary production than on other processes has improved. There is also a clear tendency towards more data archived from multifactorial studies after 2010. For easier and more effective access to ocean acidification data, the ocean acidification community is strongly encouraged to contribute to the data archiving effort, and help develop standard vocabularies describing the variables and define best practices for archiving ocean acidification data.

Petrology and geochemistry of peridotites from IODP Site 304-U1309

Peridotite samples recovered from IODP Site U1309 at the Atlantis Massif in the Mid-Atlantic Ridge were examined to understand magmatic processes for the oceanic core complex formation. Original peridotite was fragmented, and the limited short peridotite intervals are now surrounded by a huge gabbro body probably formed by late-stage melt injections. Each peridotite interval has various petrographical and geochemical features. A spinel harzburgite in contact with gabbro shows evidence of limited melt penetrations causing gradual compositional change, in terms of trace-element compositions of pyroxenes, as well as modal change near the boundary. Geochemistry of clinopyroxenes with least melt effects indicates that the harzburgite is originally mantle residue formed by partial melting under polybaric conditions, and that such a depleted peridotite is one of the components of the oceanic core complex. Some of plagioclase-bearing peridotites, on the other hand, have more complicated origin. Although their original features were partly overprinted by the injected melt, the original peridotites, both residual and non-residual materials, were possibly derived from the upper mantle. This suggests that the melt injected around an upper mantle region or into mantle material fragments. The injected melt was possibly generated at the ridge-segment center and, then, moved and evolved toward the segment end beneath the oceanic core complex.

Composition of rocks, minerals, water, and gases from uplift areas of the Central Atlantic

Original geological, geophysical, lithological, mineralogical data on uplifts of the Central Atlantic are given in the book based on materials of Cruise 1 of the R/V Akademik Nikolaj Strakhov. Geological and geophysical studies include description of the obtained material and analysis of structural and morphological elements of the ocean floor. Results of lithological, petrochemical and geochemical studies were extremely innovative and develop a conceptual model. The latter include studies of petrochemical evolution of tholeiitic alkaline plate volcanism, large-scale hydrothermal transformation of basement rocks - palygorskitization, phosphatization and ferromanganese mineralization. Showing imposition Superposition of hydrogenic alteration on hydrothermally altered rocks and its role in Cenozoic history of sedimentation is shown.

Organic compounds and bitumen in surface sediments from the Pechora Bay

Detailed geochemical investigations of bottom sediments in the Pechora Bay were carried out under a monitoring regime. The regional geochemical background is characterized. Organic matter of sediments is found to be clastic, formed under the influence of Pechora River run-off, and determined by genetic and lithofacial factors. An application of geochemical methodology is suggested for estimating hydrocarbon contamination of bottom sediments. As an example consequences of the accidental Usinsky oil spill are studied. They are based on analysis of composition of molecular markers. It is shown that increasing technogenic impact on Pechora Bay sediments is fixed only at molecular level and is not disastrous.

Microfossils and chemical elements in bottom sediments of the Ashadze-1 Hydrothermal Field (tropical Mid-Atlantic Ridge)

The first thorough analysis of microfossils from ore-bearing sediments of the Ashadze-1 Hydrothermal Field in the Mid-Atlantic Ridge sampled during Cruise 26 of R/V Professor Logachev in 2005 revealed substantial influence of hydrothermal processes on preservation of planktonic calcareous organisms as well as on preservation and composition of benthic foraminifera. From lateral and vertical distribution patterns and secondary alterations of microfossils it is inferred that the main phase of hydrothermal mineralization occurred in Holocene. Heavy metals (Cu, Co, Cr, and Ag) were accumulated by foraminiferal tests and in their enveloping Fe-Mn crusts. Distribution of authigenic minerals replacing foraminiferal tests demonstrates local zoning related to hydrothermal activity. There are three mineral-geochemical zones defined: sulfide zone, zone with elevated Mg content, and zone of Fe-Mn crusts.

Sedimentary facies, clay mineralogy and geochemistry of the Paleogene sediments of ODP Site 105-647

Claystones immediately overlying the early Eocene age ocean-floor basalt, cored at Ocean Drilling Program (ODP) Site 647, underwent hydrothermal and thermal alterations originating from the basalt, which resulted in changes in both the mineralogical and chemical composition of the sediments. Chlorites and higher magnesium and iron concentrations were found in the lowermost sediment sequence. Upcore, changes in the bulk chemical composition of the sediments become smaller, when compensated for variations in the carbonate content originating from biogenic and authigenic components. Chlorite disappears upcore, but still only part of the swelling clay minerals have survived the thermal influence. Thirty meters above the basalt, the clay mineralogy and chemical composition become uniform throughout the Paleogene section. Iron-rich smectites (i.e., nontronitic types), totally dominate the clay mineral assemblage. Biogenic components, responsible for the dominant part of the calcite and cristobalite contents, vary in amount in the upper part, and so do the authigenic carbonate and sulfide contents. Detrital components, such as kaolinite, illite, quartz, and feldspars, make up a very small proportion of the sediment record. The nontronitic smectites are believed to be authigenic, formed by a supply of iron from the continuous formation of ocean-floor basalt in the ridge area that reacted with the detrital and biogenic silicates and alumina silicates.

Trace and rare elements and factors at DSDP Hole 71-511

The distribution of paragenetic assemblages of trace and rare elements, as revealed by factor analysis (R-mode, Q-mode), the ratios of elements to Zr and the interpretation of these data in the context of the known mineralogy, lithology, and geology of the region, provide the bases for the outline of the geochemical history of sedimentation in the study area that forms the subject of this chapter. Two stages may be discerned. 1. Late-Middle Jurassic-Early Cretaceous (160-106? Ma). The sediments that accumulated in relatively shallow water (shelf) were predominantly clay, with dispersed sapropelic organic matter, plant fragments, pyrite, admixtures of acid-medium volcanic glass, and epigenetic crystals of gypsum. The bottom water layers of the basin are notably stagnant. The sediments are characterized by higher amounts of V, Zn, Cu, Cr, Rb, and Be associated with organic matter. Lower Cretaceous sediments, separated from those of the Upper Jurassic by a hiatus, accumulated in a deepened and enlarging basin. These Lower Cretaceous deposits are chemically similar to those of the Upper Jurassic, but contain diagenetic concentrations of Zn, Ni, and La. 2. Early-middle Albian (Unit 5)-middle Maestrichtian (1067-66.6Ma). The prevailing regime was that of an open ocean basin that tended to expand and deepen. During the second half of the early-middle Albian, the biogenic components Ba, Sr, and CaCO3 accumulated. By the end of this interval, Ti/Zr values had increased. In conjunction data on mineral composition, they testify to an outburst of basaltoid volcanism related to tectonic activity before an erosional hiatus (late Albian-Cenomanian). At the end of the Cenomanian-Turonian, residual deposits of predominantly clay sediments with relatively high amounts of Ti and Zr and associated rare alkalis (Li, Rb) accumulated. Clay sediments deposited during the Coniacian-Santonian were characterized by higher concentrations of Ti, Zr, Li, and Rb, by diagenetic carbonate phases of Ni, Zn, and La, and by sulphides and Fe-oxides with an admixture of Ni and Co. The latter half of the interval saw the deposition of fine basaltoid volcanoclastic material, diagenetically altered by zeolitization and carbonatization and enriched with Se, Pb, Ti, Sr, Ba, Y, and Yb. Sediments with a similar chemistry accumulated in the Campanian-middle Maestrichtian. Strong current activity preceding a global hiatus at the Mesozoic/Cenozoic boundary is reflected in both lower sedimentation rates and the presence of higher residual concentrations of Ti, Zr, Ba, Sr, and other elements studied in this chapter.

Chemical and mineral compositions of basalts from the Pacific Ocean, DSDP data

Mineral and chemical alterations of basalts were studied in the upper part of the ocean crust using data of deep-sea drilling from D/S Glomar Challenger in the main structures of the Pacific floor. Extraction of majority of chemical elements (including heavy metals) from basalts results mainly from their interaction with heated sea water. As a result mineralized hydrothermal solutions are formed. On entering the ocean they influence greatly on ocean sedimentation and ore formation.

Experimental data on photophysiology and growth rates of Pararotalia calcariformata

The eastern Mediterranean is a hotspot of biological invasions. Numerous species of Indo-pacific origin have colonized the Mediterranean in recent times, including tropical symbiont-bearing foraminifera. Among these is the species Pararotalia calcariformata. Unlike other invasive foraminifera, this species has been discovered only two decades ago and is restricted to the eastern Mediterranean coast. Combining ecological, genetic and physiological observations, we attempt to explain the recent invasion of this species in the Mediterranean Sea. Using morphological and genetic data, we confirm the species attribution to P. calcariformata McCulloch 1977 and identify its symbionts as a consortium of diatom species dominated by Minutocellus polymorphus. We document photosynthetic activity of its endosymbionts using Pulse Amplitude Modulated Fluorometry and test the effects of elevated temperatures on growth rates of asexual offspring. The culturing of asexual offspring for 120 days shows a 30-day period of rapid growth followed by a period of slower growth. A subsequent 48-day temperature sensitivity experiment indicates a similar developmental pathway and high growth rate at 28°C, whereas an almost complete inhibition of growth was observed at 20°C and 35°C. This indicates that the offspring of this species may have lower tolerance to cold temperatures than what would be expected for species native to the Mediterranean. We expand this hypothesis by applying a Species Distribution Model (SDM) based on modern occurrences in the Mediterranean using three environmental variables: irradiance, turbidity and yearly minimum temperature. The model reproduces the observed restricted distribution and indicates that the range of the species will drastically expand westwards under future global change scenarios. We conclude that P. calcariformata established a population in the Levant because of the recent warming in the region. In line with observations from other groups of organisms, our results indicate that continued warming of the eastern Mediterranean will facilitate the invasion of more tropical marine taxa into the Mediterranean, disturbing local biodiversity and ecosystem structure.

Seawater carbonate chemistry and MgCO3 concentration in bryozoan Myriapora truncata branches during experiments, 2011

There are serious concerns that ocean acidification will combine with the effects of global warming to cause major shifts in marine ecosystems, but there is a lack of field data on the combined ecological effects of these changes due to the difficulty of creating large-scale, long-term exposures to elevated CO2 and temperature. Here we report the first coastal transplant experiment designed to investigate the effects of naturally acidified seawater on the rates of net calcification and dissolution of the branched calcitic bryozoan Myriapora truncata (Pallas, 1766). Colonies were transplanted to normal (pH 8.1), high (mean pH 7.66, minimum value 7.33) and extremely high CO2 conditions (mean pH 7.43, minimum value 6.83) at gas vents off Ischia Island (Tyrrhenian Sea, Italy). The net calcification rates of live colonies and the dissolution rates of dead colonies were estimated by weighing after 45 days (May-June 2008) and after 128 days (July-October) to examine the hypothesis that high CO2 levels affect bryozoan growth and survival differently during moderate and warm water conditions. In the first observation period, seawater temperatures ranged from 19 to 24 °C; dead M. truncata colonies dissolved at high CO2 levels (pH 7.66), whereas live specimens maintained the same net calcification rate as those growing at normal pH. In extremely high CO2 conditions (mean pH 7.43), the live bryozoans calcified significantly less than those at normal pH. Therefore, established colonies of M. truncata seem well able to withstand the levels of ocean acidification predicted in the next 200 years, possibly because the soft tissues protect the skeleton from an external decrease in pH. However, during the second period of observation a prolonged period of high seawater temperatures (25-28 °C) halted calcification both in controls and at high CO2, and all transplants died when high temperatures were combined with extremely high CO2 levels. Clearly, attempts to predict the future response of organisms to ocean acidification need to consider the effects of concurrent changes such as the Mediterranean trend for increased summer temperatures in surface waters. Although M. truncata was resilient to short-term exposure to high levels of ocean acidification at normal temperatures, our field transplants showed that its ability to calcify at higher temperatures was compromised, adding it to the growing list of species now potentially threatened by global warming.

Biometry, isotopic composition and diet of Arctic charr (Salvelinus alpinus) from Lake Aigneau, Northern Quebec

Two modal size groups of sexually mature Arctic charr (Salvelinus alpinus) differing in shape and found at different depths in Lake Aigneau in the Canadian sub-Arctic are described and tested for genetic and ecological differentiation. Forms consisted of a small littoral resident, mean size 21.7 cm, and a large profundal resident, mean size 53.9 cm. Mitochondrial DNA analysis indicated that seven of eight haplotypes were diagnostic for either the littoral or profundal fish, with 66.6% of the variation being found within form groupings. Pairwise tests of microsatellite data indicated significant differences in nine of 12 loci and a significant difference between the forms across all tested loci. Molecular variation was partitioned to 84.1% within and 15.9% between forms and suggestive of either restricted interbreeding over time or different allopatric origins. Stable isotope signatures were also significantly different, with the profundal fish having higher d13C and d15N values than the littoral fish. Overlap and separation, respectively, in the range of form d13C and d15N signatures indicated that carbon was obtained from similar sources, but that forms fed at different trophic levels. Littoral fish relied on aquatic insects, predominantly chironomids. Profundal fish were largely piscivorous, including cannibalism. Predominantly empty stomachs and low per cent nitrogen muscle-tissue composition among profundal fish further indicated that the feeding activity was limited to the winter when ice-cover increases the density of available prey at depth. Results provide evidence of significant differences between the modal groups, with origins in both genetics and ecology.