Sampling sites, sampled birds and plants of young larch plantations in Tokachi district, eastern Hokkaido, northern Japan, 2011

Models and data used to describe species-area relationships confound sampling with ecological process as they fail to acknowledge that estimates of species richness arise due to sampling. This compromises our ability to make ecological inferences from and about species-area relationships. We develop and illustrate hierarchical community models of abundance and frequency to estimate species richness. The models we propose separate sampling from ecological processes by explicitly accounting for the fact that sampled patches are seldom completely covered by sampling plots and that individuals present in the sampling plots are imperfectly detected. We propose a multispecies abundance model in which community assembly is treated as the summation of an ensemble of species-level Poisson processes and estimate patch-level species richness as a derived parameter. We use sampling process models appropriate for specific survey methods. We propose a multispecies frequency model that treats the number of plots in which a species occurs as a binomial process. We illustrate these models using data collected in surveys of early-successional bird species and plants in young forest plantation patches. Results indicate that only mature forest plant species deviated from the constant density hypothesis, but the null model suggested that the deviations were too small to alter the form of species-area relationships. Nevertheless, results from simulations clearly show that the aggregate pattern of individual species density-area relationships and occurrence probability-area relationships can alter the form of species-area relationships. The plant community model estimated that only half of the species present in the regional species pool were encountered during the survey. The modeling framework we propose explicitly accounts for sampling processes so that ecological processes can be examined free of sampling artefacts. Our modeling approach is extensible and could be applied to a variety of study designs and allows the inclusion of additional environmental covariates.

Pollen, DNA and Vegetation records from surface sediments of lacustrine lakes along a forest tundra - tundra transect at the Taymyr peninsula, northern Siberia

Reliable information of past vegetation changes are important to project future changes, especially for areas undergoing rapid transitioning such as the boreal treeline. The application of detailed sedDNA records has the potential to enhance our understanding of vegetation changes gained mainly from pollen studies of lake sediments. This study investigates sedDNA and pollen records from 31 lakes along a gradient of increasing larch forest cover in northern Siberia (Taymyr Peninsula) and compares them with vegetation field surveys within the lake's catchment. With respect to vegetation richness, sedDNA recorded 114 taxa, about half of them to species level, while pollen analyses identified 43 pollen taxa. Both approaches exceed the 31 taxa revealed by vegetation field surveys of 400 m**2 plots. From north to south, Larix percentages increase, as is consistently recorded by all three methods. Furthermore, tundra sites are separated from forested sites in the plots of the principal component analyses. Comparison of ordination results by Procrustes and Protest analyses yields a significant fit among all compared pairs of records. Despite the overall comparability of sedDNA and pollen analyses certain idiosyncrasies in the compositional signal are observed, such as high percentages of Alnus and Betula in all pollen spectra and high percentages of Salix in all sedDNA spectra. In conclusion, our results from the treeline show that sedDNA analyses perform better than pollen in recording site-specific richness (i.e. presence/absence of certain vegetation taxa in the direct vicinity of the lake) and perform as good as pollen in tracing regional vegetation composition.

Properties of seawater and particulate matter from a WETLabs AC-S spectrophotometer and a WETLabs chlorophyll fluorometer mounted on the continuous surface water sampling system during the Tara Oceans expedition 2009-2013

The Tara Oceans Expedition (2009-2013) was a global survey of ocean ecosystems aboard the Sailing Vessel Tara. It carried out extensive measurements of evironmental conditions and collected plankton (viruses, bacteria, protists and metazoans) for later analysis using modern sequencing and state-of-the-art imaging technologies. Tara Oceans Data are particularly suited to study the genetic, morphological and functional diversity of plankton. The present data publication provides permanent links to original and updated versions of validated data files containing measurements from the Continuous Surface Sampling System [CSSS]. Water was pumped at the front of the vessel from ~2m depth, then de-bubbled and circulated to a WETLabs AC-S spectrophotometer and a WETLabs chlorophyll fluorometer. Systems maintenance (instrument cleaning, flushing) was done approximately once a week and in port between successive legs. All data were stamped with a GPS.