ALBERT

Description: Omic BON is a thematic Biodiversity Observation Network under the Group on Earth Observations Biodiversity Observation Network (GEO BON), focused on coordinating the observation of biomolecules in organisms and the environment. Our founding partners include representatives from national, regional, and global observing systems; standards organizations; and data and sample management infrastructures. By coordinating observing strategies, methods, and data flows, Omic BON will facilitate the co-creation of a global omics meta-observatory to generate actionable knowledge. Here, we present key elements of Omic BON's founding charter and first activities.

Description: Palaeoenvironmental records from permafrost sequences complemented by infrared stimulated luminescence (IRSL) and 230Th/U dates from Bol'shoy Lyakhovsky Island (7320'N, 14130'E) document the environmental history in the region for at least the past 200 ka. Pollen spectra and insect fauna indicate that relatively wet grass-sedge tundra habitats dominated during an interstadial c. 200–170 ka BP. Summers were rather warm and wet, while stable isotopes reflect severe winter conditions. The pollen spectra reflect sparser grass-sedge vegetation during a Taz (Late Saalian) stage, c. 170–130 ka BP, with environmental conditions much more severe compared with the previous interstadial. Open Poaceae and Artemisia plant associations dominated vegetation at the beginning of the Kazantsevo (Eemian) c. 130 ka BP. Some shrubs (Alnus fruticosa, Salix, Betula nana) grew in more protected and wetter places as well. The climate was relatively warm during this time, resulting in the melting of Saalian ice wedges. Later, during the interglacial optimum, shrub tundra with Alnus fruticosa and Betula nana s.l. dominated vegetation. Climate was relatively wet and warm. Quantitative pollen-based climate reconstruction suggests that mean July temperatures were 4–5 C higher than the present during the optimum of the Eemian, while late Eemian records indicate significant climate deterioration.

Description: In this pilot study, we describe a high-pressure incubation system allowing multiple subsampling of a pressurized culture without decompression. The system was tested using one piezophilic (Photobacterium profundum), one piezotolerant (Colwellia maris) bacterial strain and a decompressed sample from the Mediterranean deep sea (3044 m) determining bacterial community composition, protein production (BPP) and cell multiplication rates (BCM) up to 27 MPa. The results showed elevation of BPP at high pressure was by a factor of 1.5 ± 1.4 and 3.9 ± 2.3 for P. profundum and C. maris, respectively, compared to ambient-pressure treatments and by a factor of 6.9 ± 3.8 fold in the field samples. In P. profundum and C. maris, BCM at high pressure was elevated (3.1 ± 1.5 and 2.9 ± 1.7 fold, respectively) compared to the ambient-pressure treatments. After 3 days of incubation at 27 MPa, the natural bacterial deep-sea community was dominated by one phylum of the genus Exiguobacterium, indicating the rapid selection of piezotolerant bacteria. In future studies, our novel incubation system could be part of an isopiestic pressure chain, allowing more accurate measurement of bacterial activity rates which is important both for modeling and for predicting the efficiency of the oceanic carbon pump.

Description: Permafrost deposits were studied along the Olenyeksky and the Arinsky distributaries in the western Lena delta using a multidisciplinary approach that included sedimentological, mineralogical, stable-isotope, and paleoecological analyses in order to reconstruct the Late Quaternary landscape and environmental history of this Northeast.

Description: The origin of novel phenotypic characters is a key component in organismal diversification; yet, the mechanisms underlying the emergence of such evolutionary novelties are largely unknown. Here we examine the origin of egg-spots, an evolutionary innovation of the most species-rich group of cichlids, the haplochromines, where these conspicuous male fin colour markings are involved in mating. Applying a combination of RNAseq, comparative genomics and functional experiments, we identify two novel pigmentation genes, fhl2a and fhl2b, and show that especially the more rapidly evolving b-paralog is associated with egg-spot formation. We further find that egg-spot bearing haplochromines, but not other cichlids, feature a transposable element in the cis-regulatory region of fhl2b. Using transgenic zebrafish, we finally demonstrate that this region shows specific enhancer activities in iridophores, a type of pigment cells found in egg-spots, suggesting that a cis-regulatory change is causally linked to the gain of expression in egg-spot bearing haplochromines

Description: A new method of generating two-dimensional and three-dimensional cloud fields is presented, which share several important statistical properties with real measured cloud fields.Well-known algorithms such as the Fourier method and the Bounded Cascade method generate fields with a specified Fourier spectrum. The new iterative method allows for the specification of both the power spectrum and the amplitude distribution of the parameter of interest, e.g. the liquid water content or liquid water path. As such, the method is well suited to generate cloud fields based on measured data, and it is able to generate broken cloud fields. Important applications of such cloud fields are e.g. closure studies. The algorithm can be supplied with additional spatial constraints which can reduce the number of measured cases needed for such studies. In this study the suitability of the algorithm for radiative questions is evaluated by comparing the radiative properties of cloud fields from cloud resolving models of cumulus and stratocumulus with their surrogate fields at nadir, and for a solar zenith angle of 0◦ and 60◦. The cumulus surrogate clouds ended up to be identical to the large eddy simulation (LES) clouds on which they are based, except for translations and reflections. The root mean square differences of the stratocumulus transmittance and reflectance fields are less than 0.03% of the radiative budget. The radiances and mean actinic fluxes fit better than 2%. These results demonstrate that these LES clouds are well described from a radiative point of view, using only a power spectrum together with an amplitude distribution.

Description: Cichlid fishes provide textbook examples of explosive phenotypic diversification and sympatric speciation, thereby making them ideal systems for studying the molecular mechanisms underlying rapid lineage divergence. Despite the fact that gene regulation provides a critical link between diversification in gene function and speciation, many genomic regulatory mechanisms such as microRNAs (miRNAs) have received little attention in these rapidly diversifying groups. Therefore, we investigated the posttranscriptional regulatory role of miRNAs in the repeated sympatric divergence of Midas cichlids (Amphilophus spp.) from Nicaraguan crater lakes. Using miRNA and mRNA sequencing of embryos from five Midas species, we first identified miRNA binding sites in mRNAs and highlighted the presences of a surprising number of novel miRNAs in these adaptively radiating species. Then, through analyses of expression levels, we identified putative miRNA/gene target pairs with negatively correlated expression level that were consistent with the role of miRNA in downregulating mRNA. Furthermore, we determined that several miRNA/gene pairs show convergent expression patterns associated with the repeated benthic/limnetic sympatric species divergence implicating these miRNAs as potential molecular mechanisms underlying replicated sympatric divergence. Finally, as these candidate miRNA/gene pairs may play a central role in phenotypic diversification in these cichlids, we characterized the expression domains of selected miRNAs and their target genes via in situ hybridization, providing further evidence that miRNA regulation likely plays a role in the Midas cichlid adaptive radiation. These results provide support for the hypothesis that extremely quickly evolving miRNA regulation can contribute to rapid evolutionary divergence even in the presence of gene flow.

Description: Parasites are arguably among the strongest drivers of natural selection, constraining hosts to evolve resistance and tolerance mechanisms. Although, the genetic basis of adaptation to parasite infection has been widely studied, little is known about how epigenetic changes contribute to parasite resistance and eventually, adaptation. Here, we investigated the role of host DNA methylation modifications to respond to parasite infections. In a controlled infection experiment, we used the three-spined stickleback fish, a model species for host-parasite studies, and their nematode parasite Camallanus lacustris. We showed that the levels of DNA methylation are higher in infected fish. Results furthermore suggest correlations between DNA methylation and shifts in key fitness and immune traits between infected and control fish, including respiratory burst and functional trans-generational traits such as the concentration of motile sperm. We revealed that genes associated with metabolic, developmental and regulatory processes (cell death and apoptosis) were differentially methylated between infected and control fish. Interestingly, genes such as the neuropeptide FF receptor 2 and the integrin alpha 1 as well as molecular pathways including the Th1 and Th2 cell differentiation were hypermethylated in infected fish, suggesting parasite-mediated repression mechanisms of immune responses. Altogether, we demonstrate that parasite infection contributes to genome-wide DNA methylation modifications. Our study brings novel insights into the evolution of vertebrate immunity and suggests that epigenetic mechanisms are complementary to genetic responses against parasite-mediated selection.

Description: The two toothed jaws of cichlid fishes provide textbook examples of convergent evolution. Tooth phenotypes such as enlarged molar-like teeth used to process hard-shelled molluscs have evolved numerous times independently during cichlid diversification. While the ecological benefit of molar-like teeth to crush prey is known, it is unclear whether the same molecular mechanisms underlie these convergent traits. To identify genes involved in the evolution and development of enlarged cichlid teeth, we performed RNA-seq on the serially homologous toothed oral and pharyngeal jaws as well as the fourth toothless gill arch of Astatoreochromis alluaudi. We identified 27 genes that are highly upregulated on both tooth-bearing jaws compared to the toothless gill arch. Most of these genes have never been reported to play a role in tooth formation. Two of these genes (unk, rpfA) are not found in other vertebrate genomes but are present in all cichlid genomes. They also cluster genomically with two other highly expressed tooth genes (odam, scpp5) that exhibit conserved expression during vertebrate odontogenesis. Unk and rpfA were confirmed via in situ hybridization to be expressed in developing teeth of Astatotilapia burtoni. We then examined expression of the cluster's four genes in six evolutionarily independent and phylogenetically disparate cichlid species pairs each with a large- and a small-toothed species. Odam and unk commonly and scpp5 and rpfA always showed higher expression in larger-toothed cichlid jaws. Convergent trophic adaptations across cichlid diversity are associated with the repeated developmental deployment of this genomic cluster containing conserved and novel cichlid-specific genes.