HPH3B20

Exam paper for second semester: HPH3B2

Remarkable Capacity for Anaerobic Oxidation of Methane at High Methane Concentration

Anaerobic oxidation of methane (AOM), a central process in the carbon cycle of anoxic environments, moderates the release of methane from soils and sediments to water bodies and, ultimately, the atmosphere. The regulation of AOM in the environment remains poorly constrained. Here we quantified AOM and sulfate reduction (SR) rates in diverse deep seafloor samples at in situ pressure and methane concentration and discovered that, in some cases, AOM exceeded SR rates by more than four times when methane concentrations were above 5 mM. Methane concentration also affected other carbon-cycling processes (e.g., carbon assimilation) in addition to SR. These results illustrate that substantial amounts of methane may be oxidized independent of SR under in situ conditions, reshaping our view of the capacity and mechanism of AOM in methane-rich environments, including the deep biosphere, where sulfate availability is considered to limit AOM

Affinities of some common estuarine macroinvertebrates to salinity and sediment type: Empirical data from Eastern Cape estuaries, South Africa

Fourteen species of subtidal macrobenthos present in thirteen Eastern Cape estuaries, South Africa, were compared with regard to correlations with two important environmental variables (salinity and sediment mud content). Species were divided into five different faunal components based on their affinity with one of the two variables, namely marine species, oligohaline species, estuarine sand species, estuarine mud species, and species whose distribution seemed independent of either environmental variable. Although most species exhibited wide tolerance ranges to both environmental variables, preference ranges could be identified in many cases. Among the fourteen species studied, three were found mostly at high salinities, two were confined to sandy substratum, and four showed a clear preference for muddy sediment. The crab Paratylodiplax algoense was identified as a euryhaline marine species and the larvae of chironomid midges, previously believed to be oligohaline species, were found to be tolerant to near-seawater salinities.Articl

The evolutionary history of seahorses (Syngnathidae: Hippocampus): Molecular data suggest a West Pacific origin and two invasions of the Atlantic Ocean

Sequence data derived from four markers (the nuclear RP1 and Aldolase and the mitochondrial 16S rRNA and cytochrome b genes) were used to determine the phylogenetic relationships among 32 species belonging to the genus Hippocampus. There were marked differences in the rate of evolution among these gene fragments, with Aldolase evolving the slowest and the mtDNA cytochrome b gene the fastest. The RP1 gene recovered the highest number of nodes supported by >70% bootstrap values from parsimony analysis and >95% posterior probabilities from Bayesian inference. The combined analysis based on 2317 nucleotides resulted in the most robust phylogeny. A distinct phylogenetic split was identified between the pygmy seahorse, Hippocampus bargibanti, and a clade including all other species. Three species from the western Pacific Ocean included in our study, namely H. bargibanti, H. breviceps, and H. abdominalis occupy basal positions in the phylogeny. This and the high species richness in the region suggests that the genus evolved somewhere in the West Pacific. There is also fairly strong molecular support for the remaining species being subdivided into three main evolutionary lineages: two West Pacific clades and a clade of species present in both the Indo-Pacific and the Atlantic Ocean. The phylogeny obtained herein suggests at least two independent colonization events of the Atlantic Ocean, once before the closure of the Tethyan seaway, and once afterwards. © 2003 Elsevier Science (USA). All rights reserved.Articl

Development of genetic tools for the redbait species Pyura herdmani and P. stolonifera, important bioengineers along African coastlines

The development of new genetic resources is key for biological conservation in an era when the preservation of biodiversity is crucial. Here, we report the development of microsatellites and mitochondrial markers for the redbait species Pyura herdmani and P. stolonifera, both important bioengineers along African coastlines. Specifically, we identified microsatellites by means of pyrosequencing and variable regions in the mitochondrial genome using RAD-seq libraries that were generated with Illumina sequencing. A total of 4 339 putative microsatellites were found, of which 32 were tested on individuals collected along the southeast coast of South Africa. Of those, five  microsatellites cross-amplified consistently in both species, and these were tested on a total of 260 samples. Additionally, we mapped the partial mitochondrial genome of a small number of  individuals from both species and identified the most-variable regions by comparing a small number of individuals from all regions where these species have been recorded (including western South Africa and northwest Africa). The genetic markers developed here can be used to conduct population genetic studies, to monitor range shifts under   contemporary climate change, and to help in preserving ecosystem functioning along African coastlines

Comparative genetic structure in two high-dispersal prawn species from the south-west Indian Ocean

The penaeid prawns Fenneropenaeus indicus and Metapenaeus monoceros support shallow-water prawn fisheries in the south-west Indian Ocean. They are sympatric and have similar life histories, including developmental stages that depend on estuarine and marine habitats and a short dispersal duration. Nevertheless, M. monoceros juveniles display a more generalist habitat preference in estuaries and recruit to offshore habitats during a different season than F. indicus. We hypothesised that these differences would affect dispersal patterns, leading to dissimilar geographic genetic structure between the two taxa. Given their short dispersal phase, we also hypothesised that the Mozambique Channel would form a barrier to dispersal between the southeastern African mainland and Madagascar sites. Population differentiation was assessed based on analysis of mitochondrial DNA control-region sequences. Both species displayed high haplotype and low nucleotide diversity. Pairwise φST statistics supported the existence of admixed populations along the African mainland sites for both species, with geographic distance isolating populations at the extremes of the sampled range (Kenya and east coast of South Africa). The Madagascar population differed significantly from African mainland populations. The concordant patterns in population differentiation suggest that F. indicus and M. monoceros can be considered as single African stocks, or fisheries management units.Keywords: analysis of molecular variance, Fenneropenaeus indicus, fisheries management, haplotype sharing analysis, larval dispersal, Metapenaeus monoceros, mitochondrial DNA control region, western Indian Ocea

Diversification and coevolution of the ghrelin/growth hormone secretagogue receptor system in vertebrates.

The gut hormone ghrelin is involved in numerous metabolic functions, such as the stimulation of growth hormone secretion, gastric motility, and food intake. Ghrelin is modified by ghrelin O-acyltransferase (GOAT) or membrane-bound O-acyltransferase domain-containing 4 (MBOAT4) enabling action through the growth hormone secretagogue receptors (GHS-R). During the course of evolution, initially strong ligand/receptor specificities can be disrupted by genomic changes, potentially modifying physiological roles of the ligand/receptor system. Here, we investigated the coevolution of ghrelin, GOAT, and GHS-R in vertebrates. We combined similarity search, conserved synteny analyses, phylogenetic reconstructions, and protein structure comparisons to reconstruct the evolutionary history of the ghrelin system. Ghrelin remained a single-gene locus in all vertebrate species, and accordingly, a single GHS-R isoform was identified in all tetrapods. Similar patterns of the nonsynonymous (dN) and synonymous (dS) ratio (dN/dS) in the vertebrate lineage strongly suggest coevolution of the ghrelin and GHS-R genes, supporting specific functional interactions and common physiological pathways. The selection profiles do not allow confirmation as to whether ghrelin binds specifically to GOAT, but the ghrelin dN/dS patterns are more similar to those of GOAT compared to MBOAT1 and MBOAT2 isoforms. Four GHS-R isoforms were identified in teleost genomes. This diversification of GHS-R resulted from successive rounds of duplications, some of which remained specific to the teleost lineage. Coevolution signals are lost in teleosts, presumably due to the diversification of GHS-R but not the ghrelin gene. The identification of the GHS-R diversity in teleosts provides a molecular basis for comparative studies on ghrelin's physiological roles and regulation, while the comparative sequence and structure analyses will assist translational medicine to determine structure-function relationships of the ghrelin/GHS-R system

A comparison of genetic structure in two low-dispersal crabs from the Wild Coast, South Africa

The Wild Coast in south-eastern South Africa is strongly influenced by the warm, southward-flowing Agulhas Current. This current has a significant impact on dispersal in the coastal biota of the region, and facilitates high levels of connectivity among populations. However, it is not known how the region’s high-velocity hydrology affects genetic population structure in endemic estuarine species, populations of which are frequently isolated from the sea. Here, we compared genetic structure in two estuarine crabs of the family Hymenosomatidae. Both are presumed to have low dispersal potential, but they differ in terms of their life histories. Hymenosoma longicrure has abbreviated larval development and can complete its entire life cycle within estuaries, whereas Neorhynchoplax bovis is a direct developer that lacks planktonic larvae. Using DNA sequence data from the mitochondrial COI gene and the intron of the nuclear ANT gene, we found that levels of genetic structure differ considerably between the species. Depending on the genetic marker used, H. longicrure is genetically homogeneous (COI) or displays low levels of genetic structure and minor evidence of recruitment near natal sites (ANT). In contrast, connectivity in N. bovis is much lower, as this species has a unique combination of alleles at each site, indicating that recruitment is mostly local. These results support previous findings suggesting that even a short larval dispersal phase is sufficient to maintain high levels of connectivity and prevent genetic divergence among populations.Keywords: Agulhas Current, direct development, Hymenosoma longicrure, Neorhynchoplax bovis, phylogeography, planktonic larval dispersal, raftin

Genomic resources for the spotted ragged-tooth shark Carcharias taurus

Genomic data can be a useful tool in the management and conservation of biodiversity. Here, we report the development of genomic resources for the spotted ragged-tooth shark Carcharias taurus using genome-wide DNA data from Illumina next-generation sequencing. We explored two commonly used genetic marker types: microsatellites and mitochondrial DNA. A total of 4 394 putative microsatellites were identified, of which 10 were tested on 24 individuals and found to have ideal properties for population genetic analyses. Additionally, we reconstructed the first complete mitochondrial genome of a South African spotted ragged-tooth shark, and highlight the most informative gene regions to facilitate future primer design. The data reported here may serve as a resource for future studies and can ultimately be applied in the sustainable conservation and fisheries management of this apex predator.Keywords: genotype, grey nurse shark, Illumina next-generation sequencing, microsatellites, mitogenome, primer design, sand tiger shar