Biology subjects

Malham, S. K.

Publications and source records attributed to Malham, S. K..

3 recordsLinked to original sources

bioRxiv2020

Biotic and abiotic factors shaping the genome of cockle (Cerastoderma edule) in the Northeast Atlantic: a baseline for sustainable management of its wild resources

Knowledge on how environmental factors shape the genome of marine species is crucial for sustainable management of fisheries and wild populations. The edible cockle (Cerastoderma edule) is a marine bivalve distributed along the Northeast Atlantic coast of Europe and is an important resource from both commercial and ecological perspectives. We performed a population genomics screening using 2b-RAD genotyping on 9,309 SNPs localised in the cockles genome on a sample of 536 specimens pertaining to 14 beds in the Northeast Atlantic to ascertain its genetic structure regarding environmental variation. Larval dispersal modelling considering species behaviour and interannual variability in ocean conditions was carried out, as an essential background to compare genetic information with. Cockle populations in the Northeast Atlantic were shown to be panmictic and displayed low but significant geographical differentiation across populations (FST = 0.0240; P < 0.001), albeit not across generations. We identified 441 outlier SNPs related to divergent selection, sea surface temperature being the main environmental driver following a latitudinal axis. Two main genetic groups were identified, northwards and southwards of French Brittany, in accordance with our modelling, which demonstrated a barrier for larval dispersal linked to the Ushant front. Further genetic subdivision was observed using outlier loci and considering larval behaviour. The northern group was divided into the Irish/Celtic Seas and the English Channel/North Sea, while the southern group was divided into three subgroups. This information represents the baseline for management of cockles, designing conservation strategies, founding broodstock for depleted beds, and producing suitable seed for aquaculture production.

genomics↗

bioRxiv2019

Fine-scale seascape genomics of an exploited marine species, the common cockle Cerastoderma edule, using a multi-modelling approach

Population dynamics of marine species that are sessile as adults are driven by oceanographic dispersal of larvae from spawning to nursery grounds. This is mediated by life-history traits such as the timing and frequency of spawning, larval behaviour and duration, and settlement success. Here, we use 1725 single nucleotide polymorphisms (SNPs) to study the fine scale spatial genetic structure in the commercially important cockle species Cerastoderma edule and compare it to environmental variables and current-mediated larval dispersal within a modelling framework. Hydrodynamic modelling employing the NEMO Atlantic Margin Model (AMM15) was used to simulate larval transport and estimate connectivity between populations during spawning months (April - September), factoring in larval duration and seasonal variability of ocean currents. Results at neutral loci reveal the existence of three separate genetic clusters (mean FST=0.021) within a relatively fine spatial scale in the northwest Atlantic. Environmental association (EA) analysis indicates that oceanographic currents and geographical distance between the populations explain over 20% of the variance observed at neutral loci, while genetic variance (71%) at outlier loci was explained by sea surface temperatures extremes. These results fill an important knowledge gap in the management of a commercially important, overexploited species, and bring us closer to understanding the role of larval dispersal in connecting populations at a fine geographical scale.

evolutionary biology↗

bioRxiv2018

Two-step concentration of complex water samples for the detection of viruses

The accurate detection and quantification of pathogenic viruses in water is essential to understand and reduce the risk of human infection. In this paper, we validated a two-step method for the concentration of enteric viruses in water and wastewater samples. The method involves a tangential flow ultrafiltration step that reduces the sample volume of 1 - 10 L to approx. 50 mL, followed by secondary precipitation using polyethylene glycol 6000 that reduces the volume to 1 - 4 mL. For method validation, surface water samples were spiked with different concentrations of enteric viruses and viral recoveries in the concentrates exceeded 10% in all experiments. The method is suitable for water samples with high and low salinity and turbidity, allowing the accurate comparison of viral titers in a diverse range of water types. Furthermore, the method has the potential to concentrate other pathogens, e.g. bacteria or protozoa. Hence, the use of this method can improve the holistic assessment of risks associated with wastewater contaminated environments.\n\nO_LIModified tangential flow ultrafiltration method that reduces membrane clogging.\nC_LIO_LISecondary concentration with a beef extract-elution step to remove solid matter.\nC_LIO_LIThe two-step concentration method enables at least 10% recovery for different enteric viruses in difficult matrices.\nC_LIO_LIUsing the two-step concentration method 10,000x concentration can be achieved.\nC_LI\n\nSpecifications Table:\n\n\n\nO_TBL View this table:\norg.highwire.dtl.DTLVardef@12d4fceorg.highwire.dtl.DTLVardef@1d2880borg.highwire.dtl.DTLVardef@e1acf6org.highwire.dtl.DTLVardef@226492org.highwire.dtl.DTLVardef@1f8edf0_HPS_FORMAT_FIGEXP M_TBL C_TBL

microbiology↗