Biology subjects

Loh, R. K.

Publications and source records attributed to Loh, R. K..

4 recordsLinked to original sources

bioRxiv2025

Evolution under Domestication: Genetic differentiation in black soldier fly (Hermetia illucens) populations subjected to recent selective breeding

The black soldier fly (BSF; Hermetia illucens) is widely utilized in commercial and research applications for waste bioconversion and sustainable protein production. However, prolonged captivity and artificial selection can shape genetic diversity, potentially influencing adaptability and long-term population stability. This study examined how recent selective breeding, genetic drift, and relaxed selection have influenced genetic differentiation in BSF populations over a short timeframe. Using mitochondrial cytochrome oxidase I (CO1) and genome-wide RAD sequencing, population structure, heterozygosity, and selection signatures across eleven BSF populations, including selectively bred, wild-derived, and commercial strains were analysed. Results revealed that rapid genetic shifts have occurred within selectively bred populations (LA to LE) over [~]5 years, driven by artificial selection, subsequent relaxation, and environmental adaptation. The decline in effective population size (Ne) observed post-COVID-19 suggests recent bottlenecks, which may have further contributed to genetic drift and differentiation. While domesticated populations exhibited reduced genetic diversity and signs of inbreeding, wild-type population under short captivity retained higher heterozygosity. Genome-wide analyses further identified adaptive divergence among populations, with balancing selection and selective sweeps shaping genetic variation. Notably, despite shared ancestry, genetic differentiation persisted in selectively bred populations, reinforcing that selection and environmental pressures continue to influence their genomic landscape even after targeted selection was relaxed. These findings underscore the need to monitor genetic diversity in BSF breeding programs to maintain adaptability, enhance resilience, and mitigate risks from artificial selection and population collapse.

evolutionary biology↗

bioRxiv2022

Network analysis with either Illumina or MinION reveals that detecting vertebrate species requires metabarcoding of iDNA from a diverse fly community

Metabarcoding of vertebrate DNA obtained from invertebrates (iDNA) has been used to survey vertebrate communities, but we here show that it can also be used to study species interactions between invertebrates and vertebrates in a spatial context. We sampled the dung and carrion fly community of a swamp forest remnant along a disturbance gradient (10 sites: 80-310m from a road). Approximately, 60% of the baited 407 flies yield 294 vertebrate identifications based on two COI fragments and 16S sequenced with Illumina and/or MinION. A bipartite network analysis finds no specialization in the interaction between flies and vertebrate species, but a spatial analysis revealed that surprisingly 18 of the 20 vertebrate species can be detected within 150m of the road. We show that the fly community sourced for iDNA was unexpectedly rich (24 species, 3 families) and carried DNA for mammals, birds, and reptiles. They included common and rare ground-dwelling (e.g., wild boar, Sunda pangolin), and arboreal species (e.g., long-tailed macaque, Raffles banded langur) as well as small bodied vertebrates (skinks, rats). All of our results were obtained with a new, greatly simplified iDNA protocol that eliminates DNA extraction by obtaining template directly through dissolving feces and regurgitates from individual flies with water. Lastly, we show that MinION- and Illumina-based metabarcoding yield similar results. Overall, flies from several families (calliphorids, muscids and sarcophagids) should be used in iDNA surveys because we show that uncommon fly species carry the signal for several vertebrate species that are otherwise difficult to detect with iDNA.

ecology↗

bioRxiv2021

Towards environmental DNA-based bioassessment of freshwater reservoirs with small volumes of water: robust molecular protocols

Bioassessment of freshwater quality via eDNA is rapidly developing into a powerful alternative to traditional methods involving collecting, sorting, and identifying macroinvertebrates based on morphology. Particularly attractive would be methods that can use remote-controlled boats for sampling because it would allow for cost-effective, and frequent monitoring at multiple sites. The latter will be particularly important for tropical reservoirs that require year-around surveillance. We here optimize molecular protocols for capturing reservoir-specific differences in metazoan communities based on small water volumes (15 mL). The optimization is based on samples from two freshwater reservoirs with very different water qualities ("reservoir signal"). Each reservoir was sampled at three sites ("biological replicates"). For each water sample, the DNA was extracted twice ("technical replicates"). We then tested how much DNA template (0.1 ng to 15 ng) and how many PCR cycles (25 or 35) minimized variance between technical replicates. We find that 15 mL is sufficient for capturing the reservoir signal regardless of sampling time, template amounts, or PCR cycle numbers. Indeed, extrapolation from our results suggests that <1 mL would be sufficient because only 17 of 59 metazoan mOTUs (mainly planktonic crustaceans and rotifers) detected with a 313bp COI minibarcode were shared. We find that the use of 35 PCR cycles significantly lowered the number of detected species and that template amounts <0.5 ng yielded somewhat higher variance between technical replicates. Despite extensive trials, the variance between technical replicates remained high (Bray-Curtis: 5-20%; Jaccard: 10-40%) and we predict that it will be difficult to reduce this variance further. However, the overall reservoir differences are so strong that all biological and technical replicates can be correctly assigned.

ecology↗

bioRxiv2016

Silversword and lobeliad reintroduction linked to landscape restoration on Mauna Loa and Kilauea, and its implications for plant adaptive radiation in Hawaii

The endemic Hawaiian silversword and lobeliad lineages, which are two of the worlds premier examples of plant adaptive radiation, exemplify the severity of the threats confronting the Hawaiian flora, especially the threats posed by alien species. We have implemented collaborative reintroduction efforts with the endangered Ka[u] silversword (Argyroxiphium kauense) and Pele lobeliad (Clermontiapeleana) in Hawaii Volcanoes National Park. The efforts with the Ka[u] silversword have involved rediscovery, helicopter assisted rescue of diminutive remnant founders, managed breeding, outplanting at two sites in the Park of more than 21,000 seedlings deriving from 169 founders, and facilitated achene dispersal following flowering. The efforts with the Pele lobeliad have involved rediscovery, air-layering of remnant founders while suspended on climbing ropes, managed breeding, and outplanting at two sites in the Park of more than 1,000 seedlings (to date) deriving from six of the seven known founders. We have linked the reintroduction efforts to landscape restoration at large scales in the Park and in adjacent State and private lands, thereby increasing the opportunities for substantial population growth and expansion of the Ka[u] silversword and Pele lobeliad in the future. Additionally, we have extended the reintroduction efforts, including the link to landscape restoration, to encompass all other endangered silversword and lobeliad taxa occurring historically on the eastern slopes of Mauna Loa or on K[i]lauea. In so doing, we seek to restore the possibility of adaptive radiation of the silversword and lobeliad lineages going forward, especially on the youngest and most geologically active, and thus perhaps most evolutionarily dynamic, part of the Hawaiian archipelago.\n\nDedicationThis paper celebrates the centennial of Hawaii Volcanoes National Park, which was founded in August 1916.

evolutionary biology↗