Biology subjects

Capstick, M.

Publications and source records attributed to Capstick, M..

7 recordsLinked to original sources

bioRxiv2026

A mosaic of genomic architectures underpins parasitism loss in a jawless vertebrate

Lampreys are the only ancestrally parasitic vertebrate lineage, yet parasitism has been repeatedly lost alongside a suite of life-history changes, such as loss of migration and juvenile feeding and accelerated maturation. Combining whole-genome resequencing, haplotype-resolved assemblies, hybrid-zone genotyping, multi-tissue transcriptomics, and sperm phenotyping, we map this life-history syndrome in European Lampetra to six chromosomes spanning a mosaic of genomic architectures: a [~]20 Mb low-recombination region on chromosome 1 lacking chromosomal rearrangements within Lampetra but involving inter-specific rearrangements across deep lamprey lineages; a translocated inversion with ecotype-dependent sperm-velocity effects; and ecotype-divergent deletions overlapping genes crucial for nervous system (CNTNAP2) and reproductive development (FSHR). However, this genomic basis is not shared with a convergent sister lineage, pointing to independent routes to a recurring life-history transition in lampreys.

evolutionary biology↗

bioRxiv2026

Revisiting the genetics of Lake Constance Coregonids using lake-wide whole genome sequencing

Anthropogenic pressures can have detrimental impacts on fish populations, with their effective management and conservation requiring accurate monitoring tools. Yet, this is not straightforward for closely-related, co-existing species that are difficult to distinguish using simple phenotypic or genetic approaches. Coregonids are of cultural and economic importance across Europe but have faced a multitude of pressures over the last century. Yet genomic management tools are lacking. In Lake Constance, a large pre-alpine lake, stocks have drastically collapsed due to a multitude of pressures, leading to a fishery closure. Here, we adopt a cost-effective, whole genome sequencing approach for lake-wide assessment of stock composition, spatial distribution and genetic diversity of highly admixed Lake Constance whitefish (Coregonus spp.). By sequencing 983 adult and larval genomes, we show that nearly 90% of the stock is made up by one of three species, the Gangfisch (C. macrophthalmus), and define the genetic relationship between Upper and Lower Lake Constance whitefish stocks. We also identified strong mixing between Gangfisch and Blaufelchen (C. wartmanni) on traditionally specific-specific spawning grounds, and detected strong admixture in larvae, with potentially drastic impacts on the effectiveness of hatchery supplementation and stocking. Despite the collapse and admixture, species still exhibit low to moderate levels of genetic diversity, maintain ecologically-relevant genetic differences, and seem to show differences in habitat use. Overall, we present a cost-effective, translatable tool for stock-wide sequencing and genetically-informed fisheries management, with our results calling for the re-evaluation of current management practices to avoid the potential genetic mixing between species.

ecology↗

bioRxiv2025

Prevalence of zoonotic hepatic nematode varies with small mammal community diversity across a heterogenous landscape in Eastern Uganda

Identifying key drivers of pathogen infection prevalence and intensity in wildlife is essential to understand disease dispersal and transmission. Calodium hepatica (syn. Capillaria hepatica) is a generalist nematode that infects liver parenchyma of mammals worldwide and is capable of human infections. Prevalence ranges from 0-100% in wildlife, often varying across small geographic areas, making it an ideal parasite for understanding ecological drivers of variation. Here, we quantify prevalence of Calodium hepatica and present initial surveys of synanthropic small mammals in four villages representing differing land cover. Cross-sectional rodent trapping was conducted within and around households over consecutive dry seasons in Eastern Uganda. 18s rRNA gene of C. hepatica was amplified and a sub-set of PCR products sequenced to confirm presence of C. hepatica. Landscape structural diversity was classified by tree crown density and mean canopy height derived from 30m LiDAR data within a 0.5km buffer. Multivariable binomial generalised linear models were fit to C. hepatica prevalence. C. hepatica infection was common (overall 34.5%, CI95% 27.9-41.0) and found in rodent and shrew species inside and outside residences. We observe village-level differences in prevalence (18.2%-75.0%), with higher C. hepatica prevalence associated with higher relative proportion of Rattus rattus to other species (aOR=2.22 CI95% 1.30-3.85). Host diversity appears to be protective against parasite prevalence. Differences in molecular and macroscopy identification highlight challenges in diagnosis and a need for more specialized molecular tools. Further investigation is required to understand individual host and community variation in pathogen infection intensity and implications for zoonotic risk. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=127 SRC="FIGDIR/small/674808v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@e9cfdaorg.highwire.dtl.DTLVardef@4d0f6dorg.highwire.dtl.DTLVardef@12fe43dorg.highwire.dtl.DTLVardef@1318d83_HPS_FORMAT_FIGEXP M_FIG C_FIG Key FindingsO_LIZoonotic reservoirs, including Rattus rattus, Mastomys erythroleucus and Crocidura olivieri, are abundant in human-modified habitats and show elevated levels of household incursion C_LIO_LIHigh prevalence of Calodium hepatica, a nematode endoparasite, was identified in a range of small mammal species C_LIO_LIHigher proportion of native small mammal species relative to Rattus rattus appears protective against zoonotic pathogen load, with higher village-level C. hepatica prevalence in ecologically depleted sites C_LIO_LISmall-holder agriculture may provide a dilution effect through secondary wildlife support and small mammal competition, while dense village settings potentiate C. hepatica prevalence C_LI

ecology↗

bioRxiv2025

Human Skin Model from 15 GHz to 110 GHz

In the recently revised guidelines for electromagnetic safety, basic restrictions expressed in terms of the absorbed power density (APD) at frequencies higher than 6 GHz were introduced. Testing for APD compliance of wireless devices requires experimental and numerical body models or phantoms that conservatively reproduce the absorption characteristics of human skin. Previous studies of APD indicate that frequency-dependent impedance-matching effects are caused by the low-permittivity stratum corneum (SC) layer. The objective of this study is to complement previous work (Christ et al., 2020) and to develop dispersive dielectric models to represent reflection and absorption of electromagnetic fields at the surface of the skin across a frequency range up to 110 GHz. The reflection coefficient of the skin of human volunteers was measured at frequencies of 15 to 43 GHz with open waveguide probes, complementing previous data from 45 to 110 GHz (Christ et al., 2020). The volunteers represented both sexes and different age groups and occupations; measurements were made at various regions of the body. The statistical analysis of the results show that the reflection coefficient follows a normal distribution in regions where the SC is relatively thin, which permits development of a conservative skin model that covers the 95th percentile of the tested population. As expected, in regions where the SC is thicker, e.g., the palms, the reflection coefficient is not normally distributed, because the thickness of the SC depends on the mechanical stress and friction to which the hands are exposed during routine daily activities. There was no evidence of relevant differences due to sex, but there is evidence for a slight age-dependent difference. The measured data - via fitting to the numerical model - allow the derivation of two-layer dielectric dispersive models that represent absorption and reflection at the surface of the skin with known uncertainty. The proposed models can be used to conservatively demonstrate compliance with the APD limits of wireless devices operating at frequencies of up to 110 GHz in any of the 5G and 6G bands defined. HighlightsO_LIbroadband evaluation of the skin reflection coefficient with open waveguide probes; C_LIO_LIcorroboration of increased absorption of millimeter wave radiation in body regions with increased stratum corneum thickness; C_LIO_LIdispersive dielectric models representing reflection and absorption at the skin surface with known population coverage. C_LI

bioengineering↗

bioRxiv2024

Genetic diversity, population structure and differentiation of farmed and wild African catfish (Clarias gariepinus) in Nigeria

The African catfish (Clarias gariepinus) is a commercially important species, for both fisheries and aquaculture, and is now the most commonly farmed fish in sub-Saharan Africa. However, knowledge about the genetic diversity and population structure of wild and farmed populations, which is crucial for effective conservation and sustainable aquaculture management, is scarce. Using mitochondrial DNA (mtDNA) cytochrome c oxidase 1 gene (COI) sequencing and genomic analysis using triple restriction site-associated DNA sequencing (3RAD), we investigated the genetic diversity and population structure of farmed and wild C. gariepinus populations from Nigeria, including an albino form found in the wild. Eleven COI haplotypes were identified, of which seven were unique to wild samples. Wild sampling sites had a slightly broader range and higher maximum values for observed heterozygosity (Ho = 0.109 - 0.165), expected heterozygosity (He = 0.111 - 0.216), and nucleotide diversity (pi = 0.125 - 0.225) compared to the farmed populations (Ho = 0.118 - 0.147, He = 0.112-0.144, pi = 0.117 - 0.151). Conversely, genetic differentiation (Fst) was higher among farmed sampling sites compared to the wild ones and there was high genetic differentiation between the farmed and wild C. gariepinus sampling sites (Fst = 0.31 - 0.47). Despite evidence for admixture for both farmed and wild fish, there was little evidence of admixture between the two groups. Nevertheless, both mtDNA and 3RAD data strongly suggested that the albino fish, collected from the wild, were in fact farm escapees. Despite overall differentiation farmed genotypes suggesting that overall genetic integrity of wild fish has been maintained, this evidence of escape provides a warning about potential risks of increasing aquaculture activities. Specifically, this indicates the need for greater regulation of fish farms to monitor and reduce the risk of escapes.

genomics↗

bioRxiv2024

Safety of Non-invasive Brain Stimulation in Patients with Implants: A Computational Study

ObjectiveNon-invasive brain stimulation (NIBS) methodologies, such as transcranial electric (tES) and magnetic stimulation are increasingly employed for therapeutic, diagnostic, or research purposes. The concurrent presence of active or passive implants can pose safety risks, affect the NIBS delivery, or generate confounding signals. A systematic investigation is required to understand the interaction mechanisms, quantify exposure, assess safety, and establish guidance for NIBS applications. ApproachWe used measurements, simplified generic, and detailed anatomical modeling to: (i) systematically analyze exposure conditions with passive and active implants, considering local field enhancement, exposure dosimetry, tissue heating and neuromodulation, capacitive lead current injection, low-impedance pathways between electrode contacts, and insulation damage; (ii) identify safety metrics and efficient prediction strategies; (iii) quantify these metrics in relevant exposure cases and (iv) identify worst case conditions. Various aspects including implant design, positioning, scar tissue formation, anisotropy, and frequency were investigated. ResultsAt typical tES frequencies, local enhancement of dosimetric exposure quantities can reach up to one order of magnitude for DBS and SEEG implants (more for elongated passive implants), potentially resulting in unwanted neuromodulation that can confound results but is still 2-3 orders of magnitude lower than active DBS. Under worst-case conditions, capacitive current injection in the lead of active implants can produce local exposures of similar magnitude as the passive field enhancement, while capacitive pathways between contacts are negligible. Above 10 kHz, applied current magnitudes increase, necessitating consideration of tissue heating. Furthermore, capacitive effects become more prominent, leading to current injection that can reach DBS-like levels. Adverse effects from abandoned/damaged leads in direct electrode vicinity cannot be excluded. SignificanceSafety related concerns of tES application in the presence of implants are systematically identified and explored, resulting in specific and quantitative guidance and establishing a basis for safety standards. Furthermore, several methods for reducing risks are suggested.

bioengineering↗

bioRxiv2023

Exploring the impact of read clustering thresholds on RADseq-based systematics: an empirical example from European amphibians.

Restriction site-Associated DNA sequencing (RADseq) has great potential for genome-wide systematics studies of non-model organisms. However, accurately assembling RADseq reads into orthologous loci remains a major challenge in the absence of a reference genome. Traditional assembly pipelines cluster putative orthologous sequences based on a user-defined clustering threshold. Because improper clustering of orthologs is expected to affect results in downstream analyses, it is crucial to design pipelines for empirically optimizing the clustering threshold. While this issue has been largely discussed from a population genomics perspective, it remains understudied in the context of phylogenomics and coalescent species delimitation. To address this issue, we generated RADseq assemblies of representatives of the amphibian genera Discoglossus, Rana, Lissotriton and Triturus using a wide range of clustering thresholds. Particularly, we studied the effects of the intra-sample Clustering Threshold (iCT) and between-sample Clustering Threshold (bCT) separately, as both are expected to differ in multi-species data sets. The obtained assemblies were used for downstream inference of concatenation-based phylogenies, and multi-species coalescent species trees and species delimitation. The results were evaluated in the light of a reference genome-wide phylogeny calculated from newly generated Hybrid-Enrichment markers, as well as extensive background knowledge on the species systematics. Overall, our analyses show that the inferred topologies and their resolution are resilient to changes of the iCT and bCT, regardless of the analytical method employed. Except for some extreme clustering thresholds, all assemblies yielded identical, well-supported inter-species relationships that were mostly congruent with those inferred from the reference Hybrid-Enrichment data set. Similarly, coalescent species delimitation was consistent among similarity threshold values. However, we identified a strong effect of the bCT on the branch lengths of concatenation and species trees, with higher bCTs yielding trees with shorter branches, which might be a pitfall for downstream inferences of evolutionary rates. Our results suggest that the choice of assembly parameters for RADseq data in the context of shallow phylogenomics might be less challenging than previously thought. Finally, we propose a pipeline for empirical optimization of the iCT and bCT, implemented in optiRADCT, a series of scripts readily usable for future RADseq studies.

evolutionary biology↗