Biology subjects

Peck, M. A.

Publications and source records attributed to Peck, M. A..

7 recordsLinked to original sources

bioRxiv2026

Projected ecosystem responses to environmental changes associated with offshore wind farms and ocean warming

Offshore wind farms (OWFs) are rapidly expanding to meet growing demands for renewable energy, with development expected to extend further offshore into deeper waters. Given this expanded human footprint, it is important to better understand the long-term ecological consequences of OWFs and how these may interact with ongoing climate change. We used the coupled hydrodynamic-ecosystem-biogeochemical water-column model (GOTM-ERSEM-BFM) to investigate ecosystem-wide responses to environmental changes associated with OWFs and climate warming. Specifically, we examined OWF-related scenarios of reduced benthic suspension-feeding activity, representing potential effects of contaminant emissions from OWFs, and reduced wind forcing, together with increased sea surface temperature. The scenarios were simulated individually and in combination to explore potential interactive effects. These scenarios were simulated at two contrasting locations in the North Sea, representing a well-mixed coastal site and a seasonally stratified offshore site. The coastal site exhibited comparatively modest ecosystem responses across the scenarios, whereas responses were generally stronger at the deeper offshore site. At the offshore site, changes in stratification altered vertical nutrient dynamics and contributed to pronounced differences in ecosystem responses between the surface and bottom layers. Our results demonstrate that ecosystem responses to OWF-related and climate-driven environmental changes are strongly dependent on local environmental conditions, suggesting that ecological consequences may differ substantially as wind farm development expands from shallower to deeper environments.

ecology↗

bioRxiv2023

Acclimation Capacity to Global Warming of Amphibians and Freshwater Fishes: Drivers, Patterns, and Data Limitations

Amphibians and fishes play a central role in shaping the structure and function of freshwater environments. These organisms have a limited capacity to disperse across different habitats and the thermal buffer offered by freshwater systems is small. Understanding determinants and patterns of their physiological sensitivity across life history is, therefore, imperative to predicting the impacts of climate change in freshwater systems. Based on a systematic literature review including 345 experiments with 998 estimates on 96 amphibian (Anura/Caudata) and 93 freshwater fish species (Teleostei), we conducted a quantitative synthesis to explore phylogenetic, ontogenetic, and biogeographic (thermal adaptation) patterns in upper thermal tolerance (CTmax) and thermal acclimation capacity (Acclimation Response Ratio, ARR) as well as the influence of the methodology used to assess these thermal traits using a conditional inference tree analysis. We found globally consistent patterns in CTmax and ARR, with phylogeny (taxa/order), experimental methodology, climatic origin, and life stage as significant determinants of thermal traits. The analysis demonstrated that CTmax does not primarily depend on the climatic origin but on experimental acclimation temperature and duration, and life stage. Higher acclimation temperatures and longer acclimation times led to higher CTmax values, whereby Anuran larvae revealed a higher CTmax than older life stages. The ARR of freshwater fishes was more than twice that of amphibians. Differences in ARR between life stages were not significant. In addition to phylogenetic differences, we found that ARR also depended on acclimation duration, ramping rate, and adaptation to local temperature variability. However, the amount of data on early life stages is too small, methodologically inconsistent, and phylogenetically unbalanced to identify potential life cycle bottlenecks in thermal traits. We therefore propose methods to improve the robustness and comparability of CTmax/ARR data across species and life stages, which is crucial for the conservation of freshwater biodiversity under climate change.

ecology↗

bioRxiv2023

Local reflects global: Life-stage dependent changes in the phenology of coastal habitat use by North Sea herring

Climate warming is affecting the suitability and utilisation of coastal habitats by marine fishes around the world. Phenological changes are an important indicator of population responses to climate-induced changes but remain difficult to detect in marine fish populations. The design of large-scale monitoring surveys does not allow fine-grained temporal inference of population responses, while the responses of ecologically and economically important species groups such as small pelagic fish are particularly sensitive to temporal resolution. Here, we use the longest, highest-resolution time series of species composition and abundance of marine fishes in northern Europe to detect possible phenological shifts in the small pelagic North Sea herring. We detect a clear forward temporal shift in the phenology of nearshore habitat use by small juvenile North Sea herring. This forward shift can best be explained by changes in water temperatures in the North Sea. We find that reducing the temporal resolution of our data to reflect the resolution typical of larger surveys makes it difficult to detect phenological shifts and drastically reduces the effect sizes of environmental covariates such as seawater temperature. Our study therefore shows how local, long-term, high-resolution time series of fish catches are essential to understand the general phenological responses of marine fishes to climate warming and to define ecological indicators of system-level changes.

ecology↗

bioRxiv2022

k2v: A Containerized Workflow for Creating VCF Files from Kintelligence Targeted Sequencing Data

The ForenSeq Kintelligence kit developed by Verogen is a targeted Illumina sequencing assay that genotypes 10,230 single nucleotide polymorphisms designed for forensic genetic genealogy, forensic DNA phenotyping, and ancestry inference. We developed k2v, a containerized workflow for creating standard specification-compliant variant call format (VCF) files from the custom output data produced by the Kintelligence Universal Analysis Software. VCF files produced with k2v enable the use of many pre-existing, widely used, community-developed tools for manipulating and analyzing genetic data in the standard VCF format. Here we describe the k2v implementation, demonstrate its usage, and use the VCF produced by k2v to demonstrate downstream analyses that can easily be performed with pre-existing tools using VCF data as input: concordance analysis, ancestry inference, and relationship estimation. k2v is distributed as a Docker container available on Docker Hub. Documentation and source code for k2v is freely available under the GNU Public License (GPL-3.0) at https://github.com/signaturescience/k2v.

bioinformatics↗

bioRxiv2022

Internal Validation of the ForenSeq Kintelligence Kit for Application to Forensic Genetic Genealogy

Forensic Genetic Genealogy (FGG) requires high density single nucleotide polymorphism (SNP) profiles to infer distant relationships. The ForenSeq Kintelligence kit is a recently developed method targeting approximately 10,000 SNPs that were selected to be compatible with genetic genealogy databases, while avoiding medically relevant SNPs. The targeted PCR method is ideal for low input and degraded samples, which are particularly challenging for microarray analysis. We made modifications to library preparation and sample pooling to further enhance the performance of low input samples. To align this FGG method with forensic laboratory standards, we performed an internal validation study in accordance with the Scientific Working Group on DNA Analysis Methods Validation Guidelines for DNA Analysis Methods. The sensitivity and precision and accuracy studies produced accurate and reliable profiles down to 0.05 ng of DNA. The mixture and contamination studies demonstrated that the method could detect the presence of a minor contributor down to 0.02 ng, while system wide contamination was negligible. Nonprobative bone, fired shell casing, and adhesive tape samples performed well with inputs ranging from 0.05 to 1.0 ng of DNA. A bone with a high degradation index and tested at 0.1 ng DNA input resulted in a call rate of 92.9% and a heterozygosity rate of 0.387. We demonstrated the importance of both call rate and heterozygosity rate to assess profile performance. Validating FGG methods is critical to ensuring the reliability and utility of SNP profiles that will be uploaded to genetic genealogy databases for the purpose of generating investigative leads.

genomics↗

bioRxiv2022

Developmental Validation of the Illumina Infinium Assay using the Global Screening Array (GSA) on the iScan System for use in Forensic Laboratories

Microarray processing, which interrogates hundreds of thousands of single nucleotide polymorphisms (SNPs) across the human genome, has recently gained traction in forensics due to its use in forensic genetic genealogy, which is based on analysis using SNPs to compare distant relatives in publicly curated databases for the purposes of developing investigative leads or identifying human remains. To date, there has been no published developmental validation of microarray processing using the Scientific Working Group on DNA Analysis Methods (SWGDAM) Validation Guidelines for DNA Analysis Methods and Federal Bureau of Investigation Quality Assurance Standards. Validation of these methods are warranted to identify samples suitable for microarray analysis and to assess the quality of the data obtained prior to upload to genealogical databases. In this study, we validated the Global Screening Array (GSA) for use in forensic investigations according to SWGDAM guidelines, including the following studies: precision and accuracy, sensitivity, contamination, degradation, species specificity, mock case-type samples, mixtures, repeatability and reproducibility, and stability. Results indicated accurate genotype calls with SNP call rates >95% at DNA input as low as 0.20 ng. In addition to SNP call rate, we developed interpretation thresholds for signal intensity and heterozygosity to allow for sample quality assessment and identification of highly degraded and/or non-human DNA. This study demonstrates that high quality data can be generated from multiple sample types, including mock forensic evidence that simulated the challenges that are often encountered in forensic cold cases.

genomics↗

bioRxiv2020

Climate-risk to European fisheries and coastal communities

With the majority of the global human population living in coastal regions, correctly characterising the climate risk that ocean-dependent communities and businesses are exposed to is key to prioritising the finite resources available to support adaptation. We apply a climate risk analysis across the European fisheries sector for the first time to identify the most at-risk fishing fleets and coastal regions and then link the two analyses together. We employ a novel approach combining biological traits with physiological metrics to differentiate climate hazards between 556 populations of fish and use these to assess the relative climate risk for 380 fishing fleets and 105 coastal regions in Europe. Countries in southeast Europe as well as the UK have the highest risks to both fishing fleets and coastal regions overall while, in other countries, the risk-profile is greater at either the fleet level or at the regional level. European fisheries face a diversity of challenges posed by climate change and climate adaptation, therefore, needs to be tailored to each country, region and fleets specific situation. Our analysis supports this process by highlighting where and what adaptation measures might be needed and informing where policy and business responses could have the greatest impact. Significance StatementWe present a novel climate risk analysis for i) 105 ocean-dependent communities and ii) 380 fishing fleets in Europe. Our unique approach provides a perspective over the climate risks in this diverse and populous continent that is unprecedented in both its breadth and detail. We show that countries in southeast Europe as well as the UK have the highest climate risk overall, both in terms of fishing fleets and coastal communities. Substantial variation in climate risk is seen even within countries, emphasizing that climate adaptation interventions need to be tailored to the specific characteristics of the fleet or community. A focus on sustainable fisheries management and diversification of fish portfolios can reduce climate risks across the board.

ecology↗