Markussen, B. | Search bioRxiv

bioRxiv2023

Rapid and continuing regional decline of butterflies in eastern Denmark 1993-2019

O_LIMany butterfly populations respond negatively to land-use intensification in human-dominated landscapes. However, networks of protected sites have been established with the aim to halt species loss. C_LIO_LIWe undertook annual surveys of all populations of 22 uncommon butterfly species in eastern Denmark during the period 2014-2019 and compared to a systematic atlas survey done 1989-1993, in order to assess trends in regional occupancy of species. C_LIO_LIThree out of 22 species went regionally extinct between 1993 and 2015. One species sustained a single population through the study period. Logistic regression for the remaining 18 species showed 10 to be in strong decline from 1993 to 2015, two showed a declining trend and six had stable trends. For all species except one, the declining trend continued 2015-2019. For five species, a sustained strong decline was evident. C_LIO_LIIn 1993, the total count of populations for all 22 butterfly species was 565, which by 2019 had declined to 158 populations (a 72 % loss over 26 years). From 2015 to 2019, the total count of populations further shrank from 200 to 158 (a 21 % decline over just four years). C_LIO_LILegal protection of areas (Natura 2000 and Danish Nature Protection Act [§]3) was, unexpectedly, not associated with lower probability of local extinction for butterfly population. The observed sustained decline across species suggests an overall low efficiency of the network of protected sites, probably due to a combination of misguided management regimes and payment of extinction debts from the past. C_LI

ecology↗

bioRxiv2022

Parchment Glutamine Index (PQI): A novel method to estimate glutamine deamidation levels in parchment collagen obtained from low-quality MALDI-TOF data

Parchment was used as a writing material in the Middle Ages and was made using animal skins by liming them with Ca(OH)2. During liming, collagen peptides containing Glutamine (Q) undergo deamidation resulting in a mass shift of 0.984 Da. Assessing the extent of deamidation can inform us about parchment production patterns and quality. In this study, we propose a simple three-step workflow, developed as an R package called MALDIpqi(), to estimate deamidation in parchment derived collagen using low-resolution MALDI-TOF spectra. After pre-processing raw spectra, we used weighted least-squares linear regression to estimate Q deamidation levels from the convoluted isotopic envelope for seven collagen-peptide markers. Finally, we employed a linear mixed effect model to predict the overall deamidation level of a parchment sample termed Parchment Glutamine Index (PQI). To test the robustness of the workflow, we applied MALDIpqi() to previously published ZooMS data generated from almost an entire library of the Cistercian monastery at Orval Abbey, Belgium. In addition to reliably predicting PQI, we observed interesting patterns pertaining to parchment production. MALDIpqi() holds excellent potential for biocodicological and other archaeological studies involving collagen, such as bone, but we also foresee its application in the food and biomedical industry.

bioinformatics↗