Biology subjects

Madden, J. R.

Publications and source records attributed to Madden, J. R..

5 recordsLinked to original sources

bioRxiv2026

The dispersal of released pheasants and the risk of their intrusion into English protected areas

Large-scale annual releases of pheasants Phasianus colchicus and their subsequent management for recreational shooting create various ecological impacts in the UK. While effects at release sites are fairly well understood, dispersing birds may influence areas farther away. If they enter ecologically important but sensitive protected areas (PAs), any negative impacts could be especially harmful. Using tracking data, from 766 birds across 10 sites, we estimated survival and dispersal of released pheasants and applied these patterns to gamebird release records near English PAs to gauge intrusion risk. Of 2,885 registered release sites, just over half lay within 2 km of a PA. A large number of shoots release relatively few birds while a small number release many birds. Thus, numbers expected to enter a particular PA likely depend both on the size of releases and proximity to the PA. We estimate that, at a national level, a maximum of between 525,000 and 784,000 pheasants might be found within PAs very soon after release, representing around 1.7% of all the pheasants released annually. This number declines over the months after release until in February, we estimate that there are between 131,000 and 196,000 pheasants (0.4% of the total release) might be found within PAs. The critical metric by which ecological damage might occur is their density within PAs. Mean densities soon after release averaged 12.0 birds/ha in PAs within 250 m of release sites. This density declined markedly both in time (as birds died) and space (as they moved further from the pen as potential areas increased). By November, densities in PAs 500-1000m from release sites peaked at 0.5 birds/ha, falling to 0.16 birds/ha in February. These estimated densities are around two orders of magnitude lower than those known to cause strong, lasting impacts within release pens. The results are subject to assumptions about movement behaviour, game management and bias in registration. Despite these constraints, considerable local variation exists, with a minority of high-volume release sites very near PAs posing the greatest potential ecological risk.

ecology↗

bioRxiv2022

A twin UGUA motif directs the balance between gene isoforms through CFIm and the mTORC1 signaling pathway.

Alternative polyadenylation (APA) generates mRNA isoforms and diversifies gene expression. Here we report the identification of a twin UGUA motif, UGUAYUGUA, and its function in APA. Applying cTag-PAPERCLIP to Tsc1 conditional knockout mice, we discovered that the mTORC1 pathway balances expression of Trim9 isoforms. We showed that CFIm components, CPSF6 and NUDT21, promote Trim9/TRIM9-S expression in mouse and human, and we identified an evolutionarily conserved UGUAYUGUA motif that is critical for this regulation. We found additional CPSF6-regulated polyadenylation sites (PASs) with similar twin UGUA motifs in human, and we experimentally validated the twin UGUA motif functionality in BMPR1B, MOB4, and BRD4-L. Importantly, we showed that inserting a twin UGUA motif into a heterologous PAS was sufficient to confer regulation by CPSF6 and mTORC1. Our study reveals an evolutionarily conserved mechanism to regulate gene isoform expression and implicates possible gene isoform imbalance in cancer and neurologic disorders with mTORC1 pathway dysregulation.

molecular biology↗

bioRxiv2021

Scoping the Line Up: A Comparison of Biomonitoring Methodologies for Surf Zone Fish Communities

Surf zones are highly dynamic marine ecosystems that are subject to increasing anthropogenic and climatic pressures, posing multiple challenges for biomonitoring. Traditional methods such as seines and hook and line surveys are often labor intensive, taxonomically biased, and can be physically hazardous. Emerging techniques, such as baited remote underwater video (BRUV) and environmental DNA (eDNA) are promising nondestructive tools for assessing marine biodiversity in surf zones of sandy beaches. Here we compare the relative performance of beach seines, BRUV, and eDNA in characterizing community composition of bony (teleost) and cartilaginous (elasmobranch) fishes of surf zones at 18 open coast sandy beaches in southern California. Seine and BRUV surveys captured overlapping, but distinct fish communities with 50% (18/36) of detected species shared. BRUV surveys more frequently detected larger species (e.g. sharks and rays) while seines more frequently detected one of the most abundant species, barred surfperch (Amphistichus argenteus). In contrast, eDNA metabarcoding captured 83.3% (30/36) of all fishes observed in seine and BRUV surveys plus 59 additional species, including 13 that frequent surf zone habitats. eDNA approaches showed significantly higher sensitivity than seine and BRUV methods and more consistently detected 29 of the 30 (96.7%) jointly observed species across beaches. The six species detected by BRUV/seines, but not eDNA either lacked reference sequences, were only resolved at higher taxonomic ranks (e.g. Embiotocidae surfperches), or were detected below occupancy thresholds. Low site-species overlap between methods limited comparisons of richness and abundance estimates, highlighting the challenge of comparing biomonitoring approaches. Despite potential for improvement, results overall demonstrate that eDNA can provide a cost-effective tool for long-term surf zone monitoring that complements data from seine and BRUV surveys, allowing more comprehensive surveys of vertebrate diversity in surf zone habitats.

ecology↗

bioRxiv2020

HOW MANY GAMEBIRDS ARE RELEASED IN THE UK EACH YEAR?

Large numbers of gamebirds (pheasants Phasianus colchicus, red-legged partridges Alectoris rufa and mallard Anus platyrhynchos) are released annually in the UK to support recreational shooting. It is important to know how many of these birds are being released because their release and management has ecological effects on the wildlife and habitats of the UK. There is little regulation governing their release and consequently the numbers being released are unknown. I made 71 estimates of the numbers released based on numbers being reported formally via import controls and the Poultry Register, or extrapolated based on the breeding outputs of reared birds, or extrapolated based on the likely numbers and behaviour of shoots, or extrapolated based on observations of surviving birds. Based on the set of these estimates that fall within credible boundaries (ranging from 14.3 to 70.1 million birds), I estimate a mean of 34.5 million birds (95%CI 30.9-38.1 million) and a median value of 32.1 million (IQR 22.0-44.9 million) being released. This suggests that 24.3-25.3 million pheasants, 4.2-9.4 million partridges and 1.0-4.9 million mallard are released annually in the UK. These figures are markedly lower than previous published estimates and I discuss why such differences may occur. I set these figures in the context of the number and behaviour of shoots operating in the UK.

ecology↗

bioRxiv2019

Response learning confounds accurate assays of inhibitory control

The ability to inhibit prepotent actions towards rewards that are made inaccessible by transparent barriers has been considered to reflect capacities for inhibitory control (IC). Typically, subjects initially reach directly, and incorrectly, for the reward. With experience, subjects may inhibit this action and instead detour around barriers to access the reward. However, assays of IC are often measured across multiple trials, with the location of the reward remaining constant. Consequently, other cognitive processes, such as response learning (acquisition of a motor routine), may confound accurate assays of IC. We measured baseline IC capacities in pheasant chicks, Phasianus colchicus, using a transparent cylinder task. Birds were then divided into two training treatments, where they learned to access a reward placed behind a transparent barrier, but experienced differential reinforcement of a particular motor response. In the Stationary-Barrier treatment, the location of the barrier remained constant across trials. We therefore reinforced a fixed motor response, such as always go left, which birds could learn to aid their performance. Conversely, we alternated the location of the barrier across trials for birds in the Moving-Barrier treatment, and hence provided less reinforcement of their response learning. All birds then experienced a second presentation of the transparent cylinder task to assess whether differences in the training treatments influenced their subsequent capacities for IC. Birds in the Stationary-Barrier treatment showed a greater improvement in their subsequent IC performance after training compared to birds in the Moving-Barrier treatment. We therefore suggest that response learning aids IC performance on detour tasks. Consequently, non-target cognitive processes associated with different neural substrates appear to underlie performances on detour tasks, which may confound accurate assays of IC. Our findings question the construct validity of a commonly used paradigm that is widely considered to assess capacities for IC in humans and other animals.

animal behavior and cognition↗