Biology subjects

Lodge, D.

Publications and source records attributed to Lodge, D..

4 recordsLinked to original sources

bioRxiv2025

Environmental DNA monitoring of waterfowl reveals community changes during migration

Large-scale visual surveys are an integral part of waterfowl conservation and management programs. In this paper we explore the possibility of using environmental DNA-based surveys as a cost-efficient, complementary tool to estimate populations of North American waterfowl species. To achieve this, we first evaluated the performance of all currently available avian metabarcoding primers and compared them to newly designed primers targeting the mitochondrial ND2 gene within the Anatidae tribes of North America. All the existing avian assays showed strong cross-priming amplification with other vertebrates. In contrast, in-silico analyses of our waterfowl targeted assays showed a high degree (>90%) of avian specificity, encompassing all the 132 Anatidae species sequenced thus far. We used this targeted metabarcoding approach to track the temporal variation in the relative abundance of waterfowl species during the fall migration at Montezuma National Wildlife Refuge, New York, a major resting area for waterfowl on their journey to and from North American nesting areas. We compared eDNA results with visual surveys conducted by us and from those reported on eBird. Our results showed that eDNA detected all waterfowl species (n= 25) during fall migration. Positive correlations existed between standardized eDNA read counts and the relative abundance of waterfowl species as reported in eBird on the day of sampling and up to five days prior. However, this approach did not provide a good metric for absolute abundance of waterfowl species: only 8 out of 25 waterfowl species showed significant correlations between the number of eDNA reads and the total abundance of birds. Overall, while eDNA-targeted metabarcoding has not yet been applied to study bird communities extensively, our results demonstrate that this technique can be used as an effective complementary tool for assessing species composition of waterfowl communities and estimating relative abundance of species within those communities.

genetics↗

bioRxiv2023

Extrasynaptic localization is essential for α5GABAA receptor modulation of dopamine system function

Dopamine system dysfunction, observed in animal models with psychosis-like symptomatology, can be restored by targeting Gamma-Aminobutyric Acid type A receptors (GABAAR) containing the 5, but not 1, subunit in the ventral hippocampus (vHipp). The reason for this discrepancy in efficacy remains elusive; however, one key difference is that 1GABAARs are primarily located in the synapse, whereas 5GABAARs are mostly extrasynaptic. To test whether receptor location is responsible for this difference in efficacy, we injected a small interfering ribonucleic acid (siRNA) into the vHipp to knock down radixin, a scaffolding protein that holds 5GABAARs in the extrasynaptic space. We then administered GL-II-73, a positive allosteric modulator of 5GABAARs (5-PAM) known to reverse shock-induced deficits in dopamine system function, to determine if shifting 5GABAARs from the extrasynaptic space to the synapse would prevent the effects of 5-PAM on dopamine system function. As expected, knockdown of radixin significantly decreased radixin-associated 5GABAARs and increased the proportion of synaptic 5GABAARs, without changing the overall expression of 5GABAARs. Importantly, GL-II-73 was no longer able to modulate dopamine neuron activity in radixin-knockdown rats, indicating that the extrasynaptic localization of 5GABAARs is critical for hippocampal modulation of the dopamine system. These results may have important implications for clinical use of GL-II-73, as periods of high hippocampal activity appear to favor synaptic 5GABAARs, thus efficacy may be diminished in conditions where aberrant hippocampal activity is present. Significance StatementDopamine activity is known to be altered in both psychosis patients and in animal models, with promising new antipsychotics restoring normal dopamine system function. One such drug is GL-II-73, a positive allosteric modulator of 5GABAARs (5-PAM). Interestingly, previous research has shown that a positive allosteric modulator of 1GABAARs (1-PAM) does not share this ability, even when directly given to the ventral hippocampus, a region known to modulate dopamine activity. One potential explanation for this difference we examined in this study is that 1GABAARs are primarily located in the synapse, whereas 5GABAARs are mostly extrasynaptic. Determining the mechanism of this differential efficacy could lead to the refinement of antipsychotic treatment and improve patient outcomes overall.

neuroscience↗

bioRxiv2021

Global port survey quantifies commercial shippings effect on biodiversity

Spread of nonindigenous organisms by shipping is one of the largest threats to coastal ecosystems. Limited monitoring and understanding of this phenomenon currently hinder development of effective prevention policies. Surveying ports in North America, South America, Europe, Southeast Asia, and Australia we explored environmental DNA community profiles evident of ship-born species spread. We found that community similarities between ports increased with the number of ship voyages, particularly if the ports had similar environments, and when indirect stepping-stone connections were considered. We also found 57 known non-indigenous taxa, some in hitherto unreported locations. We demonstrate the usefulness of eDNA-based tools for global biodiversity surveys, and highlight that shipping homogenizes biodiversity in predictable that could inform policy and management.

ecology↗

bioRxiv2019

Higher-order patterns of aquatic species spread through the global shipping network

The introduction and establishment of non-indigenous species (NIS) through global ship movements is a significant threat to marine ecosystems and economies. While ballast-vectored invasions have been partly addressed by some national policies and an international agreement regulating the concentrations of organisms in ballast water, biofouling-vectored invasions remain a large risk. Development of additional realistic and cost-effective ship-borne NIS policies requires an accurate estimation of NIS spread risk from both ballast water and biofouling. In this paper, we demonstrate that first-order Markov assumptions limit accurate modeling of NIS spread risks through the global shipping network. In contrast, we show that higher-order patterns overcome this limitation by revealing indirect pathways of NIS transfer. We accomplish this by developing Species Flow Higher-Order Networks (SF-HON), which we developed independently for ballast and biofouling, for comparison with first-order Markovian models of ballast and biofouling. We evaluated SF-HON predictions using the largest available datasets of invasive species for Europe and the United States. We show that not only does SF-HON yield more accurate NIS spread risk predictions than first-order models and existing higher-order models, but also that there are important differences in NIS spread via the ballast and biofouling vectors. Our work provides information that policymakers can use to develop more efficient and targeted prevention strategies for ship-borne NIS spread management, especially as management of biofouling is of increasing concern.

ecology↗