Biology subjects

Cassey, P.

Publications and source records attributed to Cassey, P..

9 recordsLinked to original sources

bioRxiv2025

Strengthening Global Trade Regulation Through Targeted Listings on CITES Appendix III

Appendix III is an underutilized component of The Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES), comprising less than 2% (n = 519) of all listed species (January 2024). Appendix III uniquely offers unilateral protection for nationally protected species without requiring international consensus. Since CITES came into effect in 1975, 2,203 species have been added to Appendix III, including 875 endemic and 1,328 multi-country species. A total of 994 species have been delisted, mostly during CITES first decade. One-third of Appendix III species have been proposed for uplisting, with a 96% success rate and a median time of 3.3 years. Strengthening Appendix IIIs impact involves broader cooperation for species ranging from multiple countries, regular reviews, and utilizing Appendix III listings as a precursor for Appendix I and II proposals to enhance global biodiversity management.

ecology↗

bioRxiv2022

Leveraging a natural murine meiotic drive to suppress invasive populations

Invasive rodents, including house mice, are a major cause of environmental damage and biodiversity loss, particularly in island ecosystems. Eradication can be achieved through the distribution of rodenticide, but this approach is expensive to apply at scale, can have negative impacts (e.g. on non-target species, or through contamination), has animal ethics concerns, and has restrictions on where it can be used. Gene drives, which exhibit biased inheritance, have been proposed as a next generation strategy to control invasive alien pests and disease vectors. However, synthetic gene drives including CRISPR homing drives have proven to be technically challenging to develop in mice. The t haplotype is a naturally-occurring segregation distortion locus with highly biased transmission from heterozygous males. Here we propose a novel gene drive strategy for population suppression, tCRISPR, that leverages t haplotype bias and an embedded SpCas9/gRNA transgene to spread inactivating mutations in a haplosufficient female fertility gene. Using spatially explicit individual-based in silico modelling, we show that polyandry, sperm competition, dispersal, and transmission bias are critical factors for tCRISPR-mediated population suppression. Modelling of realistic parameter values indicates that tCRISPR can eradicate an island population of 200,000 mice while the unmodified t haplotype fails under the same conditions. We also demonstrate feasibility of this approach by engineering tCRISPR mice in a safe split drive format. tCRISPR mice exhibit high transmission of the modified t haplotype, and efficient generation and transmission of inactivating mutations in a recessive female fertility gene, crucially, at levels for which the modelling predicts that population eradication can occur. This is the first example of a feasible gene drive system for invasive alien rodent population control.

genetics↗

bioRxiv2022

The demand for wildlife not protected by the CITES multilateral treaty

The international wildlife trade presents severe conservation and environmental security risks. However, no international regulatory framework exists to monitor the trade of species not listed in the appendices of the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). We explored the composition and dynamics of internationally regulated versus non-regulated trade, focussing on importations of wild-caught terrestrial vertebrates entering the United States of America (US) from 2009-2018. The prominence of the US in global wildlife imports and its detailed data collection conventions allows a unique opportunity to formally assess this substantial but often overlooked and understudied component of the legal wildlife trade. We found 3.6 times the number of unlisted species in US imports compared with CITES-listed species (1,366 versus 378). CITES-listed species were more likely to face reported conservation threats relative to the unlisted species (71.7% vs 27.5%). Yet, we found 376 unlisted species facing conversation threats, 297 species with unknown population trends and 139 species without an evaluation by the IUCN Red List of Threatened Species. Unlisted species appeared novelly in imports at 5.5 times higher rates relative to CITES-listed species, where unlisted reptiles saw the largest rate of entry, averaging 53 unique species appearing in imports for the first time per year. Overall trade volumes were substantially larger for unlisted imports with approximately 11 times the number of animals relative to CITES-listed imports, however, import volumes were similar when compared at a species-by-species level. We found that the countries that were top exporters for CITES-listed shipments were mostly different from exporters of unlisted species. In highlighting the vulnerabilities of the wild-caught unlisted vertebrate trade entering the US and in the face of increasing global demand, we recommend governments adapt policies to monitor the trade of all wildlife.

ecology↗

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↗

bioRxiv2021

Concurrent invasions by European starlings (Sturnus vulgaris) suggest selection on shared genomic regions even after genetic bottlenecks

A species success during the invasion of new areas hinges on an interplay between demographic processes and the outcome of localized selection. Invasive European Starlings (Sturnus vulgaris) established populations in Australia and North America in the 19th century. Here, we compare whole-genome sequences among native and independently introduced European Starling populations from three continents to determine how demographic processes interact with rapid adaptive evolution to generate similar genetic patterns in these recent and replicated invasions. Our results confirm that a post-bottleneck expansion may in fact support local adaptation. We find that specific genomic regions have differentiated even on this short evolutionary timescale, and suggest that selection best explains differentiation in at least two of these regions. This infamous and highly mobile invader adapted to novel selection (e.g., extrinsic factors), perhaps in part due to the demographic boom intrinsic to many invasions.

evolutionary biology↗

bioRxiv2021

The integrated role of resource memory and scent-mediated territoriality in the emergence of home-ranges

Despite decades of animal movement research, an integrated understanding of the processes underlying the emergence of home-ranges remains inadequate. We explored the effects of integrating two key processes of home-ranging arising from individual movement decisions: (i) memory-based resource use; and (ii) scent-based territoriality. Both mechanisms together led to the formation of exclusive, resource- and population density-dependent home-ranges, which were responsive to perturbations in the conspecific environment (i.e., removing individuals). Home-range patterns (size, size skewness and overlap) were primarily influenced by memory and scent decay rate parameters, demonstrating that home-ranging is ultimately a balance between an animals inherent exploratory tendency and its desire to avoid conspecifics. Model application to a population of feral cats demonstrated that general space use patterns could be approximated through simulation, and replication of finer-scale space use patterns is plausible with further model development. Our modelling framework provides a foundation for sophisticated theoretical models of space use in interacting animals.

ecology↗

bioRxiv2021

Transcript- and annotation-guided genome assembly of the European starling

The European starling, Sturnus vulgaris, is an ecologically significant, globally invasive avian species that is also suffering from a major decline in its native range. Here, we present the genome assembly and long-read transcriptome of an Australian-sourced European starling (S. vulgaris vAU), and a second North American genome (S. vulgaris vNA), as complementary reference genomes for population genetic and evolutionary characterisation. S. vulgaris vAU combined 10x Genomics linked-reads, low-coverage Nanopore sequencing, and PacBio Iso-Seq full-length transcript scaffolding to generate a 1050 Mb assembly on 1,628 scaffolds (72.5 Mb scaffold N50). Species-specific transcript mapping and gene annotation revealed high structural and functional completeness (94.6% BUSCO completeness). Further scaffolding against the high-quality zebra finch (Taeniopygia guttata) genome assigned 98.6% of the assembly to 32 putative nuclear chromosome scaffolds. Rapid, recent advances in sequencing technologies and bioinformatics software have highlighted the need for evidence-based assessment of assembly decisions on a case-by-case basis. Using S. vulgaris vAU, we demonstrate how the multifunctional use of PacBio Iso-Seq transcript data and complementary homology-based annotation of sequential assembly steps (assessed using a new tool, SAAGA) can be used to assess, inform, and validate assembly workflow decisions. We also highlight some counter-intuitive behaviour in traditional BUSCO metrics, and present BO_SCPLOWUSCOMPC_SCPLOW, a complementary tool for assembly comparison designed to be robust to differences in assembly size and base-calling quality. Finally, we present a second starling assembly, S. vulgaris vNA, to facilitate comparative analysis and global genomic research on this ecologically important species.

genomics↗

bioRxiv2019

Local signatures of founding populations confound examination of adaptive divergence in invasive populations

A detailed understanding of population genetics in invasive populations helps us to identify drivers of successful introductions. Here, we investigate putative signals of selection in Australian populations of invasive common starlings, Sturnus vulgaris, and seek to understand how these have been influenced by introduction history. We use reduced representation sequencing to determine population structure, and identity Single Nucleotide Polymorphisms (SNPs) that are putatively under selection. We found that since their introduction into Australia, starling populations have become genetically differentiated despite the potential for high levels of dispersal, and that selection has facilitated their adaptation to the wide range of environmental conditions across their geographic range. Isolation by distance appears to have played a strong role in determining genetic substructure across the starlings Australian range. Analyses of candidate SNPs that are putatively under selection indicate that aridity, precipitation, and temperature may be important factors driving adaptive variation across the starlings invasive range in Australia. However, we also note that the historic introduction regime may leave footprints on sites flagged as being under adaptive selection, and encourage critical interpretation of selection analyses.

evolutionary biology↗

bioRxiv2019

Temperature drives the evolution and global distribution of avian eggshell colour

The survival of a birds egg depends upon their ability to maintain within strict thermal limits. Avian eggshell colours have long been considered a phenotype that can help them stay within these thermal limits, with dark eggs absorbing heat more rapidly than bright eggs. Although long disputed, evidence suggests that darker eggs do increase in temperature more rapidly than lighter eggs, explaining why dark eggs are often considered as a cost to trade-off against crypsis. Although studies have considered whether eggshell colours can confer an adaptive benefit, no study has demonstrated evidence that eggshell colours have actually adapted for this function. This would require data spanning a wide phylogenetic diversity of birds and a global spatial scale. Here we show evidence that darker and browner eggs have indeed evolved in cold climes, and that the thermoregulatory advantage for avian eggs is a stronger selective pressure in cold climates. Temperature alone predicted more than 80% of the global variation in eggshell colour and luminance. These patterns were directly related to avian nesting strategy, such that all relationships were stronger when eggs were exposed to incident solar radiation. Our data provide strong evidence that sunlight and nesting strategies are important selection pressures driving egg pigment evolution through their role in thermoregulation. Moreover, our study advances understanding of how traits have adapted to local temperatures, which is essential if we are to understand how organisms will be impacted by global climate change.

ecology↗