Urbanization of estuaries drastically changed existing shorelines and bathymetric contours, in turn modifying habitat for marine foundational species that host critical biodiversity. And yet we lack approaches to characterize a significant fraction of the biota that inhabit these ecosystems on time scales that align with rates of urbanization. Environmental DNA (or eDNA) metabarcoding that combines multiple assays targeting a broad range of taxonomic groups can provide a solution, but we need to determine whether the biological communities it detects ally with different habitats in these changing aquatic environments. In this study, we tested whether tree of life metabarcoding (ToL-metabarcoding) data extracted from filtered seawater samples correlated with four known geomorphic habitat zones across a heavily urbanized estuary (Sydney Harbour, Australia). Using this method, we substantially expanded our knowledge on the composition and spatial distribution of marine biodiversity across the tree of life in Sydney Harbour, particularly for organisms where existing records are sparse. Excluding terrestrial DNA inputs, we identified significant effects of both distance from the mouth of Sydney Harbour and geomorphic zone on biological community structure in the ToL-metabarcoding dataset (entire community), as well as in each of the taxonomic subgroups that we considered (fish, macroinvertebrates, algae and aquatic plants, bacteria). This effect appeared to be driven by taxa as a collective versus a few individual taxa, with each taxon explaining no more than 0.62% of the variation between geomorphic zones. Similarly, taxonomic richness was significantly higher within geomorphic zones with large sample sizes, but also decreased by 1% with each additional kilometer from the estuary mouth, a result consistent with a reduction in tidal inputs and available habitat in upper catchments. Based on these results, we suggest that ToL-metabarcoding can be used to benchmark biological monitoring in other urbanized estuaries globally, and in Sydney Harbour at future time points based on detection of bioindicators across the tree of life. We also suggest that robust biotic snapshots can be archived following extensive curation of taxonomic assignments that incorporates ecological affinities, supported by records from relevant and regional biodiversity repositories.

Fishes represent an important natural resource and yet their diversity and function in dynamic estuaries with relatively high levels of human pressure such as Sydney Harbour have rarely been quantified. Further, Eastern Australia supports the survival and persistence of an increasing number of tropical species found within temperate estuaries owing to increasing average ocean temperatures. A re-valuation of the number of fish species known from Sydney Harbour is therefore needed. In this study, we generated an up-to-date and annotated checklist of fishes recorded from Sydney Harbour based on verified natural history records as well as newly available citizen science records based on opportunistic observations and structured surveys. We explored the spatial and temporal distribution of these records. In addition, we quantified the function, conservation status, and commercial importance of the identified fishes. The number of fish species recorded from Sydney Harbour now stands at 675, an increase of 89 species (15 %) when compared to the most recent evaluation in 2013. We attribute this increase in fish diversity over a relatively short time to the contribution of newer citizen science programs as well as the influx and survival of fishes in the Harbour with preferences for warmer waters. Some fish families were also overrepresented in the more urbanized and polluted sections of the Harbour. In forecasting further environmental impacts on the fishes of Sydney Harbour, we recommend increased integration of collaborative citizen science programs and natural history collections as a means to track these changes.

Background: Human activities have resulted in a rapid increase of modified habitats in proximity to wildlife habitats in the Himalaya. However, it is crucial to understand the extent to which human habitat modification affects wildlife. Mesocarnivores generally possess broader niches than large carnivores and adapt quickly to human activities. Here, we use a case study in the western Himalaya to test the hypothesis that human disturbance influenced mesocarnivore habitat use. Methods: We used camera trapping and mitochondrial DNA-based species identification from faecal samples to obtain mesocarnivore detections. We then compared the responses of mesocarnivores between an anthropogenic site and a less disturbed park along a contiguous gradient in habitat quality. The non-linear pattern in species-specific habitat selection and factors responsible for space usage around villages was captured using hierarchical generalized additive modelling (HGAM) and non-metric multidimensional scaling (NMDS) ordination. Results: Wildlife occurrences along the gradient varied by species. Leopard cat and red fox were the only terrestrial mesocarnivores that occurred in both anthropogenic site and park. We found a shift in habitat selection from less disturbed habitat in the park to disturbed habitat in anthropogenic site for the species detected in both the habitat types. For instance, red fox showed habitat selection towards high terrain ruggedness (0.5 to 0.7 TRI) and low NDVI (-0.05 to 0.2) in the park but no such specific selection in anthropogenic site. Further, leopard cat showed habitat selection towards moderate slope (20°) and medium NDVI (0.5) in park but no prominent habitat selections in anthropogenic site. The results revealed their constrained behaviour which was further supported by the intensive site usage close to houses, agricultural fields and human trails in villages. Conclusions: Our results indicate shifts in habitat selection and intensive site usage by mesocarnivores in the human-modified habitat. In future, this suggests the possibility of conflict and disease spread affecting both the people and wildlife. Therefore, this study highlights the requisite to test the wildlife responses to rapidly growing human expansions in modified habitats to understand the extent of impact. The management strategies need to have an integrated focus for further expansions of modified habitat and garbage disposal strategies, especially in the human-wildlife interface area.

Environmental DNA (eDNA) metabarcoding is increasingly being used to assess community composition in coastal ecosystems. In this study, we chose to examine temporal and spatial changes in the aquatic community of Manly Lagoon - one of the most heavily developed and polluted estuaries in eastern Australia. Based on metabarcoding of the 16S mitochondrial gene (for fish) and the 18S nuclear gene (for macroinvertebrates), we identified seasonal differences in fish and macroinvertebrate community composition as well as species richness, which correlated, in some cases, with the environmental parameters of sea surface temperature and freshwater input. Moreover, given the greater taxonomic resolution of fish versus macroinvertebrate assignments, we identified several known migratory fish species of management importance that contributed significantly to the overall patterns observed. Overall, our data support the use of eDNA metabarcoding to track fish assemblages shifting in response to environmental drivers in polluted estuaries with increased sampling and consultation with historical data.

Endemic species distributed in fragmented habitats are highly vulnerable to extinction because they may have low genetic diversity. However, some life-history traits can mitigate the effect of genetic drift on populations. We analysed the level and distribution of genetic variation and ancestral population size of Yucca capensis, a long-lived endemic plant of the Baja California Peninsula, Mexico. Its populations are scattered across a habitat that is suffering accelerated transformation. We used six nuclear microsatellites to genotype 224 individuals from 17 locations across the entire species\' geographic range. We estimated polymorphisms, heterozygosity and genetic structure. We also evaluated the ancestral and recent effective size and time since the population started to change. We found high heterozygosity, high polymorphism and low differentiation among locations, suggesting a panmictic population across the range. We also detected a large ancestral effective population size, which suffered a strong reduction in the Mid-Holocene. Despite changes in environmental conditions caused by habitat modification, the high diversity and low differentiation in Y. capensis may result from its large ancestral effective size and life-history traits, such as plant longevity, clonal growth and mating system, which reduce the rate of loss of genetic variation. However, the dependence on a specialist pollinator that displays short flight range can reduce gene flow among the plant populations and could, shortly, lead them into an extinction vortex.