Harnessing the omics revolution to address the global biodiversity crisis

Human disturbances are altering global biodiversity in unprecedented ways. We identify three fundamental challenges underpinning our understanding of global biodiversity (namely discovery, loss, and preservation), and discuss how the omics revolution (e.g. genomics, transcriptomics, proteomics, metabolomics, and meta-omics) can help address these challenges. We also discuss how omics tools can illuminate the major drivers of biodiversity loss, including invasive species, pollution, urbanization, overexploitation, and climate change, with a special focus on highly diverse tropical environments. Although omics tools are transforming the traditional toolkit of biodiversity research, their application to addressing the current biodiversity crisis remains limited and may not suffice to offset current rates of biodiversity loss. Despite technical and logistical challenges, omics tools need to be fully integrated into global biodiversity research, and better strategies are needed to improve their translation into biodiversity policy and practice. It is also important to recognize that although the omics revolution can be considered the biologist's dream, socioeconomic disparity limits their application in biodiversity research.

Genotypic detection of barriers to rat dispersal: Rattus rattus behind a peninsula predator-proof fence

Clear delimitation of management units is essential for effective management of invasive species. Analysis of population genetic structure of target species can improve identification and interpretation of natural and artificial barriers to dispersal. In Aotearoa New Zealand where the introduced ship rat (Rattus rattus) is a major threat to native biodiversity, effective suppression of pest numbers requires removal and limitation of reinvasion from outside the managed population. We contrasted population genetic structure in rat populations over a wide scale without known barriers, with structure over a fine scale with potential barriers to dispersal. MtDNA D-loop sequences and microsatellite genotypes resolved little genetic structure in southern North Island population samples of ship rat 100 km apart. In contrast, samples from major islands differed significantly for both mtDNA and nuclear markers. We also compared ship rats collected within a small peninsula reserve bounded by sea, suburbs and, more recently, a predator fence with rats in the surrounding forest. Here, mtDNA did not differ but genotypes from 14 nuclear loci were sufficient to distinguish the fenced population. This suggests that natural (sea) and artificial barriers (town, fence) are effectively limiting gene flow among ship rat populations over the short distance (~ 500 m) between the peninsula reserve and surrounding forest. The effectiveness of the fence alone is not clear given it is a recent feature and no historical samples exist; resampling population genetic diversity over time will improve understanding. Nonetheless, the current genetic isolation of the fenced rat population suggests that rat eradication is a sensible management option given that reinvasion appears to be limited and could probably be managed with a biosecurity programme.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10530-023-03004-8.

Rats and the COVID-19 pandemic: considering the influence of social distancing on a global commensal pest

Rats contaminate foods and spread pathogens. Thus, changes in rat populations have consequences for society, especially in densely-populated cities. Following widespread social distancing and lockdown measures to curtail SARS-CoV-2, worldwide media outlets reported increased sightings of rats. To document possible changes in rat populations, we: (i) examined public service requests in the 6 years before, and during, ‘lockdown’ in New York City; (ii) used spatial analyses to identify calls in proximity to food service establishments (FSE); and (iii) surveyed pest-management companies. Over 6 years prior to the pandemic, we found a consistent moderate spatial association (r = 0.35) between FSE and rat-related calls. During the early stages of the pandemic, the association between rat reports and food services did not decrease as would be expected by restaurant closures, but instead modestly increased (r = 0.45). There was a 29.5% decrease in rat reports, overall. However, hotspot analysis showed that new reports were highly localized, yet absent in several industrial areas they were previously observed in, potentially masking a higher proportion of calls in neighborhoods near closed restaurants. Additionally, 37% of pest management companies surveyed reported that, unlike previous years, 50–100% of requests were from new clients and addresses. The finding that hotspots remained nearby dense clusters of restaurants does not support the common narrative that rats moved long distances. Rather, our results are consistent with rats finding nearby alternative food resources. Tracking these dynamics as the COVID-19 pandemic abates will be an important step to identifying how rats respond to society returning to normal activity patterns.

The effect of COVID19 pandemic restrictions on an urban rodent population

Shortly after the enactment of restrictions aimed at limiting the spread of COVID-19, various local government and public health authorities around the world reported an increased sighting of rats. Such reports have yet to be empirically validated. Here we combined data from multi-catch rodent stations (providing data on rodent captures), rodent bait stations (providing data on rodent activity) and residents' complaints to explore the effects of a six week lockdown period on rodent populations within the City of Sydney, Australia. The sampling interval encompassed October 2019 to July 2020 with lockdown defined as the interval from April 1st to May 15th, 2020. Rodent captures and activity (visits to bait stations) were stable prior to lockdown. Captures showed a rapid increase and then decline during the lockdown, while rodent visits to bait stations declined throughout this period. There were no changes in the frequency of complaints during lockdown relative to before and after lockdown. There was a non-directional change in the geographical distribution of indices of rodent abundance suggesting that rodents redistributed in response to resource scarcity. We hypothesize that lockdown measures initially resulted in increased rodent captures due to sudden shortage of human-derived food resources. Rodent visits to bait stations might not show this pattern due to the nature of the binary data collected, namely the presence or absence of a visit. Relocation of bait stations driven by pest management goals may also have affected the detection of any directional spatial effect. We conclude that the onset of COVID-19 may have disrupted commensal rodent populations, with possible implications for the future management of these ubiquitous urban indicator species.

Urban biodiversity management using evolutionary tools

Cities are fully functioning ecosystems and are home to no-analogue communities of species that interact with each other and which are subject to novel urban stressors. As such, biodiversity can evolve in response to these new urban conditions, making urban species a moving target for conservation and management efforts. An evolving urban biodiversity necessitates integrating evolutionary insights into management for these efforts to be successful in a dynamic urban milieu. Here we present a framework for categorizing urban biodiversity from a management perspective. We then discuss a suite of example management tools and their potential evolutionary implications-both their opportunities for and potential consequence to management. Urban ecosystems are proliferating but, far from being ecological lost causes, they may provide unique insights and opportunities for biodiversity conservation. Determining how to achieve urban biodiversity priorities while managing pest species requires evolutionary thinking.