Use of carrion fly iDNA metabarcoding to monitor invasive and native mammals

Severely fragmented habitats increase the risk of extirpation of native mammal populations through isolation, increased edge effects, and predation. Therefore, monitoring the movement of mammal populations through anthropogenically altered landscapes can inform conservation. We used metabarcoding of invertebrate-derived DNA (iDNA) from carrion flies (Calliphoridae and Sarcophagidae) to track mammal populations in the wheat belt of southwestern Australia, where widespread clearing for agriculture has removed most of the native perennial vegetation and replaced it with an agricultural system. We investigated whether the localization of the iDNA signal reflected the predicted distribution of 4 native species—echidna (Tachyglossus aculeatus), numbat (Myrmecobius fasciatus), woylie (Bettongia penicillata), and chuditch (Dasyurus geoffroii)—and 2 non-native, invasive mammal species—fox (Vulpes vulpes) and feral cat (Felis catus). We collected bulk iDNA samples (n = 150 samples from 3428 carrion flies) at 3 time points from 3 conservation reserves and 35 road edges between them. We detected 14 of the 40 mammal species known from the region, including our target species. Most detections of target taxa were in conservation reserves. There were a few detections from road edges. We detected foxes and feral cats throughout the study area, including all conservation reserves. There was a significant difference between the diversity (F_3, 98 = 5.91, p < 0.001) and composition (F_3, 43 = 1.72, p < 0.01) of taxa detections on road edges and conservation reserves. Conservation reserves hosted more native biodiversity than road edges. Our results suggest that the signals from iDNA reflect the known distribution of target mammals in this region. The development of iDNA methods shows promise for future noninvasive monitoring of mammals. With further development, iDNA metabarcoding could inform decision-making related to conservation of endangered taxa, invasive species management, and impacts of habitat fragmentation.     

Collaborating to Conserve Large Mammals in Southeast Asia

Abstract:  Depressed mammal densities characterize the interior of many Southeast Asian protected areas, and are the result of commercial and subsistence hunting. Local people are part of this problem but can participate in solutions through improved partnerships that incorporate local knowledge into problem diagnosis. The process of involving local people helps build a constituency that is more aware of its role (positive and negative) in a protected area and generates site-specific conservation assessments for management planning. We illustrate the practical details of initiating such a partnership through our work in a Thai wildlife sanctuary. Many protected areas in Southeast Asia present similar opportunities. In local workshops, village woodsmen were led through ranking exercises to develop a spatially explicit picture of 20-year trends in the abundance of 31 mammal species and to compare species-specific causes for declines. Within five taxonomic groups, leaf monkeys (primates), porcupines (rodents), tigers (large carnivores), civets (small carnivores), and elephants (ungulates) had declined most severely (37–74%). Commercial hunting contributed heavily to extensive population declines for most species, and subsistence hunting was locally significant for some small carnivores, leaf monkeys, and deer. Workshops thus clarified which species were at highest risk of local extinction, where the most threatened populations were, and causes for these patterns. Most important, they advanced a shared problem definition, thereby unlocking opportunities for collaboration. As a result, local people and sanctuary managers have increased communication, initiated joint monitoring and patrolling, and established wildlife recovery zones. Using local knowledge has limitations, but the process of engaging local people promotes collaborative action that large mammals in Southeast Asia need.     

Temporal and Spatial Trends in Chlorinated Hydrocarbon Concentrations of Mink in Canadian Lakes Erie and St. Clair

Mink (Mustela vison) carcasses were collected from local commercial trappers from fall 1998 to spring 2003 from tributaries and marshes within 4.8km from the shores of Lakes Erie and St. Clair, including the Wheatley Harbour and St. Clair River Areas of Concern (AOCs), as well as from inland sites (8 to 40km from shore). Liver concentrations, on a lipid weight basis, of chlorinated hydrocarbons were measured and compared among sites and to tissue concentrations of mink from two previous collections from similar sites over the past 25 years. Mink from the western Lake Erie sites, which included the Wheatley Harbour AOC, had significantly higher concentrations of sum PCBs and PCB Aroclors than those from the St. Clair corridor or inland sites, with concentrations from the rest of Lake Erie being intermediate. Dieldrin concentrations were also significantly higher in western Lake Erie than many other sites, and those of oxychlordane and mirex also tended to be higher (0.05 < p < 0.1). There were no differences in contaminant concentrations between the St. Clair River AOC and the downstream non-AOC Lake St. Clair site, with the exception of slightly higher levels of octachlorostyrene (OCS). Concentrations of PCBs and other chlorinated hydrocarbons in mink showed a general decrease over the past two decades. In contrast, PCBs and some organochlorine pesticides tended to increase, significantly so with oxychlordane, in western Lake Erie mink over the same time period. DDE declined at all sites. Currently, mink liver PCB concentrations are within the range associated with reproductive impairment, as determined from captive mink studies, in 11.7% of all animals collected from the Lakes Erie and St. Clair basin overall, but in almost 40% of individuals from western Lake Erie.     

Habitat Suitability Models and the Shortfall in Conservation Planning for African Vertebrates

Abstract:  Ongoing loss of biodiversity requires identifying large-scale conservation priorities, but the detailed information on the distribution of species required for this purpose is often missing. We present a systematic reserve selection for 1223 African mammals and amphibians in which habitat suitability models are used as estimates of the area occupied by species. In the framework of the World Conservation Union (IUCN) Global Amphibian Assessment and IUCN Global Mammal Assessment, we collected the geographic range (extent of occurrence) and habitat preferences for each species. We used the latter to build species-specific habitat suitability models inside geographic ranges, and for 181 species we verified the models by comparing suitability levels to presence-absence data collected in the field. We then used the suitable areas as estimators of the area of occupancy and compared the results of systematic reserve selection based on geographic ranges to those based on estimated areas of occupancy. Our results showed that the reserve system would need a 30-100% expansion to achieve minimal conservation targets, concentrated in the tropics, where species richness reaches a maximum. Comparative analyses revealed that using geographic ranges, which overestimate the area occupied by species, underestimates the total amount of area that needs to be conserved. The area selected for conservation doubled when we used the estimated area of occupancy in place of the geographic ranges. This happened because the suitable areas potentially occupied by each species overlapped less than their geographic ranges. As a result, any given protected area contained fewer species than predicted by the analysis of ranges. Because species are more specialized than our estimates of distribution based on extent of occurrence suggest, we propose that this is a general effect in systematic conservation planning.     

Rabbit biocontrol and landscape‐scale recovery of threatened desert mammals

Funding for species conservation is insufficient to meet the current challenges facing global biodiversity, yet many programs use expensive single‐species recovery actions and neglect broader management that addresses threatening processes. Arid Australia has the world's worst modern mammalian extinction record, largely attributable to competition from introduced herbivores, particularly European rabbits (Oryctolagus cuniculus) and predation by feral cats (Felis catus) and foxes (Vulpes vulpes). The biological control agent rabbit hemorrhagic disease virus (RHDV) was introduced to Australia in 1995 and resulted in dramatic, widespread rabbit suppression. We compared the area of occupancy and extent of occurrence of 4 extant species of small mammals before and after RHDV outbreak, relative to rainfall, sampling effort, and rabbit and predator populations. Despite low rainfall during the first 14 years after RHDV, 2 native rodents listed by the International Union for Conservation of Nature (IUCN), the dusky hopping‐mouse (Notomys fuscus) and plains mouse (Pseudomys australis), increased their extent of occurrence by 241–365%. A threatened marsupial micropredator, the crest‐tailed mulgara (Dasycercus cristicauda), underwent a 70‐fold increase in extent of occurrence and a 20‐fold increase in area of occupancy. Both bottom‐up and top‐down trophic effects were attributed to RHDV, namely decreased competition for food resources and declines in rabbit‐dependent predators. Based on these sustained increases, these 3 previously threatened species now qualify for threat‐category downgrading on the IUCN Red List. These recoveries are on a scale rarely documented in mammals and give impetus to programs aimed at targeted use of RHDV in Australia, rather than simply employing top‐down threat‐based management of arid ecosystems. Conservation programs that take big‐picture approaches to addressing threatening processes over large spatial scales should be prioritized to maximize return from scarce conservation funding. Further, these should be coupled with long‐term ecological monitoring, a critical tool in detecting and understanding complex ecosystem change.     

Eradication of Invasive Mammals on Islands Inhabited by Humans and Domestic Animals

Abstract: Non‐native invasive mammal species have caused major ecological change on many islands. To conserve native species diversity, invasive mammals have been eradicated from several islands not inhabited by humans. We reviewed the challenges associated with campaigns to eradicate invasive mammals from islands inhabited by humans and domestic animals. On these islands, detailed analyses of the social, cultural, and economic costs and benefits of eradication are required to increase the probability of local communities supporting the eradication campaign. The ecological benefits of eradication (e.g., improvement of endemic species’ probability of survival) are difficult to trade‐off against social and economic costs due to the lack of a common currency. Local communities may oppose an eradication campaign because of perceived health hazards, inconvenience, financial burdens, religious beliefs, or other cultural reasons. Besides these social challenges, the presence of humans and domestic animals also complicates eradication and biosecurity procedures (measures taken to reduce the probability of unwanted organisms colonizing an island to near zero). For example, houses, garbage‐disposal areas, and livestock‐feeding areas can provide refuges for certain mammals and therefore can decrease the probability of a successful eradication. Transport of humans and goods to an island increases the probability of inadvertent reintroduction of invasive mammals, and the establishment of permanent quarantine measures is required to minimize the probability of unwanted recolonization after eradication. We recommend a close collaboration between island communities, managers, and social scientists from the inception of an eradication campaign to increase the probability of achieving and maintaining an island permanently free of invasive mammals.     

Null-Hypothesis Significance Testing and the Critical Weight Range for Australian Mammals

Abstract:  The critical weight range hypothesis for Australian terrestrial mammals states that species in the intermediate size range 35–5500 g are particularly susceptible to extinction. In a 2001 study Cardillo and Bromham found no statistically significant evidence for this hypothesis and suggested that research should instead focus on why small species are resistant to extinction. We used a similar data set of body sizes of Australian mammals grouped by conservation classification, but we used test statistics (mean deviation above and below the median body size) that are more statistically powerful than those of Cardillo and Bromham (quartiles, maxima, and minima of body size distributions). We found strong evidence in favor of the critical weight range hypothesis: the body size distribution of threatened species was more clustered toward the median body size from above and below. This pattern was statistically significant at the continental scale and in the arid zone, but not in the mesic zone. Confusing statistical significance with evidence of no effect, as Cardillo and Bromham did, can have negative implications for conservation biology because it can result in failure to act when action is warranted or provision of incorrect advice that affects policy and planning decisions.     

Infectious Diseases and Extinction Risk in Wild Mammals

Abstract:  Parasite-driven declines in wildlife have become increasingly common and can pose significant risks to natural populations. We used the IUCN Red List of Threatened and Endangered Species and compiled data on hosts threatened by infectious disease and their parasites to better understand the role of infectious disease in contemporary host extinctions. The majority of mammal species considered threatened by parasites were either carnivores or artiodactyls, two clades that include the majority of domesticated animals. Parasites affecting host threat status were predominantly viruses and bacteria that infect a wide range of host species, including domesticated animals. Counter to our predictions, parasites transmitted by close contact were more likely to cause extinction risk than those transmitted by other routes. Mammal species threatened by parasites were not better studied for infectious diseases than other threatened mammals and did not have more parasites or differ in four key traits demonstrated to affect parasite species richness in other comparative studies. Our findings underscore the need for better information concerning the distribution and impacts of infectious diseases in populations of endangered mammals. In addition, our results suggest that evolutionary similarity to domesticated animals may be a key factor associated with parasite-mediated declines; thus, efforts to limit contact between domesticated hosts and wildlife could reduce extinction risk.     

广西大明山自然保护区哺乳动物资源调查研究

2000年9月11日至26日,在广西省大明山自然保护区采集哺乳动物81只(种),共计19种,隶属5目,11科.结合以往的调查资料,已知大明山自然保护区有哺乳动物动物60种,隶属8目,22科,47属.保护区内的哺乳动物多样性系数(H”)为2.5555,均匀度指数(J)为O.8679,动物的密度为231.23只/km2.     

Using environmental DNA to assess population‐wide spatiotemporal reserve use

Scientists increasingly rely on protected areas to assist in biodiversity conservation, yet the efficacy of these areas is rarely systematically assessed, often because of underfunding. Still, adaptive management strategies to maximize conservation success often rely on understanding the temporal and spatial dynamism of populations therein. Examination of environmental DNA (eDNA) is a time and cost‐effective way to monitor species’ distribution, and quantitative polymerase chain reaction (qPCR) provides information on organismal abundance. To date, however, such techniques remain underused for population assessments in protected areas. We determined eDNA concentration of the critically endangered Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis) to describe its occurrence, range, and use of the Tian e‐Zhou National Nature Reserve in Hubei, China, across seasons and hydrological depths. Despite the observation that total eDNA concentrations were highest in surface waters in summer, finless porpoise eDNA concentrations were significantly higher in deeper waters than in surface waters in summer. During the breeding season (spring), eDNA signals were site specific and restricted to the core area of the reserve. However, postbreeding eDNA concentrations were widespread across the reserve, encompassing sites previously thought to be unfrequented by the species. Our results suggest spatiotemporal idiosyncrasies in site, depth, and seasonal use of the reserve and a propensity for postbreeding population dispersal. With eDNA and qPCR we were able to assess an entire population's use of a protected area. Illuminating nuances in habitat use via eDNA could be valuable to set pragmatic conservation goals for this, and other, species.