A new long-read mitochondrial-genome protocol (PacBio HiFi) for haemosporidian parasites: a tool for population and biodiversity studies.

BACKGROUND: Studies on haemosporidian diversity, including origin of human malaria parasites, malaria's zoonotic dynamic, and regional biodiversity patterns, have used target gene approaches. However, current methods have a trade-off between scalability and data quality. Here, a long-read Next-Generation Sequencing protocol using PacBio HiFi is presented. The data processing is supported by a pipeline that uses machine-learning for analysing the reads. METHODS: A set of primers was designed to target approximately 6 kb, almost the entire length of the haemosporidian mitochondrial genome. Amplicons from different samples were multiplexed in an SMRTbell® library preparation. A pipeline (HmtG-PacBio Pipeline) to process the reads is also provided; it integrates multiple sequence alignments, a machine-learning algorithm that uses modified variational autoencoders, and a clustering method to identify the mitochondrial haplotypes/species in a sample. Although 192 specimens could be studied simultaneously, a pilot experiment with 15 specimens is presented, including in silico experiments where multiple data combinations were tested. RESULTS: The primers amplified various haemosporidian parasite genomes and yielded high-quality mt genome sequences. This new protocol allowed the detection and characterization of mixed infections and co-infections in the samples. The machine-learning approach converged into reproducible haplotypes with a low error rate, averaging 0.2% per read (minimum of 0.03% and maximum of 0.46%). The minimum recommended coverage per haplotype is 30X based on the detected error rates. The pipeline facilitates inspecting the data, including a local blast against a file of provided mitochondrial sequences that the researcher can customize. CONCLUSIONS: This is not a diagnostic approach but a high-throughput method to study haemosporidian sequence assemblages and perform genotyping by targeting the mitochondrial genome. Accordingly, the methodology allowed for examining specimens with multiple infections and co-infections of different haemosporidian parasites. The pipeline enables data quality assessment and comparison of the haplotypes obtained to those from previous studies. Although a single locus approach, whole mitochondrial data provide high-quality information to characterize species pools of haemosporidian parasites.

Factors and costs associated with removal of a newly established population of invasive wild pigs in Northern U.S.

The human-mediated spread of exotic and invasive species often leads to unintentional and harmful consequences. Invasive wild pigs (Sus scrofa) are one such species that have been repeatedly translocated throughout the United States and cause extensive damage to natural ecosystems, threatened and endangered species, agricultural resources, and private lands. In 2005, a newly established population of wild pigs was confirmed in Fulton County, Illinois, U.S. In 2011, a state-wide wild pig damage management program involving federal, state, and local government authorities directed a concerted effort to remove wild pigs from the county until the last wild pig (of 376 total) was successfully removed in 2016. We examined surveillance data from camera traps at bait sites and records of wild pig removals during this elimination program to identify environmental and anthropogenic factors that optimized removal of this population. Our results revealed that wild pigs used bait sites most during evening and nocturnal periods and on days with lower daily maximum temperatures. Increased removals of wild pigs coincided with periods of cold weather. We also identified that fidelity and time spent at bait sites by wild pigs was not influenced by increasing removals of wild pigs. Finally, the costs to remove wild pigs averaged $50 per wild pig (6.8 effort hours per wild pig) for removing the first 99% of the animals. Cost for removing the last 1% increased 84-fold, and averaged 122.8 effort hours per wild pig removed. Our results demonstrated that increased effort in removing wild pigs using bait sites should be focused during periods of environmental stress to maximize removal efficiency. These results inform elimination programs attempting to remove newly established populations of wild pigs, and ultimately prevent population and geographic expansion.

Locating and eliminating feral swine from a large area of fragmented mixed forest and agriculture habitats in north-central USA.

Illinois is one of the US states where elimination of feral swine (Sus scrofa) was determined practical, as only a few isolated populations were established. A particularly important step towards feral swine elimination from Illinois was to eliminate the population in Fulton County. We describe the approaches applied to systematically detect, locate, and eliminate feral swine in a successful county-wide elimination. Detecting and locating feral swine was facilitated by extensive outreach activities, aerial surveys to locate crop damage, and use of camera traps placed over bait in areas where reports, sign, or crop damage occurred. The population was eliminated after 376 feral swine were removed from 2009 to 2016 by trapping, sharpshooting over bait, and aerial shooting. Aerial surveys efficiently located feral swine activity over wide areas during times of the crop cycle when damage would occur and would be most distinguishable from other damage sources. Two applications of aerial shooting in 2014 were particularly efficient for rapidly eliminating most remaining feral swine after they had become difficult to locate and remove. Persistent efforts thereafter led to the successful elimination of feral swine in Fulton County by 2016. We believe this is the first documentation of a widespread feral swine elimination in mixed agriculture and forest habitats.

Benefits to rare plants and highway safety from annual population reductions of a "native invader," white-tailed deer, in a Chicago-area woodland.

Overabundant white-tailed deer are one of the most serious threats to woodland plant communities in the Chicago area. Moreover, the abundant deer in a highly populated area causes economic harm and poses hazards to human safety through collisions with vehicles. The artificial conditions causing the overabundance and resulting consequences qualify the white-tailed deer in the Chicago area to be considered as "native invaders". We examined the benefits of culling deer at a Chicago-area woodland preserve by comparing browse rates on four endangered plant species from years before culling began with years with culling. We also examined deer-vehicle collision and traffic flow rates on area roads from years before culling began and years with culling to assess whether population reductions may have benefited road safety in the area. All four endangered plant species (three orchid species and sweet fern) had lower browse rates in years with culls, although the decreased browsing rates were statistically distinguishable for only two of the species (grass pink orchid and sweet fern). After first verifying that traffic flow rates did not decrease from pre-cull years to years with culls, we analyzed the Illinois Department of Transportation data from area roads based on deer-vehicle collisions causing >US$500 in damage and showed a one-third reduction in deer-vehicle collisions. An economic analysis showed a cost savings during the cull years of US$0.6 million for reducing browsing to just these four monitored plant species and the reduction in deer-vehicle collisions.

Egg oiling to reduce hatch-year ring-billed gull numbers on Chicago's beaches during swim season and water quality test results.

A burgeoning ring-billed gull population along Chicago's Lake Michigan beaches contributes to degraded water quality through fecal contamination. Egg oiling was conducted at Chicago's gull colonies to reduce production and the influx of hatch-year (HY) gulls using Chicago's beaches, with a second, long-term objective of eventually reducing adult gull numbers through attrition. We also investigated swim season water quality trends through the course of this work. From 2007 to 2009, 52, 80, and 81%, of nests at the two primary nest colonies had their eggs rendered inviable by corn oil application. Counts of HY and after hatch-year (AHY) gulls were analyzed during treatment years for 10 beaches. Water quality data were available from the Chicago Park District during our three treatment years and the prior year (baseline) for 19 beaches. HY counts declined at all 10 surveyed beaches from the initial year (52% nests with oiled eggs) to subsequent years with ~80% of nests oiled. Overall, HY gulls numbers on beaches decreased 86% from 2007 to 2009. Decreases in beach usage by AHY gulls were not detected. Compared to pretreatment, the number of beaches with improved water quality test rates increased each year through the course of the study. The frequency of water quality tests showing bacterial exceedances compared to 2006 declined at 18 of 19 beaches by 2009. Egg oiling resulted in fewer HY gulls using Chicago's beaches and was likely a beneficial factor for reduced frequencies of swim advisories and swim bans.