De-novo assembly of four rail (Aves: Rallidae) genomes: A resource for comparative genomics.

Rails are a phenotypically diverse family of birds that includes 130 species and displays a wide distribution around the world. Here we present annotated genome assemblies for four rails from Aotearoa New Zealand: two native volant species, pukeko Porphyrio melanotus and mioweka Gallirallus philippensis, and two endemic flightless species takahe Porphyrio hochstetteri and weka Gallirallus australis. Using the sequence read data, heterozygosity was found to be lowest in the endemic flightless species and this probably reflects their relatively small populations. The quality checks and comparison with other rallid genomes showed that the new assemblies were of good quality. This study significantly increases the number of available rallid genomes and will enable future genomic studies on the evolution of this family.

Morphological characterisation of a novel Eimeria sp. parasite in South Island takahe (Porphyrio hochstetteri).

AIMS: A novel Eimeria sp. is described from the endangered South Island takahe (Porphyrio hochstetteri). METHODS: Faeces were collected from South Island takahe in managed populations across two geographic locations within New Zealand, linked by extensive bird translocation. Faecal flotations were performed and oocysts collected were sporulated in sterile water at 25°C for 5 days. Morphometric measurements including length:width (L:W) ratios of oocysts and sporocysts were made of 65 oocysts using light microscopy under oil immersion. A retrospective histological review of archived post-mortem material from takahe was performed. RESULTS: Oocysts were ovoid (mean L:W 1.2 (SD 0.1)) with mean dimensions of 18.0 (SD 0.8) × 15.2 (SD 0.7) µm, and walls 0.9 (SD 0.1) µm thick at the equator. A micropyle was absent and the oocyst residuum was present as a granular spherical mass. Four sporocysts were present and were elongate ovoid in shape (mean L:W ratio 1.5), with mean dimensions of 9.7 (SD 1.1) × 6.3 (SD 0.7) µm and each containing two sporozoites with anterior and posterior refractile bodies. This morphological description is distinct from other Eimeria spp. described in hosts of the family Rallidae. The retrospective review of tissue was hindered by the poor quality of the preserved gut tissue, but coccidial organisms were able to be identified in the caudal ileum and caecum of a single bird. CONCLUSIONS: A novel Eimeria sp. was identified in the faeces of takahe. We propose this species be named Eimeria takahe. CLINICAL RELEVANCE: Conservation of the endangered South Island takahe is reliant on human management of populations under varying degrees of captive management. An understanding of diseases affecting this host, including parasites and their identification as unique to the takahe or introduced from interactions with other hosts, is essential to the maintenance of overall bird health and informs management decisions in this recovery programme.Abbreviations: L:W: Length:width.

Genomic Epidemiology and Management of Salmonella in Island Ecosystems Used for Takahe Conservation.

Translocation and isolation of threatened wildlife in new environments may have unforeseen consequences on pathogen transmission and evolution in host populations. Disease threats associated with intensive conservation management of wildlife remain speculative without gaining an understanding of pathogen dynamics in meta-populations and how location attributes may determine pathogen prevalence. We determined the prevalence and population structure of an opportunistic pathogen, Salmonella, in geographically isolated translocated sub-populations of an endangered New Zealand flightless bird, the takahe (Porphyrio hochstetteri). Out of the nine sub-populations tested, Salmonella was only isolated from takahe living on one private island. The apparent prevalence of Salmonella in takahe on the private island was 32% (95% CI 13-57%), with two serotypes, Salmonella Mississippi and Salmonella houtenae 40:gt-, identified. Epidemiological investigation of reservoirs on the private island and another island occupied by takahe identified environmental and reptile sources of S. Mississippi and S. houtenae 40:gt- on the private island. Single nucleotide polymorphism analysis of core genomes revealed low-level diversity among isolates belonging to the same serotype and little differentiation according to host and environmental source. The pattern observed may be representative of transmission between sympatric hosts and environmental sources, the presence of a common unsampled source, and/or evidence of a recent introduction into the ecosystem. This study highlights how genomic epidemiology can be used to ascertain and understand disease dynamics to inform the management of disease threats in endangered wildlife populations.

Using a common commensal bacterium in endangered Takahe as a model to explore pathogen dynamics in isolated wildlife populations.

Predicting and preventing outbreaks of infectious disease in endangered wildlife is problematic without an understanding of the biotic and abiotic factors that influence pathogen transmission and the genetic variation of microorganisms within and between these highly modified host communities. We used a common commensal bacterium, Campylobacter spp., in endangered Takahe (Porphyrio hochstetteri) populations to develop a model with which to study pathogen dynamics in isolated wildlife populations connected through ongoing translocations. Takahe are endemic to New Zealand, where their total population is approximately 230 individuals. Takahe were translocated from a single remnant wild population to multiple offshore and mainland reserves. Several fragmented subpopulations are maintained and connected through regular translocations. We tested 118 Takahe from 8 locations for fecal Campylobacter spp. via culture and DNA extraction and used PCR for species assignment. Factors relating to population connectivity and host life history were explored using multivariate analytical methods to determine associations between host variables and bacterial prevalence. The apparent prevalence of Campylobacter spp. in Takahe was 99%, one of the highest reported in avian populations. Variation in prevalence was evident among Campylobacter species identified. C. sp. nova 1 (90%) colonized the majority of Takahe tested. Prevalence of C. jejuni (38%) and C. coli (24%) was different between Takahe subpopulations, and this difference was associated with factors related to population management, captivity, rearing environment, and the presence of agricultural practices in the location in which birds were sampled. Modeling results of Campylobacter spp. in Takahe metapopulations suggest that anthropogenic management of endangered species within altered environments may have unforeseen effects on microbial exposure, carriage, and disease risk. Translocation of wildlife between locations could have unpredictable consequences including the spread of novel microbes between isolated populations.