Avian malaria, caused by Plasmodium spp., has been reported as a cause of morbidity and mortality in New Zealand bird populations. The prevalence of Plasmodium lineages in the Waimarino Forest was evaluated in NZ robins (Petroica longipes), other passerines, blue ducks (Hymenolaimus malacorhynchos), and brown kiwi (Apteryx mantelli), using nested PCR. The presence of P. sp. lineage LINN1, P. (Huffia) elongatum lineage GRW06 and P. (Novyella) sp. lineage SYAT05 was demonstrated; Plasmodium (Haemamoeba) relictum lineage GRW4 was not found. The highest prevalence of infection was found in introduced European species (80.5%), followed by native (19%) and endemic species (3.5%), with a significant difference between these groups. All detected Plasmodium lineages have previously been identified in New Zealand and introduced species have been suggested as an important reservoir of infection. The results of this study will aid New Zealand conservation managers with disease risk management during bird translocations from the Waimarino forest.

Background The Aotearoa New Zealand takahē (Porphyrio hochstetteri), once thought to be extinct, is a nationally threatened flightless rail under intensive conservation management. While there has been previous research into disease-related microbes in takahē, little is known about the microbes present in the gastrointestinal tract. Given the importance of gut-associated microbes to herbivore nutrition and immunity, knowledge of these communities is likely to be of considerable conservation value. Here we examined the gut microbiotas of 57 takahē at eight separate locations across Aotearoa New Zealand. Results Faecal samples, taken as a proxy for the hindgut bacterial community, were subjected to 16S rRNA gene amplicon sequencing using Illumina MiSeq. Phylogenetic analysis of > 2200 amplicon sequence variants (ASVs) revealed nine main bacterial phyla (Acidobacteriota, Actinobacteriota, Bacteroidota, Campilobacterota, Firmicutes, Fusobacteriota, Planctomycetota, Proteobacteria, and Verrucomicrobiota) that accounted for the majority of sequence reads. Location was a significant effect (p value < 0.001, 9999 permutations) that accounted for 32% of the observed microbiota variation. One ASV, classified as Lactobacillus aviarius, was present in all samples at an average relative abundance of 17% (SD = 23.20). There was strong evidence (p = 0.002) for a difference in the abundance of the genus Lactobacillus between locations. A common commensal bacterium previously described in takahē, Campylobacter spp., was also detected in most faecal samples. Conclusions Location plays a pivotal role in the observed variation among takahē gut bacterial communities and is potentially due to factors such as supplemental feeding and medical treatment experienced by birds housed in captivity at one of the eight sampled sites. These data present a first glimpse of the previously unexplored takahē gut microbiota and provide a baseline for future microbiological studies and conservation efforts.

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Species recovery programs are increasingly using genomic data to measure neutral genetic diversity and calculate metrics like relatedness. While these measures can inform conservation management, determining the mechanisms underlying inbreeding depression requires information about functional genes associated with adaptive or maladaptive traits. Toll‐like receptors (TLRs) are one family of functional genes, which play a crucial role in recognition of pathogens and activation of the immune system. Previously, these genes have been analysed using species‐specific primers and PCR. Here, we leverage an existing short‐read reference genome, whole‐genome resequencing population data set, and bioinformatic tools to characterize TLR gene diversity in captive and wild tchūriwat’/tūturuatu/shore plover (Thinornis novaeseelandiae), a threatened bird endemic to Aotearoa New Zealand. Our results show that TLR gene diversity in tchūriwat’/tūturuatu is low, and forms two distinct captive and wild genetic clusters. The bioinformatic approach presented here has broad applicability to other threatened species with existing genomic resources in Aotearoa New Zealand and beyond.

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Abstract Anthropogenic feeding of wildlife provides a valuable opportunity for people to engage with animals, but such feeding has the potential to be detrimental to the species involved. Ducks are frequently fed at urban ponds globally, yet the health impacts of an urban lifestyle for birds are poorly documented. We studied urban and rural Mallards (Anas platyrhynchos) in the Manawatū-Whanganui region (New Zealand). Mallards are opportunistic omnivores that have a phenotypically flexible gastrointestinal system. As urban Mallards consume considerable amounts of low-fibre, high carbohydrate foods via anthropogenic feeding, we predicted that urban Mallards would have smaller gastrointestinal tract organs and higher fat levels than rural ducks. We compared gross body composition of Mallards in a modified environment with high levels of feeding by humans and in rural habitats. We also evaluated other health-associated aspects including fat deposit size, liver fat content and haemosiderin (liver iron deposit) levels. Contrary to predictions, urban birds had larger gizzards and caeca and were no fatter than rural birds; rural birds additionally had larger pectoralis major muscles. These differences are probably associated with broader ecological and behavioural factors than with the provision of anthropogenic food per se [in particular the presence of hard foods (acorns and nuts) for urban birds, and higher flight activity of rural birds]. Longer caeca in urban birds could, however, relate to immunity rather than microbial fermentation of cellulose. Overall, while the nature of the local environment does affect Mallard physiology, no detrimental effects of urban living were evident in this study.