Highly pathogenic avian influenza (HPAI) virus subtype H5N1 has never been detected in New Zealand. The potential impact of this virus on New Zealand's wild birds would be catastrophic. To expand our knowledge of avian influenza viruses across New Zealand, we sampled wild aquatic birds from New Zealand, its outer islands and its subantarctic territories. Metatranscriptomic analysis of 700 individuals spanning 33 species revealed no detection of H5N1 during the annual 2023-2024 migration. A single detection of H1N9 in red knots (Calidris canutus) was noted. This study provides a baseline for expanding avian influenza virus monitoring in New Zealand.

Wild migratory birds play a major role in the global spread of viruses, yet the diversity, host range and transmission patterns of viruses harboured by migratory species in Aotearoa/New Zealand remain largely unknown. This knowledge gap is critical given New Zealand's position along major migratory flyways spanning Oceania, Antarctica and east Asia, where understanding viral diversity is key to assessing the risk of viral introductions such as highly pathogenic avian influenza virus and viral dispersal across these regions. To address this, we conducted the first large-scale metatranscriptomic survey of wild birds from New Zealand and its subantarctic islands, collecting 1,348 samples from 31 host species spanning four avian orders. We identified 118 avian viruses from 17 families, including 107 novel species, greatly expanding our knowledge of avian viral diversity. Viral communities differed significantly by host order and foraging behaviour, with scavenger birds harbouring more diverse viromes than non-scavengers. Although no HPAI subtypes were detected, we recovered a low-pathogenic avian influenza A/H1N9 virus from red knots (Calidris canutus) and a divergent tobanivirus from Auckland Island teal (Anas aucklandica), the first putative avian member of the Tobaniviridae. Notably, we detected 12 mammalian-associated viruses, primarily in scavenger birds, including Hedgehog hepatovirus, Rabbit haemorrhagic disease virus 2, and sea lion astroviruses, with mammalian host reads confirming their dietary origin. This study establishes the first virome baseline for New Zealand's migratory birds, highlighting the ecological role of foraging in shaping viral communities and improving regional preparedness for HPAI and other emerging avian pathogens. ### Competing Interest Statement The authors have declared no competing interest. Te Niwha, New Zealand’s Infectious Disease Research Platform, TN/SWC/24/UoOJG

Ruddy turnstone (Arenaria interpres) is the third most numerous Arctic-breeding wader that occurs in New Zealand. Numbers of turnstones in New Zealand have declined but identification of potential causal factors is hampered by lack of information of the migration routes used. Re-sights of marked birds indicate that some New Zealand turnstones pass through East Asia and Australia on both northward and southward migration. Information on possible migration through the Pacific is lacking.

Co-ordinated counts of waders across New Zealand have been undertaken in November and June since 1983; the consistent timing of counts aimed to reduce variation from the effect of seasonal changes in bird numbers. The Australian Shorebird census and the wider Asian Waterbird Census, however, are conducted in January, making direct comparison with the New Zealand counts potentially problematic, especially if an attempt is to be made to assess total flyway populations. Since 1998 waders on Farewell Spit (40 degrees 30.5'S, 172 degrees 45'E to 40 degrees 33.5'N 173 degrees 02'E) have been counted in February as well as in November and June. Counts of bar-tailed godwit and ruddy turnstone were on average 20% and 35% higher in February compared to November, respectively. Also, counts of the endemic migratory South Island pied oystercatcher were 15% higher in February compared to June. The improvement of data for overall population assessments is not only important for establishing trends of species but is also important for applying the 1% population criterion for wader site assessments.

While avian migration timing is clearly influenced by both breeding and non-breeding geography, it is challenging to identify the relative and interdependent roles of endogenous programs, early-life experience, and carry-over effects in the development of adult annual schedules. Bar-tailed godwits Limosa lapponica baueri migrate northward from New Zealand toward Asian stopover sites during the boreal spring, with differences in timing between individuals known to relate to their eventual breeding-ground geography in Alaska. Here, we studied the timing of northward migration of individual godwits at three sites spanning 1,100 km of New Zealand’s 1,400-km length. A lack of morphological or genetic structure among sites indicates that the Alaskan breeding population mixes freely across all sites, and larger birds (southern breeders) tended to migrate earlier than smaller birds (northern breeders) at all sites. However, we unexpectedly found that migration timing varied between the sites, with birds from southern New Zealand departing on average 9.4–11 days earlier than birds from more northerly sites, a difference consistent across 4 years of monitoring. There is no obvious adaptive reason for migration timing differences of this magnitude, and it is likely that geographic variation in timing within New Zealand represents a direct response to latitudinal variation in photoperiod. Using resightings of marked birds, we show that immature godwits explore widely around New Zealand before embarking on their first northward migration at age 2–4 years. Thus, the process by which individual migration dates are established appears to involve: (1) settlement by sub-adult godwits at non-breeding sites, to which they are highly faithful as adults; (2) a consequent response to environmental cues (i.e., photoperiod) that sets the local population’s migration window; and (3) endogenous mechanisms, driven by breeding geography, that establish and maintain the well-documented consistent differences between individuals. This implies that behavioral decisions by young godwits have long-lasting impacts on adult annual-cycle schedules, but the factors guiding non-breeding settlement are currently unknown.

Bar-tailed godwits (Limosa lapponica) were counted throughout New Zealand and on the east coast of Australia during the 2019-2020 austral summer, in the first attempt to assess the total population of the subspecies baueri on the southern hemisphere non-breeding grounds. Survey coverage in New Zealand was nationwide (158 sites surveyed); surveys in Australia covered 314 sites between Great Sandy Strait in southern Queensland, and the Gulf St Vincent in South Australia. Areas north of Great Sandy Strait were either partially counted or were not visited over this survey period. Partial surveys were excluded from the survey results. The total number of godwits counted was 116,446. If allowance is made for an additional similar to 10,000 birds expected to have been present in northern Queensland (based on previous surveys), the total population of baueri in New Zealand and Australia would have been about 126,000. The 2019 breeding season was very successful, with the highest recorded number of juvenile birds since 2011 and 2012.

During southward migration from Alaska in 2006, a satellite-tracked female bar-tailed godwit (Limosa lapponica baueri) encountered adverse weather and stayed between 19 September and about 28 September 2006 at Ouvea (Loyalty Islands, New Caledonia), where she apparently died. Ouvea was visited between 27 September and 7 October 2007 to look for godwits. A total of eight godwits was recorded of which one, thought to be an adult female, may have been a dropout migrant. The remaining birds appeared to be immatures.

Following an initial aerial census of breeding New Zealand king shags (Leucocarbo carunculatus) in 2015, 2 further aerial censuses were carried out in 2016 and 1 census in 2017. In 2016, birds were photographed on 2 separate dates using a hand-held camera from inside a fixed wing aircraft. In 2017 the birds were photographed from a fixed-wing plane equipped with an automated camera system mounted below the aircraft. Photographs were independently assessed by 3 observers in 2016 and 2 observers in 2017. Nesting pairs were identified and the figures were averaged per colony for a final estimate of the number of active nests. The first census for 2016 was completed on 6 June and 89 active nests were estimated, compared with 117 nests counted on 1 July. For some colonies, breeding appeared to have just started in June 2016, so an underestimate of active breeders during the first aerial census was the probable cause. The 2017 aerial census was completed on 21 June and we identified 153 active nests. All follow up aerial surveys in 2016 and 2017 were well below the 187 active nests recorded in the 2015 study but within the historic variation. The exception to this trend is Trio Island, where no breeding colony was observed in 2017, the first time this has been recorded at this site.

Our understanding of the niche concept will remain limited while the quantity and range of different food types eaten remain a dominant proxy for niche breadth, as this does not account for the broad ecological context that governs diet. Linking nutrition, physiology and behaviour is critical to predict the extent to which a species adjusts its nutritional niche breadth at the levels of prey ("prey composition niche," defined as the range of prey compositions eaten) and diet ("realized nutritional niche" is the range of diets composed through feeding on the prey). Here, we studied adult chick-rearing Australasian gannets Morus serrator to propose an integrative approach using sea surface temperature anomalies (SSTa), geographic location and bathymetry over different years, to explore their relationship with the nutritional composition of prey and diets (i.e. prey composition and nutritional niche breadth), habitat use and foraging behaviour. We found that gannets feed on prey that varied widely in their nutritional composition (have a broad prey composition niche), and composed diets from these prey that likewise varied in composition (have a broad realized nutritional niche), suggesting generalism at two levels of macronutrient selection. Across seasons, we established "nutritional landscapes" (hereafter nutriscapes), linking the nutritional content of prey (wet mass protein-to-lipid ratio-P:L) to the most likely geographic area of capture and bathymetry. Nutriscapes varied in their P:L from 6.06 to 15.28, over time, space and bathymetry (0-150 m). During warm water events (strong positive SSTa), gannets expanded their foraging habitat, increased their foraging trip duration and consumed prey and diets with low macronutrient content (wet mass proportions of P and L). They were also constrained to the smallest prey composition and realized nutritional niche breadths. Our findings are consistent with previous suggestions that dietary generalism evolves in heterogeneous environments, and provide a framework for understanding the nutritional goals in wild marine predators and how these goals drive ecological interactions and are, in turn, ultimately shaped by environmental fluctuations.

New Zealand's endemic King Shag (Leucocarbo carunculatus) has occupied only a narrow portion of the northeastern South Island for at least the past 240years. However, pre-human Holocene fossil and archaeological remains have suggested a far more widespread distribution of the three Leucocarbo species (King, Otago, Foveaux) on mainland New Zealand at the time of Polynesian settlement in the late 13th Century CE. We use modern and ancient DNA, and morphometric and osteological analyses, of modern King Shags and Holocene fossil Leucocarbo remains to assess the pre-human distribution and taxonomic status of the King Shag on mainland New Zealand, and the resultant conservation implications. Our analyses show that the King Shag was formerly widespread around southern coasts of the North Island and the northern parts of the South Island but experienced population and lineage extinctions, and range contraction, probably after Polynesian arrival. This history parallels range contractions of other New Zealand seabirds. Conservation management of the King Shag should take into account this species narrow distribution and probable reduced genetic diversity. Moreover, combined genetic, morphometric and osteological analyses of prehistoric material from mainland New Zealand suggest that the now extinct northern New Zealand Leucocarbo populations comprised a unique lineage. Although these distinctive populations were previously assigned to the King Shag (based on morphological similarities and geographic proximity to modern Leucocarbo populations), we herein describe them as a new species, the Kohatu Shag (Leucocarbo septentrionalis). The extinction of this species further highlights the dramatic impacts Polynesians and introduced predators had on New Zealand's coastal and marine biodiversity. The prehistoric presence of at least four species of Leucocarbo shag on mainland NZ further highlights its status as a biodiversity hotspot for Phalacrocoracidae.

The foraging challenge for predators is to find and capture food with adequate levels of energy and nutrients. Marine predators require particularly sophisticated foraging strategies that enable them to balance self- and offspring-feeding, and also in many circumstances simultaneously consider the nutritional constraints of their partners. Here we combined the use of dietary analysis, proximate composition and nutritional geometry (right-angled mixture triangle nutritional models) to examine the macronutrient preferences of Australasian gannets (Morus serrator) at Farewell Spit gannetry in New Zealand. Our results showed intra- and inter-specific variation in the protein, lipid and water composition of prey captured by our sample of 111 Australasian gannets. In addition, we observed significant differences in the Australasian gannets’ nutritional niche between seasons. We provide evidence of sex-specific macronutrient foraging strategies in a successful marine predator in the wild. We have shown that in spite of fluctuations in the nutritional composition of foods available to Australasian gannets, males consistently capture prey with higher protein-to-lipid ratios and lower lipid-to-water ratios than females. These results aid to better understand the evolutionary relationship between macronutrient selection and sex-specific traits in wild animals. They also suggest an incentive for these predators to combine individually imbalanced but nutritionally complementary foods to achieve dietary balance, further highlighting the likelihood that prey selection is guided by the balance of macronutrients, rather than energy alone.

Like many migratory shorebird populations using the East Asian-Australasian Flyway, Bar-tailed Godwits Limosa lapponica baueri in New Zealand have significantly declined since the mid-1990s, but census data indicate a relatively stable population since 2004. The demographic drivers of both the decline and stabilisation remain unknown. We estimated annual survival from mark-recapture data of adult godwits in New Zealand during 2005-2014. Annual adult survival declined over the study period from 0.89-0.96 in 2005-2010 to 0.83-0.84 in 2011-2012. The simultaneous decline in annual survival found in a separate study of Bar-tailed Godwits L. l. menzbieri in north-west Australia suggests a common effect of their high dependence on threatened migratory staging sites in the Yellow Sea; the more extreme decline in L. l. menzbieri may reflect ecological differences between the populations, such as timing and extent of use of these sites. At current apparent recruitment rates, persistent adult survival of similar to 0.84 would lead to a population decline of 5-6% per year in L. l. baueri. Our study implies that the demographic precursors to a population decline developed during a period of apparent population stability; this suggests that monitoring a single index of population stability is insufficient for predicting future trends.

Prior to 1992 the total population of New Zealand king shag (Leucocarbo carunculatus) was estimated to be about 300 individuals. Between 1992 and 2002, colonies in the outer Marlborough Sounds, New Zealand were surveyed by boat and the total population was estimated to be 645 birds. About 92% of all birds occurred at Duffers Reef, North Trio Island, Sentinel Rock, and White Rocks, with an estimated 102-126 breeding pairs. A survey in February 2015 was the first to be conducted from the air. All colonies were photographed within 44 minutes prior to the morning departure and the total population was estimated to be 839 individuals. A total of 187 pairs/nests were recorded using aerial 3D images of all breeding colonies in June 2015. North Trio Island was the largest breeding colony with 33.7% of all nests, followed by Duffers Reef with 18.7% of all nests. Despite the larger revised population size, the species remains Nationally Endangered.

Patchily distributed marine pelagic prey present considerable challenges to predatory seabirds, including Gannets (Morus spp.) departing from large breeding colonies. Here, for the first time, we used GPS data loggers to provide detailed spatial, temporal, and habitat metrics of chick-rearing Australasian Gannets (Morus serrator) foraging behaviours from two distant colonies in New Zealand. Our goal was to examine the extent to which Gannet foraging tactics vary across disparate habitats, and determine whether the observed differences are consistent with predictions derived from foraging studies of other gannet species. Foraging trip performance was highly consistent between colonies, and sexes, and no significant differences in any of the variables analyzed were observed. However, Gannets from Farewell Spit (FS) dove in shallower waters (0–50 m) than birds from Cape Kidnappers (CK, >50 m), which is consistent with previous dietary studies suggesting that FS Gannets feed mainly on coastal prey, whereas CK birds feed on species with a more oceanic distribution. Diving frequencies were similar in the two colonies suggesting that Gannets were foraging in habitats with similar levels of food availability. Further studies are needed to understand the relationship between prey availability, oceanography and geographic features, to better interpret foraging tactics of Australasian Gannets.

Migrating birds make the longest non-stop endurance flights in the animal kingdom. Satellite technology is now providing direct evidence on the lengths and durations of these flights and associated staging episodes for individual birds. Using this technology, we compared the migration performance of two subspecies of bar-tailed godwit Limosa lapponica travelling between non-breeding grounds in New Zealand (subspecies baueri) and northwest Australia (subspecies menzbieri) and breeding grounds in Alaska and eastern Russia, respectively. Individuals of both subspecies made long, usually non-stop, flights from non-breeding grounds to coastal staging grounds in the Yellow Sea region of East Asia (average 10 060 +/- SD 290 km for baueri and 5860 +/- 240 km for menzbieri). After an average stay of 41.2 +/- 4.8 d, baueri flew over the North Pacific Ocean before heading northeast to the Alaskan breeding grounds (6770 +/- 800 km). Menzbieri staged for 38.4 +/- 2.5 d, and flew over land and sea northeast to high arctic Russia (4170 +/- 370 km). The post-breeding journey for baueri involved several weeks of staging in southwest Alaska followed by non-stop flights across the Pacific Ocean to New Zealand (11 690 km in a complete track) or stopovers on islands in the southwestern Pacific en route to New Zealand and eastern Australia. By contrast, menzbieri returned to Australia via stopovers in the New Siberian Islands, Russia, and back at the Yellow Sea; birds travelled on average 4510 +/- 360 km from Russia to the Yellow Sea, staged there for 40.8 +/- 5.6 d, and then flew another 56807180 km to Australia (10 820 +/- 300 km in total). Overall, the entire migration of the single baueri godwit with a fully completed return track totalled 29 280 km and involved 20 d of major migratory flight over a round-trip journey of 174 d. The entire migrations of menzbieri averaged 21 940 +/- 570 km, including 14 d of major migratory flights out of 154 d total. Godwits of both populations exhibit extreme flight performance, and baueri makes the longest (southbound) and second-longest (northbound) non-stop migratory flights documented for any bird. Both subspecies essentially make single stops when moving between non-breeding and breeding sites in opposite hemispheres. This reinforces the critical importance of the intertidal habitats used by fuelling godwits in Australasia, the Yellow Sea, and Alaska.

The diet of the Australasian gannet (Morus serrator) at Farewell Spit, New Zealand, was studied by the analysis of 70 regurgitations collected from the 1995 to 2001 breeding seasons. Surface schooling pilchard (Sardinops neopilchardus) was the main prey, followed by anchovy (Engraulis australis). The composition of the diet was similar in most seasons examined except in 1996 in which anchovy was the main prey item. Such a change in diet could be linked with a pilchard mass mortality in New Zealand in August 1995. The estimated annual prey consumption by birds at the Farewell Spit gannetry was 852 tonnes. Although annual catches of pilchard and anchovy by commercial fisheries in the area are still relatively small, an increase may interfere with prey availability, and in turn, increase competition between marine predators and influence the breeding success. Our analyses of diet are consistent with previous studies showing that Australasian gannets as flexible foragers and they highlight their importance as bioindicators of fish stocks in New Zealand.