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Little Spotted Kiwi (LSK; Apteryx owenii) have the lowest genetic diversity of five currently recognised kiwi species apparently due to a bottleneck when at most five individuals were translocated to Kapiti Island in 1912. Ancient DNA analyses show that LSK also had the lowest genetic diversity of kiwi species historically, possibly due to population bottlenecks during Pleistocene glaciation. We compare genetic diversity between LSK from Kapiti Island (extant), D’Urville Island (extinct) and the South Island of mainland New Zealand (extinct) at 495 bp of the mitochondrial control region (mtDNA) and 15 nuclear microsatellite loci (nDNA). Despite higher sample sizes in extant (n = 31 mtDNA, 97 nDNA) than recently extinct (n = 10 mtDNA, 9 nDNA) populations, extant LSK have at least 78% fewer mtDNA haplotypes and 52% fewer microsatellite alleles than recently extinct LSK. Extant LSK were strongly divergent from historical LSK for both mtDNA and nDNA (FST = 0.237 to 0.480), but showed greatest similarity with historical samples from Fiordland near the putative source population of Kapiti founders. Microsatellite data suggest that Kapiti LSK could have arisen from as few as three birds and our mtDNA data show that at least two of the founders were female. Our results indicate that substantial genetic diversity has been lost with the recent extinctions of remnant populations. Locating and protecting any last surviving individuals in presumed extinct populations will require intensive conservation efforts, but could also provide an invaluable source of genetic diversity for the species.

New Zealand’s iconic, flightless and endangered species of kiwi (Apterygidae) are at risk of extinction on the mainland due to predation by introduced mammals. In order to provide effective conservation management a robust understanding of genetic variation in the group is needed. Recent genomic analyses of kiwi suggest that several cryptic and as yet undescribed lineages occur in the South Island, most notably within a taxon that has until now been called Apteryx australis australis, the South Island Brown Kiwi or Tokoeka. In order for these lineages to be formally described and treated as separate conservation units it is first necessary to determine from which lineage of Tokoeka the holotype was collected. To determine this, we generated a near complete mitochondrial genome and nuclear SNP dataset for the holotype and compared these with living kiwi populations. Our results definitively assign the holotype to the Stewart Island population of brown kiwi which until now was recognized as a distinct subspecies Apteryx australis lawyri (Rothschild, 1893). This leads us to synonymize Apteryx lawryi Rothschild, 1893 within Apteryx australis Shaw, 1813. As the holotype was collected by sealers in the early 19th century, the result also provides a novel insight into the activities of early sealers in New Zealand. New names for taxa will need to be erected for any mainland South Island taxa described, because there are no scientific names available for taxonomy.

Small and fragmented populations may become rapidly differentiated due to genetic drift, making it difficult to distinguish whether neutral genetic structure is a signature of recent demographic events, or of long-term evolutionary processes that could have allowed populations to adaptively diverge. We sequenced 52 whole genomes to examine Holocene demographic history and patterns of adaptation in kiwi ( Apteryx ), and recovered 11 strongly differentiated genetic clusters corresponding to previously recognized lineages. Demographic models suggest that all 11 lineages experienced dramatic population crashes relative to early- or mid-Holocene levels. Small population size is associated with low genetic diversity and elevated genetic differentiation ( F ST ), suggesting that population declines have strengthened genetic structure and led to the loss of genetic diversity. However, population size is not correlated with inbreeding rates. Eight lineages show signatures of lineage-specific selective sweeps (284 sweeps total) that are unlikely to have been caused by demographic stochasticity. Overall, these results suggest that despite strong genetic drift associated with recent bottlenecks, most kiwi lineages possess unique adaptations and should be recognized as separate adaptive units in conservation contexts. Our work highlights how whole-genome datasets can address longstanding uncertainty about the evolutionary and conservation significance of small and fragmented populations of threatened species.

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Molecular dating largely overturned the paradigm that global cooling during recent Pleistocene glacial cycles resulted in a burst of species diversification although some evidence exists that speciation was commonly promoted in habitats near the expanding and retracting ice sheets. Here, we used a genome-wide dataset of more than half a million base pairs of DNA to test for a glacially induced burst of diversification in kiwi, an avian family distributed within several hundred kilometers of the expanding and retracting glaciers of the Southern Alps of New Zealand. By sampling across the geographic range of the five kiwi species, we discovered many cryptic lineages, bringing the total number of kiwi taxa that currently exist to 11 and the number that existed just before human arrival to 16 or 17. We found that 80% of kiwi diversification events date to the major glacial advances of the Middle and Late Pleistocene. During this period, New Zealand was repeatedly fragmented by glaciers into a series of refugia, with the tiny geographic ranges of many kiwi lineages currently distributed in areas adjacent to these refugia. Estimates of effective population size through time show a dramatic bottleneck during the last glacial cycle in all but one kiwi lineage, as expected if kiwi were isolated in glacially induced refugia. Our results support a fivefold increase in diversification rates during key glacial periods, comparable with levels observed in classic adaptive radiations, and confirm that at least some lineages distributed near glaciated regions underwent rapid ice age diversification.

Genetic effects are often overlooked in endangered species monitoring, and populations showing positive growth are often assumed to be secure. However, the continued reproductive success of a few individuals may mask issues such as inbreeding depression, especially in long-lived species. Here, we test for inbreeding depression in little spotted kiwi (Apteryx owenii) by comparing a population founded with two birds to one founded with 40 birds, both from the same source population and both showing positive population growth. We used a combination of microsatellite genotypes, nest observations and modelling to examine the consequences of assessing population viability exclusively via population growth. We demonstrate (i) significantly lower hatching success despite significantly higher reproductive effort in the population with two founders; (ii) positive growth in the population with two founders is mainly driven by ongoing chick production of the founding pair; and (iii) a substantial genetic load in the population founded with two birds (10-15 diploid lethal equivalents). Our results illustrate that substantial, cryptic inbreeding depression may still be present when a population is growing, especially in long-lived species with overlapping generations.

SummaryThe population growth of Brown Kiwi Apteryx mantelli was measured under four different management regimes: unmanaged, predator trapping, predator poisoning, and Bank of New Zealand Operation Nest Egg™ (BNZONE) — the removal of eggs for artificial incubation and return of resultant subadults to the wild. Life table analysis revealed that high adult mortality (7.3% per annum), caused mainly by domestic dog Canis familiaris and Ferret Mustela furo predation was the critical factor affecting Brown Kiwi populations in central Northland. The 13.8-year life expectancy of adults was only one-third of what can be expected in the absence of these two predators. Predation of Brown Kiwi chicks and juveniles (< 1 kg) by Stoats Mustela erminea and, to a lesser extent, domestic cats Felis catus, was also important. Unmanaged populations declined at 2.5% per annum. Trapping pests in a 200 ha area was largely ineffective, with the population declining by 1.7% per annum. Poisoning pests allowed Brown Kiwi populations to increase at 3.3% per annum. BNZONE proved to be by far the most effective tool, resulting in a 12.5% annual population increase, mainly due to 83% chick survival to six months old, compared with 10% survival in unmanaged sites. There were no observable behavioural problems associated with chicks being reared ex situ, but BNZONE was the most expensive tool and benefited only the Brown Kiwi. This study has helped to develop a range of tools that are now being used to facilitate recovery of populations of all four threatened species of kiwi in New Zealand, and the experimental approach used has wider application in management of other threatened species.

We present 14 microsatellite loci that were isolated from little spotted kiwi (LSK, Apteryx owenii). All loci cross-amplify in all kiwi species currently recognized except for one locus in a single species. Little spotted kiwi exhibited lower variation at these loci (mean number of alleles, H E) than other kiwi species, despite the markers having been developed for polymorphism in LSK and a far greater number of LSK genotyped than kiwi of other species. Reliable cross-species amplification and polymorphism make these markers promising new tools for the management of New Zealand’s threatened kiwi.

The presence of morphologically crypticlineages within the threatened brown kiwi ofNew Zealand has confounded their taxonomy. Recent genetic studies (Herbert and Daugherty1994; Baker et al. 1995) revealed that atleast two phylogenetic species exist within thebrown kiwi, and suggested that further researchshould resolve the taxonomic problems. In thispaper we extend genetic analyses to includesequences from 58 brown kiwi representing fivephylogenetic lineages for four mitochondrialloci (control region, cytochrome b,ATPase 6 and ATPase 8). Major lineages ofbrown kiwi are shown to be reciprocallymonophyletic, and align with other biologicaldifferences in the ecology, behavior,morphology and parasites of kiwi. BecausemtDNA sequences of major lineages of kiwi arenot evolving in a clocklike manner, we used anew penalized likelihood method withrate-smoothing to date the divergence of NorthIsland brown kiwi and the geographicallyisolated Okarito population (rowi) at about 6.2Mya. These lineages diverged about 8.2 Myafrom the brown kiwi in Fiordland and Haast inthe southern part of the South Island, and arethus older than the species of spotted kiwi(5.8 Mya). Given their distinctness, long-termgeographical isolation, lack of hybridizationin introduced populations, and accumulation ofnew biological characters within theselineages, we hypothesize that reproductiveincompatibilities have probably arisen as well. We therefore recommend that these divergentlineages be formally recognized as fullspecies; Apteryx mantelli should bere-instated for the North Island brown kiwi,A. australis should be restricted to thetokoeka, and a new species A. rowiishould be erected to describe the rowi atOkarito. Tokoeka should be split into at leastthree conservation management units (Haast,Fiordland and Stewart Island [Rakiura]), butfurther research is required to determine theexact relationships and status of theselineages. Further investigation is alsorequired into the genetic structuring of theNorth Island brown kiwi to confirm conservationmanagement units on the North Island.

Using allozymes and mtDNA sequences from the cytochrome b gene, we report that the brown kiwi has the highest levels of genetic structuring observed in birds. Moreover, the mtDNA sequences are, with two minor exceptions, diagnostic genetic markers for each population investigated, even though they are among the more slowly evolving coding regions in this genome. A major unexpected finding was the concordant split in molecular phylogenies between brown kiwis in the southern South Island and elsewhere in New Zealand. This basic phylogeographic boundary halfway down the South Island coincides with a fixed allele difference in the Hb nuclear locus and strongly suggests that two morphologically cryptic species are currently merged under one polytypic species. This is another striking example of how molecular genetic assays can detect phylogenetic discontinuities that are not reflected in traditional morphologically based taxonomies. However, reanalysis of the morphological characters by using phylogenetic methods revealed that the reason for this discordance is that most are primitive and thus are phylogenetically uninformative. Shared-derived morphological characters support the same relationships evident in the molecular phylogenies and, in concert with the molecular data, suggest that as brown kiwis colonized northward from the southern South Island, they retained many primitive characters that confounded earlier systematists. Strong subdivided population structure and cryptic species in brown kiwis seem to have evolved relatively recently as a consequence of Pleistocene range disjunctions, low dispersal power, and genetic drift in small populations.

Little spotted kiwi (Apteryx owenii) were located in their shelter burrows on Kapiti Island, off the south-west coast of the lower North Island, with the help of a trained dog. In total, 106 captures were made of 87 kiwi, 48 of which were adults, 36 juveniles (less than three years old) and three thought to be juvenile but overlapping in size with adults. Juveniles occupied home ranges between territories established by adult pairs, but sometimes dispersed over large distances. One juvenile moved one kilometre in one night. The sex ratio of captured adults did not deviate significantly from a 1:1 ratio. Adult mortality appears to be low: nine out of 10 banded birds were found in a study area nine to ten years later. Recruitment seems to be adequate, because juveniles quickly occupy territories when the original residents are removed and there are very few territories with only single adults. I conclude that the population of little spotted kiwi on Kapiti Island is self-sustaining. This conclusion...

The little spotted kiwi (Apteryx owenii) is probably extinct on both main islands of New Zealand. Its only known surviving population is on Kapiti Island (1,970 ha). Translocations to other offshore islands are seen as essential to the survival of the species. In this paper we discuss the criteria for assessment of islands for translocations, and the early results of two transfers. Only five of >700 known islands were identified as potentially suitable. None was greater than 500 ha in size. Between 1982 and 1989 little spotted kiwis were transferred to three islands, Long, Red Mercury, and Hen Is. All, or nearly all, of the transferred birds survived on Long and Red Mercury Islands and have since bred on both. The result of the transfer to Hen Island has yet to be determined. The limited potential carrying capacity of these islands for little spotted kiwis, and the need for a new transfer to a larger island, are discussed.

Conservation benefits of eradicating invasive species are clear, but these efforts can affect non-target species of special concern. We monitored the survival of little spotted kiwi (Apteryx owenii) during a program that eradicated Pacific rats (Rattus exulans) and Norway rats (R. norvegicus) from 1965-ha Kapiti Island, New Zealand. About 90% of the world population of this threatened bird was at risk during the poison operation. Two of 10 radiomarked kiwi died in the months following the aerial distribution of cereal baits containing 0.002% active ingredient brodifacoum. Of 50 adult birds banded before the toxin application, we found 46 still alive >6 months after the toxin application. At worst, 8% (3-19%) of little spotted kiwi were killed by accidental poisoning. Once natural mortality was taken into account, the actual toxin-induced mortality was much lower than this. The population of little spotted kiwi on Kapiti Island did not appear to be affected by brodifacoum long-term, because accidental losses were compensated by high productivity in the breeding seasons following rat eradication.