Brown Kiwi Research Articles

Aspects of the development of Ixodes anatis under different environmental conditions in the laboratory and in the field

BackgroundNumerous laboratory and fewer field-based studies have found that ixodid ticks develop more quickly and survive better at temperatures between 18 °C and 26 °C and relative humidity (RH) between 75 and 94%. Ixodes anatis Chilton, 1904, is an endophilic, nidicolous species endemic to North Island brown kiwi (Apteryx mantelli) (NIBK) and the tokoeka (Apteryx australis), and little is known about the environmental conditions required for its development. The aims of this study were to determine and compare the conditions of temperature and RH that ensure the best survival of the kiwi tick and the shortest interstadial periods, in laboratory conditions and outdoors inside artificial kiwi burrows.MethodsFree-walking engorged ticks were collected off wild kiwi hosts and placed in the laboratory under various fixed temperature and humidity regimes. In addition, sets of the collected ticks at different developmental stages were placed in artificial kiwi burrows. In both settings, we recorded the times taken for the ticks to moult to the next stage.ResultsLarvae and nymphs both showed optimum development at between 10 °C and 20 °C, which is lower than the optimum temperature for development in many other species of ixodid ticks. However, larvae moulted quicker and survived better when saturation deficits were < 1–2 mmHg (RH > 94%); in comparison, the optimum saturation deficits for nymph development were 1–10 mmHg.ConclusionsOur results suggest that the kiwi tick has adapted to the stable, but relatively cool and humid conditions in kiwi burrows, reflecting the evolutionary consequences of its association with the kiwi.Graphical

Genetic factors for short life span associated with evolution of the loss of flight ability.

Acquisition or loss of flying ability is evolutionarily linked with maximum life span (MLS) in mammals and birds. Although ecological factors, such as extrinsic mortality, may lead to either shortened or extended life spans through natural selection, MLS is influenced by complex molecular and metabolic processes, and the genetic changes associated with flying ability that have led to either a longer or shorter MLS are unknown. Here, we examine the parallel evolution of flight in mammals and birds and investigate positively selected genes at branches where either the acquisition (in little brown bats and large flying foxes) or loss (in Adélie penguins, emperor penguins, common ostriches, emus, great spotted kiwis, little spotted kiwis, okarito brown kiwis, greater rheas, lesser rheas, and cassowaries) of flight abilities occurred. Although we found no shared genes under selection among all the branches of interest, 7 genes were found to be positively selected in 2 of the branches. Among the 7 genes, only IGF2BP2 is known to affect both life span and energy expenditure. The positively selected mutations detected in IGF2BP2 likely affected the functionality of the encoded protein. IGF2BP2, which has been reported to simultaneously prolong life span and increase energy expenditure, could be responsible for the evolution of shortened MLS associated with the loss of flying ability.

Nematode larva migrans caused by Toxocara cati in the North Island brown kiwi (Apteryx mantelli)

Sporadic cases of visceral and neural nematode larva migrans have been diagnosed at necropsy in the endangered New Zealand kiwi (Apteryx spp.), but the causative organisms have not yet been definitively identified. From an initial group of five affected kiwi, PCR was performed on DNA extracted from archival formalin-fixed paraffin-embedded tissue sections in which larval nematodes had been histologically identified. Sequencing of positive results from four out of the five kiwi aligned with sequences from Toxocara cati, a nematode parasite whose definitive host is the domestic cat. PCR was then performed on a second group of 12 kiwi that had histologic inflammatory lesions consistent with larva migrans, but variable larval presence. Repeatable positive PCR results were only achieved in one tissue, in which larval organisms were histologically confirmed. This study supports the use of PCR as an alternative or adjunct to the morphological identification of nematode larvae in formalin-fixed histopathological samples, as well as showing that in investigation of larva migrans, PCR has greatest chance of success from sections where nematode larvae are evident histologically. The identification of Toxocara cati from lesions of larva migrans in kiwi reflects an indirect, parasite-mediated effect of an invasive mammalian species on a native species.

Does the economic benefit of biodiversity enhancement exceed the cost of conservation in planted forests?

This study evaluates a proposed programme that would sustain and enhance the provision of ecosystem services in planted forests. We focused on the evaluation of the benefits and costs of the conservation of the New Zealand brown kiwi, an iconic yet threatened bird species that inhabits planted forests. Yao et al. (2014) found that a sample of 209 New Zealand (NZ) households would, on average, financially support a brown kiwi conservation programme in planted forests. We extend that study using a proof of concept that integrates economic, ecological and spatial approaches. We undertake this in five steps: 1) supplementing a previous discrete choice experiment survey by interviewing more than 900 additional georeferenced households; 2) estimating household-specific means of marginal willingness-to-pay (WTP) values; 3) using econometrics and geospatial approaches to explore WTP determinants; 4) identifying 12 ecologically and economically feasible ecosystem-service sites and calculate the costs of a conservation programme at each site; and 5) aggregating the public benefits of biodiversity at the regional and national levels and calculate the cost-benefit ratio. We found that the value of the proposed biodiversity conservation initiative at the national level can be more than 100 times higher than the overall cost of the programme.

Factors affecting abundance of different stages of the endophilic tick Ixodes anatis in brown kiwi (Apteryx mantelli) shelters

Ixodes anatis is a species of endophilic (nidicolous) tick species parasitizing brown kiwi (Apteryx mantelli). Even though they are endemic to New Zealand like their host, very little is known about these ticks or their population dynamics and relationships with their hosts. We conducted a study from May 2013 to June 2014 to evaluate the effect of shelter location (one of three gullies), habitat (forest, scrub and pasture) and type (tree, soil and surface) on the abundance of the different life stages of I. anatis. In total, 12,172 ticks were collected from 63 shelters, which were sampled monthly for 11 months over the 14 month period. Un-engorged larvae predominated over other stages accounting for 87.2% of the samples collected. We found that location, habitat in which the shelters were located, and the type of shelter were significant predictors of I. anatis abundance. Tree shelters in forests had significantly higher tick abundance than those in scrub and pasture. Tree and soil shelters in general had significantly more ticks than surface shelters. Shelters located in Kauri Bush a drier site, had higher abundances than those in wetter sites. While some of these changes can be explained with the movement of the host, we believe more research needs to be done on the effect of shelters’ microclimate on I. anatis’ life cycle.

Serum prolactin and testosterone levels in captive and wild brown kiwi (Apteryx mantelli) during the prebreeding, breeding, and incubation periods.

In brown kiwi (Apteryx mantelli), the male is the primary incubator, a trait that is relatively rare among birds. The maintenance of avian incubation behavior is controlled by the protein hormone prolactin (PRL). Although steroid hormone concentrations in both wild and captive kiwi have previously been reported, this study is the first to report levels of PRL in captive and wild male and female kiwi through the prebreeding and breeding seasons, and to directly compare testosterone (T) concentrations between captive and wild males during the breeding and incubation periods. Female PRL concentrations increased at the time of oviposition, whereas male PRL concentrations rose gradually between the prebreeding and incubation periods. Although males are considered the main incubator, an increase in PRL levels could help females maintain behaviors such as nest guarding, or to take over incubation the event of mate loss. A gradual increase in PRL allows the male to be ready for incubation during the long breeding season. Interestingly, T concentrations in captive males did not decrease during incubation and was significantly higher than in wild males. Continual elevated T could have an impact on sperm production through negative feedback, thereby contributing to the low egg fertility seen in captive kiwi. Therefore, determining the underlying reason for the differences in hormone levels could be significant, if not vital, for improving the success of captive kiwi breeding programs.

Isolation and genotyping of Campylobacter species from kiwi (Apteryx spp.) in captivity: implications for transmission to and from humans

ABSTRACTAims: To investigate the presence of Campylobacter spp. in captive kiwi (Apteryx spp.) and compare their genotypic profiles with those of human and animal origin, in order to assess their potential for zoonotic or zooanthroponotic transmission.Methods: Conventional selective enrichment and filter-based isolation methods were applied to isolate Campylobacter spp. from fresh faecal samples from 12 North Island brown kiwi (Apteryx mantelli) and one great spotted kiwi (A. haastii), housed in one of five different areas in a kiwi sanctuary in Christchurch, New Zealand. Isolates were identified using multiplex PCR and 16S rRNA gene sequencing. High-resolution rapid genotyping using multiplex ligation-dependant probe amplification-based binary typing (MBiT) was applied and profiles compared with similar results from 2,165 Campylobacter spp. isolates contained in a database derived from human clinical, veterinary and environmental samples.Results: One isolate of C. jejuni, and one belonging to the C. lari phylogenetic group were recovered from faeces from two kiwi. High-resolution rapid genotyping by MBiT demonstrated these to be indistinguishable from isolates obtained previously from human cases of diarrhoea, and others from chicken, cattle, sheep and water.Conclusions: These data provide evidence for potential zoonotic or zooanthroponotic transmission of Campylobacter spp. in kiwi with implications for management of birds kept in captivity. We believe this is the first formal report of C. jejuni and a C. lari-like organism in kiwi.Abbreviations: MBiT: Multiplex ligation-dependant probe amplification-based binary typing

Apparent lack of efficacy of toltrazuril against Eimeria species affecting brown kiwi (Apteryx mantelli) at a captive rearing facility

AIM: To assess the efficacy of toltrazuril against the Eimeria spp. affecting brown kiwi (Apteryx mantelli).METHODS: Droppings were collected from three brown kiwi, aged <6 months old, at a captive rearing facility in the North Island of New Zealand, between 22 February and 20 April 2017, on 14 sampling dates. Only droppings (n=30) that were excreted between 03:00 and 07:00, as determined using video surveillance, were included for analysis, reflecting the peak time for shedding of coccidial oocysts for brown kiwi. Oocysts were quantified in each sample and Eimeria species identified on the basis of oocyst morphology. All samples were collected between 2 and 10 days after the birds had been treated with 25 mg/kg toltrazuril.RESULTS: Eimeria spp. oocysts were identified in 28/30 individual samples and on 14/14 sampling dates. Oocyst counts varied from 0 to 328,080 oocysts per gram (opg), and at least one oocyst count >10,000 opg was measured on 12/14 sampling dates. Three species of Eimeria were observed, with Eimeria apteryxii and E. kiwii most commonly encountered, whereas only one sample contained E. paraurii.CONCLUSIONS AND CLINICAL RELEVANCE: In the three birds monitored at this research site, there was a high abundance of E. apteryxii and E. kiwii oocysts in droppings despite recent administration of toltrazuril. These results suggest that the populations of Eimeria spp. affecting brown kiwi at this location appear to possess an ability to survive exposure to toltrazuril. Toltrazuril is widely used at captive rearing facilities to limit the effects of coccidiosis in juvenile kiwi. If a lack of efficacy is confirmed, it will be necessary to investigate alternative treatment regimens alongside broader environmental management strategies.

The circadian variation of oocyst shedding of Eimeria spp. affecting brown kiwi (Apteryx mantelli).

Captive rearing of wild brown kiwi (Apteryx mantelli) is widely carried out to assist in the recovery of this declining species. As a consequence, high densities of immunologically naïve kiwi are commonly housed in semi-captive conditions, with the potential to result in substantial morbidity and mortality from coccidiosis caused by multiple species of Eimeria. Previous research has described circadian variation in oocyst shedding across multiple avian host species. The aim of this research was to describe any circadian variation in oocyst shedding in brown kiwi. Droppings were collected from brown kiwi (n = 4) at a single captive rearing facility using video surveillance to determine the time of excretion, and oocyst counts were undertaken. Results show that two of the Eimeria spp. affecting brown kiwi exhibit a peak in oocyst shedding between 03.00 and 07.00 with few or no oocysts shed between 08.00 and midnight. These results are not able to be explained by the current hypotheses theorising the evolutionary forces behind the development of this adaptive trait. Our findings increase the current understanding of the biology of the Eimeria spp. affecting brown kiwi and have important implications for the management of captive-reared kiwi, in particular for the accurate interpretation of faecal oocyst counts.

New Zealand's kiwis may be losing eyesight

Blind kiwis seem able to survive quite happily using other senses. It's possible that the flightless birds are evolving to lose their sight--so vision might actually be a waste of energy for them. The discovery of the blind birds came when researchers studied a group of 160 endangered Okarito brown kiwis in the Okarito forest on New Zealand's South Island. We found a very high prevalence of birds with eye lesions, says Alan Tennyson at the Museum of New Zealand Te Papa Tongarewa in Wellington. A third of them had eye problems. But the biggest surprise was chancing upon three sightless birds. No other birds are known to have a free-living population of blind [individuals], says Tennyson.

Interspecies differences in plasma concentrations of 25-hydroxyvitamin D3 and dermal Vitamin D synthesis of kiwi (Apteryx mantelli), tuatara (Sphenodon punctatus), and New Zealand sea lions (Phocarctos hookeri).

Vitamin D plays a central role in calcium homeostasis of most vertebrates, and is obtained in different species through diet, dermal synthesis, or a combination of both. The aim of this study was to determine the predominant routes of Vitamin D synthesis in three disparate species, brown kiwi (Apteryx mantelli), tuatara (Sphenodon punctatus), and New Zealand sea lions (Phocarctos hookeri). We surveyed plasma concentrations of 25-hydroxyvitamin D2 and D3, analysed environmental conditions and life history factors, and determined the ability of skin samples to synthesise Vitamin D3 on exposure to ultraviolet-B radiation. There was variation in the plasma/serum 25-hydroxyvitamin D3 concentrations between and within the species studied, with wild kiwi having the lowest concentrations and NZ sea lions the highest. Kiwi skin produced small but measurable amounts of Vitamin D3, while tuatara skin produced Vitamin D3 concentrations higher than that of kiwi. New Zealand sea lion skin produced the highest amount of Vitamin D3 and differed from the other two species in this study in that Vitamin D3 was present in skin before UV-B exposure. The results from this study show that all three species studied retained the ability to use both dietary and dermal sources of Vitamin D, although there was interspecies variation in the magnitude of dermal synthesis. Comparisons between these species show that there are differences in their Vitamin D pathways, but suggest that there are more factors contributing to these pathways than might be expected solely from life history characteristics.

Description of four new species of coccidia (Apicomplexa: Eimeriidae) from brown kiwi, Apteryx mantelli, in New Zealand.

This study used morphological techniques to describe and name four new species of coccidia from the brown kiwi (Apteryx mantelli). Four distinct eimerian oocyst species were recovered that we describe as new species. The largest of these, Eimeria paraurii n. sp. measured 32.2×19.8μm and is morphologically similar to gametocytes previously described histologically in colorectal polyps (Morgan et al. in Parasitol Res 111(4):1689-1699, 2012). Eimeria apteryxii n. sp. measured 23.9×14.9μm and is similar to renal oocysts described histologically in brown, rowi (A. rowii) and Haast tokoeka kiwi (A. australis "Haast") (Morgan et al. in Avian Pathol 42(2):137-146, 2013). Eimeria kiwii n. sp. measured 14.8×13.9μm and resembled gametocytes described previously in kiwi intestinal epithelial cells in brown kiwi (Morgan et al. in Parasitol Res 111(4):1689-1699, 2012). Eimeria mantellii n. sp. measured 17.8×10.7μm and did not appear similar to any coccidia previously described in histological studies in kiwi. These are the first species of Eimeria to be described and named from brown kiwi. Because the morphological descriptions in the present study were determined from a limited number of kiwi droppings from two geographical locations, it is likely that these represent only a portion of Eimeria species present in other populations of both brown kiwi and other Apteryx species from around New Zealand.

The complete mitochondrial genome of North Island brown kiwi (Apteryx mantelli)

Here, we report the complete mitochondrial genome sequence of North Island brown kiwi(Apteryx mantelli). The genome is found to be 16,694 bp in length and has a base composition of A (30.74%), G (13.46%), C (26.50%), and T (29.30%). Similar to other Apteryx species, it contains a typically conserved structure including 13 protein-coding genes, 2 rRNA genes, 1 control region (D-loop), and 22tRNA genes. The proportion of coding sequences with a total length of 11,431 bp is 68.47%, which encodes 3776 amino acids. All protein-coding genes started with Met, and ND2, COX2, and COX3 ended by TAA as a stop codon. The lengths of 12S ribosomal RNA and 16S ribosomal RNA are 973 bp and 1596 bp, respectively. The length of control region is 1112 bp, ranging from 15,583 bp to 16,694 bp. The complete mitochondrial genome sequence provided here would be useful for further understanding the evolution of ratite and conservation genetics of A. mantelli.

Roosting Preferences of North Island Brown Kiwis (Apteryx mantelli)

ABSTRACT The North Island Brown Kiwi (Apteryx mantelli) is a nocturnal endangered species endemic to New Zealand. The protection of suitable habitat is key to the species' recovery; however, little is known about their habitat requirements. We studied the diurnal roosting behaviours of kiwis by intensely tracking 41 radio-tagged, non-breeding adults from May 2010 to February 2012 on Ponui Island, New Zealand. From these birds, we collected 3,997 roosting locations in three different macro-habitat types (scrub, forest, and swamp) and described 223 roosting burrows in the forest macro-habitat. Overall, we discovered that kiwis were roosting generalists; three quarters of the study population was found in more than one macro-habitat and just 5% used only a single type of micro-habitat. However, using compositional analyses, we found that they did show some clear preferences. On a macro-habitat level, kiwis preferred forest habitat over scrub or swamp. Furthermore, on a micro-habitat level, they preferred roo...

A new marker based on the avian spindlin gene that is able to sex most birds, including species problematic to sex with CHD markers.

We have developed a new marker (Z43B) that can be successfully used to identify the sex of most birds (69%), including species difficult or impossible to sex with other markers. We utilized the zebra finch Taeniopygia guttata EST microsatellite sequence (CK309496) which displays sequence homology to the 5' untranslated region (UTR) of the avian spindlin gene. This gene is known to be present on the Z and W chromosomes. To maximize cross-species utility, the primer set was designed from a consensus sequence created from homologs of CK309496 that were isolated from multiple distantly related species. Both the forward and reverse primer sequences were 100% identical to 14 avian species, including the Z chromosome of eight species and the chicken Gallus gallus W chromosome, as well as the saltwater crocodile Crocodylus porosus. The Z43B primer set was assessed by genotyping individuals of known sex belonging to 61 non-ratite species and a single ratite. The Z and W amplicons differed in size making it possible to distinguish between males (ZZ) and females (ZW) for the majority (69%) of non-ratite species tested, comprising 10 orders of birds. We predict that this marker will be useful for obtaining sex-typing data for ca 6,869 species of birds (69% of non-ratites but not galliforms). A wide range of species could be sex-typed including passerines, shorebirds, eagles, falcons, bee-eaters, cranes, shags, parrots, penguins, ducks, and a ratite species, the brown kiwi, Apteryx australis. Those species sexed include species impossible or problematic to sex-type with other markers (magpie, albatross, petrel, eagle, falcon, crane, and penguin species). Zoo Biol. 35:533-545, 2016. © 2016 The Authors. Zoo Biology published by Wiley Periodicals, Inc.

Short pulse of 1080 improves the survival of brown kiwi chicks in an area subjected to long-term stoat trapping

ABSTRACTMany mainland populations of kiwi are declining because stoats (Mustela erminea) kill most of their chicks. Stoats are often trapped during conservation programmes, but the long-term effectiveness of trapping has not been measured. During continuous trapping of mammalian predators in the 9800 ha Whangarei Kiwi Sanctuary, the survival of brown kiwi (Apteryx mantelli) chicks declined over time. Following the use of sodium fluoroacetate (1080) to kill rats (Rattus spp.) and possums (Trichosurus vulpecula) and likely secondary poisoning of stoats, chick survival at Riponui increased from 5% to 56%, and the 62% chick survival at Rarewarewa was better than the 20% recorded in a trapped-only area nearby. We suggest that untrappable stoats accumulate in areas subjected to continuous predator trapping. Conservation managers should build into their long-term pest control programmes a periodic pulse of an alternative tool to kill pests that, for whatever reason, actively avoid the primary control tool.

Description, molecular characterisation, diagnostics and life cycle of Plasmodium elongatum (lineage pERIRUB01), the virulent avian malaria parasite

Plasmodium elongatum causes severe avian malaria and is distributed worldwide. This parasite is of particular importance due to its ability to develop and cause lethal malaria not only in natural hosts, but also in non-adapted endemic birds such as the brown kiwi and different species of penguins. Information on vectors of this infection is available but is contradictory. PCR-based analysis indicated the possible existence of a cluster of closely related P. elongatum lineages which might differ in their ability to develop in certain mosquitoes and birds. This experimental study provides information about molecular and morphological characterisation of a virulent P. elongatum strain (lineage pERIRUB01) isolated from a naturally infected European robin, Erithacus rubecula. Phylogenetic analysis based on partial cytochrome b gene sequences showed that this parasite lineage is closely related to P. elongatum (lineage pGRW6). Blood stages of both parasite lineages are indistinguishable, indicating that they belong to the same species. Both pathogens develop in experimentally infected canaries, Serinus canaria, causing death of the hosts. In both these lineages, trophozoites and erythrocytic meronts develop in polychromatic erythrocytes and erythroblasts, gametocytes parasitize mature erythrocytes, exoerythrocytic stages develop in cells of the erythrocytic series in bone marrow and are occasionally reported in spleen and liver. Massive infestation of bone marrow cells is the main reason for bird mortality. We report here on syncytium-like remnants of tissue meronts, which slip out of the bone marrow into the peripheral circulation, providing evidence that the syncytia can be a template for PCR amplification. This finding contributes to better understanding positive PCR amplifications in birds when parasitemia is invisible and improved diagnostics of abortive haemosporidian infections. Sporogony of P. elongatum (pERIRUB01) completes the cycle and sporozoites develop in widespread Culex quinquefasciatus and Culex pipiens pipiens form molestus mosquitoes. This experimental study provides information on virulence and within species lineage diversity in a single pathogenic species of haemosporidian parasite.

The UCSC Genome Browser database: 2017 update.

Since its 2001 debut, the University of California, Santa Cruz (UCSC) Genome Browser (http://genome.ucsc.edu/) team has provided continuous support to the international genomics and biomedical communities through a web-based, open source platform designed for the fast, scalable display of sequence alignments and annotations landscaped against a vast collection of quality reference genome assemblies. The browser's publicly accessible databases are the backbone of a rich, integrated bioinformatics tool suite that includes a graphical interface for data queries and downloads, alignment programs, command-line utilities and more. This year's highlights include newly designed home and gateway pages; a new ‘multi-region’ track display configuration for exon-only, gene-only and custom regions visualization; new genome browsers for three species (brown kiwi, crab-eating macaque and Malayan flying lemur); eight updated genome assemblies; extended support for new data types such as CRAM, RNA-seq expression data and long-range chromatin interaction pairs; and the unveiling of a new supported mirror site in Japan.

Avian malaria in introduced, native and endemic New Zealand bird species in a mixed ecosystem

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.

Kiwi genome provides insights into evolution of a nocturnal lifestyle.

BackgroundKiwi, comprising five species from the genus Apteryx, are endangered, ground-dwelling bird species endemic to New Zealand. They are the smallest and only nocturnal representatives of the ratites. The timing of kiwi adaptation to a nocturnal niche and the genomic innovations, which shaped sensory systems and morphology to allow this adaptation, are not yet fully understood.ResultsWe sequenced and assembled the brown kiwi genome to 150-fold coverage and annotated the genome using kiwi transcript data and non-redundant protein information from multiple bird species. We identified evolutionary sequence changes that underlie adaptation to nocturnality and estimated the onset time of these adaptations. Several opsin genes involved in color vision are inactivated in the kiwi. We date this inactivation to the Oligocene epoch, likely after the arrival of the ancestor of modern kiwi in New Zealand. Genome comparisons between kiwi and representatives of ratites, Galloanserae, and Neoaves, including nocturnal and song birds, show diversification of kiwi’s odorant receptors repertoire, which may reflect an increased reliance on olfaction rather than sight during foraging. Further, there is an enrichment of genes influencing mitochondrial function and energy expenditure among genes that are rapidly evolving specifically on the kiwi branch, which may also be linked to its nocturnal lifestyle.ConclusionsThe genomic changes in kiwi vision and olfaction are consistent with changes that are hypothesized to occur during adaptation to nocturnal lifestyle in mammals. The kiwi genome provides a valuable genomic resource for future genome-wide comparative analyses to other extinct and extant diurnal ratites.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-015-0711-4) contains supplementary material, which is available to authorized users.