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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.

Maintaining genetic diversity and genetic structure in threatened species is recognised as important, but genetic data are frequently missing from management plans. We use a panel of 11 highly poly...

Kiwi (Apteryx spp.) are highly threatened flightless birds endemic to New Zealand. They are members of the most basal extant avian lineage, the paleognaths, and exhibit a suite of traits that are unusual in birds. Despite their iconic and imperiled status, there have been only four genomic studies of kiwi to date with only two of these aimed at improving conservation. There is, therefore, massive opportunity to use genomic techniques to elucidate the genetic basis and consequences of the strange ecology and evolution of kiwi and to inform their intensive management. In this chapter, we review genomic studies in paleognaths, assess prospects for the future of kiwi genomics, and define some lessons for population genomics and conservation of at-risk taxa generally. We also present an analysis of genomic signatures associated with the evolution of Apterygidae and the genes involved in diversification of kiwi via comparison of 3,774 orthologous protein coding genes among 28 avian species. We found strong signals of selection in genes associated with dwarfism, neurogenesis, retinal development, and temperature regulation. Our results provide clues as to why kiwi have such small body size (relative to other paleognaths), large egg size (relative to their body size), excellent olfaction, and poor vision. The data further suggest that coping with highly divergent temperature regimes may be a defining feature of the spotted kiwi clade which includes the only kiwi species that inhabits the alpine zone. Considerable genomic resources are now available for kiwi, including whole-genome sequences, transcriptome assemblies, thousands of SNP markers, and numerous candidate genes. There is also a myriad of outstanding questions about kiwi that genomic studies can inform. The challenge now is to bring these new genomic tools to bear on conservation and management of kiwi.

Pedigrees are frequently recommended for estimating inbreeding coefficients (F PED ), but are error-prone due to missing behavioural data in wild populations. Genetic marker-based pedigrees have been suggested as a remedy to this problem, but their accuracy depends on the number and polymorphism of loci available, and the completeness of population sampling. We used simulations to examine how accuracy of marker-based pedigrees varies with number of loci and sampling regime when allelic diversity is low (2.2–4 alleles per locus in founders), as is often the case in threatened species. We also examined the impact of pedigree errors on the validity of F PED estimated from marker-based pedigrees. Our results indicate that accurate parentage assignments are only feasible if genotypes are available for all individuals that ever existed in the population, and that accuracy does not improve past 40 loci. Errors in marker-based pedigrees resulted in underestimation of F PED by up to 27 % and overestimation of the variance in F PED by up to 182 %. At least 80 % pedigree accuracy was required to produce unbiased estimates of F PED , which were still highly imprecise. Given the degree of sampling required, it is not currently feasible to measure inbreeding in wild populations of threatened species with a pedigree based solely on microsatellite data. Resources may be better directed towards developing more robust genetic tools (whole genome sequencing and large SNP panels) to facilitate direct estimation of inbreeding coefficients without a pedigree. Where this is not possible, long-term monitoring projects will be required to accurately estimate inbreeding coefficients via a combination of behavioural and genetic data.

Measuring hatching success in birds is important for assessing population viability, but nests are often cryptic and may be abandoned if birds are disturbed during nesting. We evaluated the suitability of Wildtech New Zealand Ltd's Chick Timer™ radio telemetry software for monitoring hatching success in little spotted kiwi (Apteryx owenii). The software provided accurate reports of activity levels and times of nest emergence by adult birds. Eighty four per cent of incubation attempts and 70% of first hatching events were detected, with no false indications of incubation or hatching. Our results suggest that this technology will facilitate studies of hatching success in little spotted kiwi and other large birds with cryptic or inaccessible nests. A ground truthing study such as this one, however, is required before full implementation of the software in any species.

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.

Major histocompatibility complex (MHC) genes are important for vertebrate immune response and typically display high levels of diversity due to balancing selection from exposure to diverse pathogens. An understanding of the structure of the MHC region and diversity among functional MHC genes is critical to understanding the evolution of the MHC and species resilience to disease exposure. In this study, we characterise the structure and diversity of class II MHC genes in little spotted kiwi Apteryx owenii, a ratite bird representing the basal avian lineage (paleognaths). Results indicate that little spotted kiwi have a more complex MHC structure than that of other non-passerine birds, with at least five class II MHC genes, three of which are expressed and likely to be functional. Levels of MHC variation among little spotted kiwi are extremely low, with 13 birds assayed having nearly identical MHC genotypes (only two genotypes containing four alleles, three of which are fixed). These results suggest that recent genetic drift due to a species-wide bottleneck of at most seven birds has overwhelmed past selection for high MHC diversity in little spotted kiwi, potentially leaving the species highly susceptible to disease.

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.

Salmonids spawn in highly diverse habitats, exhibit strong genetic population structuring, and can quickly colonize newly created habitats with few founders. Spawning traits often differ among populations, but it is largely unknown if these differences are adaptive or due to genetic drift. To test if sockeye salmon (Oncorhynchus nerka) populations are adapted to glacial, beach, and tributary spawning habitats, we examined variation in heritable phenotypic traits associated with spawning in 13 populations of wild sockeye salmon in Lake Clark, Alaska. These populations were commonly founded between 100 and 400 hundred sockeye salmon generations ago and exhibit low genetic divergence at 11 microsatellite loci (FST < 0.024) that is uncorrelated with spawning habitat type. We found that mean PST (phenotypic divergence among populations) exceeded neutral FST for most phenotypic traits measured, indicating that phenotypic differences among populations could not be explained by genetic drift alone. Phenotypic divergence among populations was associated with spawning habitat differences, but not with neutral genetic divergence. For example, female body color was lighter and egg color was darker in glacial than non-glacial habitats. This may be due to reduced sexual selection for red spawning color in glacial habitats and an apparent trade-off in carotenoid allocation to body and egg color in females. Phenotypic plasticity is an unlikely source of phenotypic differences because Lake Clark sockeye salmon spend nearly all their lives in a common environment. Our data suggest that Lake Clark sockeye salmon populations are adapted to spawning in glacial, beach and tributary habitats and provide the first evidence of a glacial spawning ecotype in salmonids. Glacial spawning habitats are often young (i.e.

Traditional ecological knowledge can be highly informative and integrated with complementary scientific knowledge to improve species management. This is especially true for abundant species with which indigenous peoples have frequent interactions (e.g., through harvest), but has been studied less frequently in isolated or declining species. We examined Maori traditional ecological knowledge of tuatara (Sphenodon spp., reptiles that resemble lizards but are the last living representatives of the order Sphenodontia) through semidirected interviews of elders of Te Atiawa, Ngati Koata, and Ngati Wai Iwi (similar to tribes), the guardians of several islands currently inhabited by tuatara. Maori are indigenous to New Zealand, having settled 800 to 1000 years ago. Tuatara are endemic to New Zealand, have declined in numbers since human settlement, and are now restricted to 37 offshore islands. The detail and volume of tuatara traditional ecological knowledge were less than that recorded in studies of more abundant or accessible species. In addition, traditional knowledge of the cultural significance of tuatara was more common and detailed among the elders than traditional knowledge of tuatara biology or ecology. The traditional knowledge collected, however, provided the first evidence of seven former sites of tuatara occupation, suggested five additional sites tuatara may currently occupy, contained novel hypotheses for scientific testing, and described tuatara cultural roles that have not been reported previously. We conclude that, in at least some cases, traditional ecological knowledge may persist as species decline and may serve as a valuable source of ecological information for conservation.

Background Kiwi represent the most basal extant avian lineage (paleognaths) and exhibit biological attributes that are unusual or extreme among living birds, such as large egg size, strong olfaction, nocturnality, flightlessness and long lifespan. Despite intense interest in their evolution and their threatened status, genomic resources for kiwi were virtually non-existent until the recent publication of a single genome. Here we present the most comprehensive kiwi transcriptomes to date, obtained via Illumina sequencing of whole blood and de novo assembly of mRNA sequences of eight individuals from each of the two rarest kiwi species, little spotted kiwi (LSK; Apteryx owenii) and rowi (A. rowi). Results Sequences obtained were orthologous with a wide diversity of functional genes despite the sequencing of a single tissue type. Individual and composite assemblies contain more than 7900 unique protein coding transcripts in each of LSK and rowi that show strong homology with chicken (Gallus gallus), including those associated with growth, development, disease resistance, reproduction and behavior. The assemblies also contain 66,909 SNPs that distinguish between LSK and rowi, 12,384 SNPs among LSK (associated with 3088 genes), and 29,313 SNPs among rowi (associated with 4953 genes). We found 3084 transcripts differentially expressed between LSK and rowi and 150 transcripts differentially expressed between the sexes. Of the latter, 83 could be mapped to chicken chromosomes with 95% syntenic with chromosome Z. Conclusions Our study has simultaneously sequenced multiple species, sexes, and individual kiwi at thousands of genes, and thus represents a significant leap forward in genomic resources available for kiwi. The expression pattern we observed among chromosome Z related genes in kiwi is similar to that observed in ostriches and emu, suggesting a common and ancestral pattern of sex chromosome homomorphy, recombination, and gene dosage among living paleognaths. The transcriptome assemblies described here will provide a rich resource for polymorphic marker development and studies of adaptation of these highly unusual and endangered birds. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2714-2) contains supplementary material, which is available to authorized users.

Bottlenecks can have lasting effects on genetic population structure that obscure patterns of contemporary gene flow and drift. Sockeye salmon are vulnerable to bottleneck effects because they are a highly structured species with excellent colonizing abilities and often occupy geologically young habitats. We describe genetic divergence among and genetic variation within spawning populations of sockeye salmon throughout the Lake Clark area of Alaska. Fin tissue was collected from sockeye salmon representing 15 spawning populations of Lake Clark, Six-mile Lake, and Lake Iliamna. Allele frequencies differed significantly at 11 microsatellite loci in 96 of 105 pairwise population comparisons. Pairwise estimates of FST ranged from zero to 0.089. Six-mile Lake and Lake Clark populations have historically been grouped together for management purposes and are geographically proximate. However, Six-mile Lake populations are genetically similar to Lake Iliamna populations and are divergent from Lake Clark populations. The reduced allelic diversity and strong divergence of Lake Clark populations relative to Six-mile Lake and Lake Iliamna populations suggest a bottleneck associated with the colonization of Lake Clark by sockeye salmon. Geographic distance and spawning habitat differences apparently do not contribute to isolation and divergence among populations. However, temporal isolation based on spawning time and founder effects associated with ongoing glacial retreat and colonization of new spawning habitats contribute to the genetic population structure of Lake Clark sockeye salmon. Nonequilibrium conditions and the strong influence of genetic drift caution against using estimates of divergence to estimate gene flow among populations of Lake Clark sockeye salmon.

The effective conservation of salmonids requires the recognition and preservation of populations that are diverse in genetic composition and life history. The management of sockeye salmon Oncorhynchus nerka in Bear Lake, Alaska, is based on the presumption that there are two, genetically isolated seasonal runs that exhibit a bimodal escapement pattern. We investigated the genetic composition and life history of the putative early and late runs in two consecutive years. Significant allele frequency differences at six microsatellite loci demonstrate restricted gene flow between the early and late runs (F ST = 0.017). There were also significant, and presumably adaptive, differences between the runs with respect to body weight, somatic weight, ovary weight, and egg size among females after correction to equal body sizes. Further, scale pattern analysis revealed highly significant differences in the growth-at-age patterns of these runs. These results demonstrate that there are significant genetic dif...

Tag retention and tag-related mortality are concerns for any tagging study but are rarely estimated. We assessed retention and mortality rates for esophageal radio tag implants in adult sockeye salmon Oncorhynchus nerka. Migrating sockeye salmon captured at the outlet of Lake Clark, Alaska, were implanted with one of four different radio tags (14.5 × 43 mm (diameter × length), 14.5 × 49 mm, 16 × 46 mm, and 19 × 51 mm). Fish were observed for 15 to 35 d after tagging to determine retention and mortality rates. The overall tag retention rate was high (0.98; 95% confidence interval (CI), 0.92-1.00; minimum, 33 d), with one loss of a 19-mm × 51- mm tag. Mortality of tagged sockeye salmon (0.02; 95% CI, 0-0.08) was similar to that of untagged controls (0.03 (0-0.15)). Sockeye salmon with body lengths (mid-eye to tail fork) of 585-649 mm retained tags as large as 19 × 51 mm and those with body lengths of 499-628 mm retained tags as small as 14.5 × 43 mm for a minimum of 33 d with no increase in mortali...

(2009). Effective partnerships between universities and indigenous communities: A case study in tuatara conservation in Aotearoa. Journal of the Royal Society of New Zealand: Vol. 39, No. 4, pp. 229-231.

Marine, coastal and freshwater fisheries are culturally, ecologically, recreationally and economically important in New Zealand (NZ) and across the world. Over-exploitation of stocks has resulted in declining catches, particularly in the last 50 years, which has signalled the need for strategies to protect these valuable resources, while allowing sustainable exploitation (Pauly 1995; Jackson et. al. 2001; Myers and Worm 2003; Hutchings and Reynolds 2004; Hilborn 2006, 2007). This article outlines an ambitious and novel community-led approach to engage regional stakeholders in local fisheries management, initiated and led by Ng�ti Kahungunu (a M�ori iwi or tribal grouping) in NZ. This initiative is a significant move away from today?s highly centralised national form of fisheries management, and is a step towards a regional form of management that is led by the community for the benefit of the community (e.g., Govan et al. 2006). As such, this proposal represents a challenge to modern management practices, but more importantly it may represent the future for the sustainable utilization of fisheries resources.