Search

CASE HISTORY: Salmonellosis was suspected as the cause of death in eight wild animals on Tiritiri Matangi Island, in the Hauraki Gulf of New Zealand, between November and September 2011, including three hihi (Notiomystis cincta), a tuatara (Sphenodon punctatus), a masked lapwing (Vanellus miles novaehollandiae), and a saddleback (Philesturnus carunculatus). An outbreak investigation to identify the source and distribution of infection was undertaken over the summer of 2011–2012. CLINICAL AND LABORATORY FINDINGS: Surveillance of five species of forest bird (n=165) in December 2011 returned a single positive result forSalmonellaspp. Environmental sampling of 35 key water sources and hihi supplementary feeding stations conducted in December 2011 and March 2012 returned isolates ofS. entericasubspecieshoutenaeandS. entericaserovar Saintpaul from a stream, a dam and a supplementary feeding station. The same serotypes were identified in tissue samples collected from post mortem specimens of the affected birds, and their similarity was confirmed by pulsed-field gel electrophoresis. DIAGNOSIS: Mortality in wildlife associated with infection withS. entericasubspecieshoutenaeandS. entericaserovar Saintpaul. CLINICAL RELEVANCE: This is the first detection of theseSalmonellaspp. from wild birds in New Zealand. Our study highlights how active surveillance in response to observed disease emergence (here mortalities) can provide important insight for risk assessment and management within populations of endangered species and inform risk assessment in translocation planning. [ABSTRACT FROM PUBLISHER]

Recombination, the process of DNA exchange between homologous chromosomes during meiosis, plays a major role in genomic diversity and evolutionary change. Variation in recombination rate is widespread despite recombination often being essential for progression of meiosis. One such variation is heterochiasmy, where recombination rates differ between sexes. Heterochiasmy has been observed across broad taxonomic groups, yet it remains an evolutionary enigma. We used Lep-MAP3, a pedigree-based software that is efficient in handling large datasets, to generate linkage maps for the hihi or stitchbird (Notiomystis cincta), utilising information from >36 K SNPs and 36 families. We constructed 29 linkage maps, including for the previously unscaffolded Z chromosome. The hihi is an endangered passerine endemic to Aotearoa New Zealand that is sexually dimorphic and exhibits high levels of sexual conflict, including sperm competition. Patterns in recombination in the hihi are consistent with those in other birds, including higher recombination rates in micro-chromosomes. Heterochiasmy in the hihi is male-biased, in line with predictions of the Haldane-Huxley rule, with the male linkage map being 15% longer. Micro-chromosomes exhibit heterochiasmy to a greater extent, contrary to that reported in other birds. At the intra-chromosomal level, heterochiasmy is higher nearer to chromosome ends and in gene-rich regions. Regions of extreme heterochiasmy are enriched for genes implicated in cell structure. This study adds an important contribution in assessing evolutionary theories of heterochiasmy and provides a framework for future studies investigating fine-scale heterochiasmy., (© 2024. The Author(s).)

Hatching failure affects up to 77% of eggs laid by threatened bird species, yet the true prevalence and drivers of egg fertilization failure versus embryo mortality as underlying mechanisms of hatching failure are unknown. Here, using ten years of data comprising 4,371 eggs laid by a population of a threatened bird, the hihi ( Notiomystis cincta) , we investigate the relative importance of infertility and embryo death as drivers of hatching failure and explore population-level factors associated with them. We show that of the 1,438 eggs that failed to hatch (33% of laid eggs) between 2010 and 2020, 83% failed due to embryo mortality, with the majority failing in the early stages of embryonic development. In the most comprehensive estimates of infertility rates in a wild bird population to date, we find that fertilization failure accounts for around 17% of hatching failure overall and is more prevalent in years where the population is smaller and more male biased. Male embryos are more likely to die during early development than females, but we find no overall effect of sex on the successful development of embryos. Offspring fathered by within-pair males have significantly higher inbreeding levels than extra-pair offspring; however, we find no effect of inbreeding nor extra-pair paternity on embryo mortality. Accurately distinguishing between infertility and embryo mortality in this study provides unique insight into the underlying causes of reproductive failure over a long-term scale and reveals the complex risks of small population sizes to the reproduction of threatened species., Competing Interests: Competing interests statement:The authors declare no competing interest.

Mark-recapture surveys are commonly used to monitor translocated populations globally. Data gathered are then used to estimate demographic parameters, such as abundance and survival, using Jolly-Seber (JS) models. However, in translocated populations initial population size is known and failure to account for this may bias parameter estimates, which are important for informing conservation decisions during population establishment. Here, we provide methods to account for known initial population size in JS models by incorporating a separate component likelihood for translocated individuals, using a maximum-likelihood estimation, with models that can be fitted using either R or MATLAB. We use simulated data and a case study of a threatened lizard species with low capture probability to demonstrate that unconstrained JS models may overestimate the size of translocated populations, especially in the early stages of post-release monitoring. Our approach corrects this bias; we use our simulations to demonstrate that overestimates of population size between 78% and 130% can occur in the unconstrained JS models when the detection probability is below 0.3 compared to 1%-8.9% for our constrained model. Our case study did not show an overestimate; however accounting for the initial population size greatly reduced error in all parameter estimates and prevented boundary estimates. Adopting the corrected JS model for translocations will help managers to obtain more robust estimates of the population sizes of translocated animals, better informing future management including reinforcement decisions, and ultimately improving translocation success., (© 2023 The Authors. Ecological Applications published by Wiley Periodicals LLC on behalf of The Ecological Society of America.)

Telomeres are well known for their associations with lifespan and ageing across diverse taxa. Early-life telomere length can be influenced by developmental conditions and has been shown positively affect lifetime reproductive success in a limited number of studies. Whether these effects are caused by a change in lifespan, reproductive rate or perhaps most importantly reproductive senescence is unclear. Using long-term data on female breeding success from a threatened songbird (the hihi, Notiomystis cincta), we show that the early-life telomere length of individuals predicts the presence and rate of future senescence of key reproductive traits: clutch size and hatching success. In contrast, senescence of fledging success is not associated with early-life telomere length, which may be due to the added influence of biparental care at this stage. Early-life telomere length does not predict lifespan or lifetime reproductive success in this species. Females may therefore change their reproductive allocation strategy depending on their early developmental conditions, which we hypothesise are reflected in their early-life telomere length. Our results offer new insights on the role that telomeres play in reproductive senescence and individual fitness and suggest telomere length can be used as a predictor for future life history in threatened species., (© 2023 The Authors. Molecular Ecology published by John Wiley & Sons Ltd.)

A high-quality reference genome can be a valuable resource for threatened species by providing a foundation to assess their evolutionary potential to adapt to future pressures such as environmental change. We assembled the genome of a female hihi (Notiomysits cincta), a threatened passerine bird endemic to Aotearoa New Zealand. The assembled genome is 1.06 Gb, and is of high quality and highly contiguous, with a contig N50 of 7.0 Mb, estimated QV of 44 and a BUSCO completeness of 96.8%. A male assembly of comparable quality was generated in parallel. A population linkage map was used to scaffold the autosomal contigs into chromosomes. Female and male sequence coverage and comparative genomics analyses were used to identify Z-, and W-linked contigs. In total, 94.6% of the assembly length was assigned to putative nuclear chromosome scaffolds. Native DNA methylation was highly correlated between sexes, with the W chromosome contigs more highly methylated than autosomal chromosomes and Z contigs. 43 differentially methylated regions were identified, and these may represent interesting candidates for the establishment or maintenance of sex differences. By generating a high-quality reference assembly of the heterogametic sex, we have created a resource that enables characterization of genome-wide diversity and facilitates the investigation of female-specific evolutionary processes. The reference genomes will form the basis for fine-scale assessment of the impacts of low genetic diversity and inbreeding on the adaptive potential of the species and will therefore enable tailored and informed conservation management of this threatened taonga (treasured) species., (© 2023 The Authors. Molecular Ecology Resources published by John Wiley & Sons Ltd.)

For small and isolated populations, the increased chance of mating between related individuals can result in a substantial reduction in individual and population fitness. Despite the increasing availability of genomic data to measure inbreeding accurately across the genome, inbreeding depression studies for threatened species are still scarce due to the difficulty of measuring fitness in the wild. Here, we investigate inbreeding and inbreeding depression for the extensively monitored Tiritiri Mātangi island population of a threatened Aotearoa New Zealand passerine, the hihi (Notiomystis cincta). First, using a custom 45 k single nucleotide polymorphism (SNP) array, we explore genomic inbreeding patterns by inferring homozygous segments across the genome. Although all individuals have similar levels of ancient inbreeding, highly inbred individuals are affected by recent inbreeding, which can probably be explained by bottleneck effects such as habitat loss after European arrival and their translocation to the island in the 1990s. Second, we investigate genomic inbreeding effects on fitness, measured as lifetime reproductive success, and its three components, juvenile survival, adult annual survival and annual reproductive success, in 363 hihi. We find that global inbreeding significantly affects juvenile survival but none of the remaining fitness traits. Finally, we employ a genome-wide association approach to test the locus-specific effects of inbreeding on fitness, and identify 13 SNPs significantly associated with lifetime reproductive success. Our findings suggest that inbreeding depression does impact hihi, but at different genomic scales for different traits, and that purging has therefore failed to remove all variants with deleterious effects from this population of conservation concern., (© 2023 The Authors. Molecular Ecology published by John Wiley & Sons Ltd.)

Extinct in the Wild (EW) species are placed at the highest risk of extinction under the International Union for Conservation of Nature Red List, but the extent and variation in this risk have never been evaluated. Harnessing global databases of ex situ animal and plant holdings, we report on the perilous state of EW species. Most EW animal species-already compromised by their small number of founders-are maintained at population sizes far below the thresholds necessary to ensure demographic security. Most EW plant species depend on live propagation by a small number of botanic gardens, with a minority secured at seed bank institutions. Both extinctions and recoveries are possible fates for EW species. We urgently call for international effort to enable the latter.

The shape and intensity of natural selection can vary between years, potentially resulting in a chronic reduction of fitness as individuals need to track a continually changing optimum of fitness (i.e., a "lag load"). In endangered species, often characterized by small population size, the lack of genetic diversity is expected to limit the response to this constant need to adjust to fluctuating selection, increasing the fitness burden and thus the risk of extinction. Here, we use long-term monitoring data to assess whether the type of selection for a key fitness trait (i.e., lay date) differs between two reintroduced populations of a threatened passerine bird, the hihi (Notiomystis cincta). We apply recent statistical developments to test for the presence or absence of fluctuation in selection in both the Tiritiri Mātangi Island and the Kārori sanctuary populations. Our results support the presence of stabilizing selection in Tiritiri Mātangi with a potential moving optimum for lay date. In Kārori our results favour a regime of directional selection. Although the shape of selection may differ, for both populations an earlier lay date generally increases fitness in both environments. Further, the moving optimum models of lay date on Tiritiri Mātangi, suggesting that selection varies between years, imply a substantial lag load in addition to the fitness burden caused by the population laying too late. Our results highlight the importance of characterizing the form and temporal variation of selection for each population to predict the effects of environmental change and to inform management., (© 2022 European Society for Evolutionary Biology.)

Conservation translocation is a common method for species recovery, for which one increasingly frequent objective is restoring lost ecological functions to promote ecosystem recovery. However, few conservation translocation programs explicitly state or monitor function as an objective, limiting the ability to test assumptions, learn from past efforts, and improve management. We evaluated whether translocations of hihi (Notiomystis cincta), a threatened New Zealand passerine, achieved their implicit objective of restoring lost pollination function. Through a pollinator-exclusion experiment, we quantified, with log response ratios (lnR), the effects of birds on fruit set and seed quality in hangehange (Geniostoma ligustrifolium), a native flowering shrub. We isolated the contributions of hihi by making comparisons across sites with and without hihi. Birds improved fruit set more at sites without hihi (lnR = 1.27) than sites with hihi (lnR = 0.50), suggesting other avian pollinators compensated for and even exceeded hihi contributions to fruit set. Although birds improved seed germination only at hihi sites (lnR = 0.22-0.41), plants at sites without hihi had germination rates similar to hihi sites because they produced 26% more filled seeds, regardless of pollination condition. Therefore, although our results showed hihi improved seed quality, they also highlighted the complexity of ecological functions. When an important species is lost, ecosystems may be able to achieve similar function through different means. Our results underscore the importance of stating and monitoring the ecological benefits of conservation translocations when functional restoration is a motivation to ensure these programs are achieving their objectives., (© 2022 The Authors. Conservation Biology published by Wiley Periodicals LLC on behalf of Society for Conservation Biology.)

Sample mix-ups occur when samples have accidentally been duplicated, mislabelled or swapped. When samples are subsequently genotyped or sequenced, this can lead to individual IDs being incorrectly linked to genetic data, resulting in incorrect or biased research results, or reduced power to detect true biological patterns. We surveyed the community and found that almost 80% of responding researchers have encountered sample mix-ups. However, many recent studies in the field of molecular ecology do not appear to systematically report individual assignment checks as part of their publications. Although checks may be done, lack of consistent reporting means that it is difficult to assess whether sample mix-ups have occurred or been detected. Here, we present an easy-to-follow sample verification framework that can utilise existing metadata, including species, population structure, sex and pedigree information. We demonstrate its application to a data set representing individuals of a threatened Aotearoa New Zealand bird species, the hihi, genotyped on a 50K SNP array. We detected numerous incorrect genotype-ID associations when comparing observed and genetic sex or comparing to relationships in a verified microsatellite pedigree. The framework proposed here helped to confirm 488 individuals (39%), correct another 20 bird-genotype links, and detect hundreds of incorrect sample IDs, emphasizing the value of routinely checking genetic and genomic data sets for their accuracy. We therefore promote the implementation and reporting of this simple yet effective sample verification framework as a standardized quality control step for studies in the field of molecular ecology., (© 2021 John Wiley & Sons Ltd.)

The rate of adaptive evolution, the contribution of selection to genetic changes that increase mean fitness, is determined by the additive genetic variance in individual relative fitness. To date, there are few robust estimates of this parameter for natural populations, and it is therefore unclear whether adaptive evolution can play a meaningful role in short-term population dynamics. We developed and applied quantitative genetic methods to long-term datasets from 19 wild bird and mammal populations and found that, while estimates vary between populations, additive genetic variance in relative fitness is often substantial and, on average, twice that of previous estimates. We show that these rates of contemporary adaptive evolution can affect population dynamics and hence that natural selection has the potential to partly mitigate effects of current environmental change.

Next-generation sequencing has transformed the fields of ecological and evolutionary genetics by allowing for cost-effective identification of genome-wide variation. Single nucleotide polymorphism (SNP) arrays, or "SNP chips", enable very large numbers of individuals to be consistently genotyped at a selected set of these identified markers, and also offer the advantage of being able to analyse samples of variable DNA quality. We used reduced representation restriction-aided digest sequencing (RAD-seq) of 31 birds of the threatened hihi (Notiomystis cincta; stitchbird) and low-coverage whole genome sequencing (WGS) of 10 of these birds to develop an Affymetrix 50 K SNP chip. We overcame the limitations of having no hihi reference genome and a low quantity of sequence data by separate and pooled de novo assembly of each of the 10 WGS birds. Reads from all individuals were mapped back to these de novo assemblies to identify SNPs. A subset of RAD-seq and WGS SNPs were selected for inclusion on the chip, prioritising SNPs with the highest quality scores whose flanking sequence uniquely aligned to the zebra finch (Taeniopygia guttata) genome. Of the 58,466 SNPs manufactured on the chip, 72% passed filtering metrics and were polymorphic. By genotyping 1,536 hihi on the array, we found that SNPs detected in multiple assemblies were more likely to successfully genotype, representing a cost-effective approach to identify SNPs for genotyping. Here, we demonstrate the utility of the SNP chip by describing the high rates of linkage disequilibrium in the hihi genome, reflecting the history of population bottlenecks in the species., (© 2021 John Wiley & Sons Ltd.)

Inbreeding can lead to a loss of heterozygosity in a population and when combined with genetic drift may reduce the adaptive potential of a species. However, there is uncertainty about whether resequencing data can provide accurate and consistent inbreeding estimates. Here, we performed an in-depth inbreeding analysis for hihi (Notiomystis cincta), an endemic and nationally vulnerable passerine bird of Aotearoa New Zealand. We first focused on subsampling variants from a reference genome male, and found that low-density data sets tend to miss runs of homozygosity (ROH) in some places and overestimate ROH length in others, resulting in contrasting homozygosity landscapes. Low-coverage resequencing and 50 K SNP array densities can yield comparable inbreeding results to high-coverage resequencing approaches, but the results for all data sets are highly dependent on the software settings employed. Second, we extended our analysis to 10 hihi where low-coverage whole genome resequencing, RAD-seq and SNP array genotypes are available. We inferred ROH and individual inbreeding to evaluate the relative effects of sequencing depth versus SNP density on estimating inbreeding coefficients and found that high rates of missingness downwardly bias both the number and length of ROH. In summary, when using genomic data to evaluate inbreeding, studies must consider that ROH estimates are heavily dependent on analysis parameters, data set density and individual sequencing depth., (© 2021 John Wiley & Sons Ltd.)

The art of population modelling is to incorporate factors essential for capturing a population's dynamics while otherwise keeping the model as simple as possible. However, it is unclear how optimal model complexity should be assessed, and whether this optimal complexity has been affected by recent advances in modelling methodology. This issue is particularly relevant to small populations because they are subject to complex dynamics but inferences about those dynamics are often constrained by small sample sizes. We fitted Bayesian hierarchical models to long-term data on vital rates (survival and reproduction) for the toutouwai Petroica longipes population reintroduced to Tiritiri Matangi, a 220-ha New Zealand island, and quantified the performance of those models in terms of their likelihood of replicating the observed population dynamics. These dynamics consisted of overall growth from 33 (±0.3) to 160 (±6) birds from 1992-2018, including recoveries following five harvest events for further reintroductions to other sites. We initially included all factors found to affect vital rates, which included inbreeding, post-release effects (PRE), density-dependence, sex, age and random annual variation, then progressively removed these factors. We also compared performance of models where data analysis and simulations were done simultaneously to those produced with the traditional two-step approach, where vital rates are estimated first then fed into a separate simulation model. Parametric uncertainty and demographic stochasticity were incorporated in all projections. The essential factors for replicating the population's dynamics were density-dependence in juvenile survival and PRE, i.e. initial depression of survival and reproduction in translocated birds. Inclusion of other factors reduced the precision of projections, and therefore the likelihood of matching observed dynamics. However, this reduction was modest when the modelling was done in an integrated framework. In contrast, projections were much less precise when done with a two-step modelling approach, and the cost of additional parameters was much higher under the two-step approach. These results suggest that minimization of complexity may be less important than accounting for covariances in parameter estimates, which is facilitated by integrating data analysis and population projections using Bayesian methods., (© 2021 British Ecological Society.)

Ko koe ki tēnā, ko ahau ki tēnai kīwai o te kete (you at that, and I at this handle of the basket). This Māori (New Zealanders of indigenous descent) saying conveys the principle of cooperation-we achieve more through working together, rather than separately. Despite decades of calls to rectify cultural imbalance in conservation, threatened species management still relies overwhelmingly on ideas from Western science and on top-down implementation. Values-based approaches to decision making can be used to integrate indigenous peoples' values into species conservation in a more meaningful way. We used such a values-based method, structured decision making, to develop comanagement of pekapeka (Mystacina tuberculata) (short-tailed bat) and tara iti (Sternula nereis davisae) (Fairy Tern) between Māori and Pākehā (New Zealanders of European descent). We implemented this framework in a series of workshops in which facilitated discussions were used to gather expert knowledge to predict outcomes and make management recommendations. For both species, stakeholders clearly stated their values as fundamental objectives from the start, which allowed alternative strategies to be devised that naturally addressed their diverse values, including mātauranga Māori (Māori knowledge and perspectives). On this shared basis, all partners willingly engaged in the process, and decisions were largely agreed to by all. Most expectations of conflicts between values of Western science and Māori culture were unfounded. Where required, positive compromises were made by jointly developing alternative strategies. The values-based process successfully taha wairua taha tangata (brought both worlds together to achieve the objective) through codeveloped recovery strategies. This approach challenges the traditional model of scientists first preparing management plans focused on biological objectives, then consulting indigenous groups for approval. We recommend values-based approaches, such as structured decision making, as powerful methods for development of comanagement conservation plans between different peoples., (© The Authors. Conservation Biology published by Wiley Periodicals LLC on behalf of Society for Conservation Biology.)

Inbreeding depression is an important long-term threat to reintroduced populations. However, the strength of inbreeding depression is difficult to estimate in wild populations because pedigree data are inevitably incomplete and because good data are needed on survival and reproduction. Predicting future population consequences is especially difficult because this also requires projecting future inbreeding levels and their impacts on long-term population dynamics, which are subject to many uncertainties. We illustrate how such projections can be derived through Bayesian state-space modeling methods based on a 26-year data set for North Island Robins (Petroica longipes) reintroduced to Tiritiri Matangi Island in 1992. We used pedigree data to model increases in the average inbreeding level (F) over time based on kinship of possible breeding pairs and to estimate empirically N e /N (effective/census population size). We used multiple imputation to model the unknown components of inbreeding coefficients, which allowed us to estimate effects of inbreeding on survival for all 1458 birds in the data set while modeling density dependence and environmental stochasticity. This modeling indicated that inbreeding reduced juvenile survival (1.83 lethal equivalents [SE 0.81]) and may have reduced subsequent adult survival (0.44 lethal equivalents [0.81]) but had no apparent effect on numbers of fledglings produced. Average inbreeding level increased to 0.10 (SE 0.001) as the population grew from 33 (0.3) to 160 (6) individuals over the 25 years, giving a N e / N ratio of 0.56 (0.01). Based on a model that also incorporated habitat regeneration, the population was projected to reach a maximum of 331-1144 birds (median 726) in 2130, then to begin a slow decline. Without inbreeding, the population would be expected stabilize at 887-1465 birds (median 1131). Such analysis, therefore, makes it possible to empirically derive the information needed for rational decisions about inbreeding management while accounting for multiple sources of uncertainty., (© 2020 Society for Conservation Biology.)

A key goal of ecological research is to obtain reliable estimates of population demographic rates, abundance and trends. However, a common challenge when studying wildlife populations is imperfect detection or breeding observation, which results in unknown survival status and reproductive output for some individuals. It is important to account for undetected individuals in population models because they contribute to population abundance and dynamics, and can have implications for population management. Promisingly, recent methodological advances provide us with the tools to integrate data from multiple independent sources to gain insights into the unobserved component of populations. We use data from five reintroduced populations of a threatened New Zealand bird, the hihi (Notiomystis cincta), to develop an integrated population modelling framework that allows missing values for survival status, sex and reproductive output to be modelled. Our approach combines parallel matrices of encounter and reproduction histories from marked individuals, as well as counts of unmarked recruits detected at the start of each breeding season. Integrating these multiple data types enabled us to simultaneously model survival and reproduction of detected individuals, undetected individuals and unknown (never detected) individuals to derive parameter estimates and projections based on all available data, thereby improving our understanding of population dynamics and enabling full propagation of uncertainty. The methods presented will be especially useful for management programmes for populations that are intensively monitored but where individuals are still imperfectly detected, as will be the case for most threatened wild populations.

Inbreeding can depress individuals' fitness traits and reduce population viability. However, studies that directly translate inbreeding depression on fitness traits into consequences for population viability, and further, into consequences for management choices, are lacking. Here, we estimated impacts of inbreeding depression (B, lethal equivalents) across life-history stages for an extinct-in-the-wild species, the sihek (Guam kingfisher, Todiramphus cinnamominus). We then projected population growth under different management alternatives with our B estimates incorporated, as well as without inbreeding depression (B = 0) or with a conventional default B. We found that inbreeding depression severely impacted multiple life-history stages, and directly translated into an effect on population viability under management alternatives. Simulations including our B estimates indicated rapid population decline, whereas projections without inbreeding depression or with default B suggested very gradual population decline. Further, our results demonstrate that incorporation of B across life-history stages can influence management decisions, as projections with our B estimates suggested a need to switch to increased breeding management to avoid species extinction and support wild releases. Our results demonstrate that magnitude of B across life-history stages can translate into demographic consequences, such that incorporation of multiple life-stage B into population models can be important for informed conservation management decision-making.

Early independence from parents is a critical period where social information acquired vertically may become outdated, or conflict with new information. However, across natural populations, it is unclear if newly independent young persist in using information from parents, or if group-level effects of conformity override previous behaviours. Here, we test if wild juvenile hihi ( Notiomystis cincta , a New Zealand passerine) retain a foraging behaviour from parents, or if they change in response to the behaviour of peers. We provided feeding stations to parents during chick-rearing to seed alternative access routes, and then tracked their offspring's behaviour. Once independent, juveniles formed mixed-treatment social groups, where they did not retain preferences from their time with parents. Instead, juvenile groups converged over time to use one access route- per group, and juveniles that moved between groups switched to copy the locally favoured option. Juvenile hihi did not copy specific individuals, even if they were more familiar with the preceding bird. Our study shows that early social experiences with parents affect initial foraging decisions, but social environments encountered later on can update transmission of arbitrary behaviours. This suggests that conformity may be widespread in animal groups, with potential cultural, ecological and evolutionary consequences.

To predict if a threatened species can adapt to changing selective pressures, it is crucial to understand the genetic basis of adaptive traits, especially in species historically affected by severe bottlenecks. We estimated the heritability of three hihi ( Notiomystis cincta ) morphological traits known to be under selection (nestling tarsus length, body mass and head-bill length) using 523 individuals and 39 699 single nucleotide polymorphisms (SNPs) from a 50 K Affymetrix SNP chip. We then examined the genetic architecture of the traits via chromosome partitioning analyses and genome-wide association scans (GWAS). Heritabilities estimated using pedigree relatedness or genomic relatedness were low. For tarsus length, the proportion of genetic variance explained by each chromosome was positively correlated with its size, and more than one chromosome explained significant variation for body mass and head-bill length. Finally, GWAS analyses suggested many loci of small effect contributing to trait variation for all three traits, although one locus (an SNP within an intron of the transcription factor HEY2 ) was tentatively associated with tarsus length. Our findings suggest a polygenic nature for the morphological traits, with many small effect size loci contributing to the majority of the variation, similar to results from many other wild populations. However, the small effective population size, polygenic architecture and already low heritabilities suggest that both the total response and rate of response to selection are likely to be limited in hihi.

Human activity affecting the welfare of wild vertebrates, widely accepted to be sentient, and therefore deserving of moral concern, is widespread. A variety of motives lead to the killing of individual wild animals. These include to provide food, to protect stock and other human interests, and also for sport. The acceptability of such killing is widely believed to vary with the motive and method. Individual vertebrates are also killed by conservationists. Whether securing conservation goals is an adequate reason for such killing has recently been challenged. Conventional conservation practice has tended to prioritise ecological collectives, such as populations and species, when their interests conflict with those of individuals. Supporters of the 'Compassionate Conservation' movement argue both that conservationists have neglected animal welfare when such conflicts arise and that no killing for conservation is justified. We counter that conservationists increasingly seek to adhere to high standards of welfare, and that the extreme position advocated by some supporters of 'Compassionate Conservation', rooted in virtue ethics, would, if widely accepted, lead to considerable negative effects for conservation. Conservation practice cannot afford to neglect consequences. Moreover, the do-no-harm maxim does not always lead to better outcomes for animal welfare.

There is growing recognition that variation in animal personality traits can influence survival and reproduction rates, and consequently may be important for wildlife population dynamics. Despite this, the integration of personality research into conservation has remained uncommon. Alongside the establishment of personality as an important source of individual variation has come an increasing interest in factors affecting the development of personality. Recent work indicates the early environment, including natal nutrition, may play a stronger role in the development of personality than previously thought. In this study, we investigated the importance of three personality metrics (activity, boldness and acclimation time) for estimating survival of a threatened species, the hihi (Notiomystis cincta), and evaluated the influence of early natal nutrition on those metrics. Our results showed that boldness (as measured from a one-off cage test) had a positive effect on the probability of juvenile hihi surviving to adulthood. There was also a tendency for juveniles that received carotenoid supplementation in the nest to be bolder than those that did not, suggesting that the early environment had some influence on the expression of boldness in juvenile hihi. Linking the development of personality traits with ultimate effects on vital rates may benefit conservation management, as it could enable developmentally targeted management interventions. To our knowledge, this study is the first to identify potential linkages between early natal nutrition, personality and fitness in a wild-living population. This article is part of the theme issue 'Linking behaviour to dynamics of populations and communities: application of novel approaches in behavioural ecology to conservation'.

Emerging Infectious Diseases (EIDs) are recognised as global extinction drivers of threatened species. Unfortunately, biodiversity managers have few tested solutions to manage them when often the desperate need for solutions necessitates a response. Here we test in situ biosecurity protocols to assess the efficacy of managing Psittacine beak and feather disease (PBFD), one of the most common and emergent viral diseases in wild parrots (Psittaciformes) that is currently affecting numerous threatened species globally. In response to an outbreak of PBFD in Mauritius "echo" parakeets (Psittacula eques), managers implemented a set of biosecurity protocols to limit transmission and impact of Beak and feather disease virus (BFDV). Here we used a reciprocal design experiment on the wild population to test whether BFDV management reduced viral prevalence and viral load, and improved nestling body condition and fledge success. Whilst management reduced the probability of nestling infection by approximately 11% there was no observed impact on BFDV load and nestling body condition. In contrast to expectations there was lower fledge success in nests with added BFDV biosecurity (83% in untreated vs. 79% in treated nests). Our results clearly illustrate that management for wildlife conservation should be critically evaluated through targeted monitoring and experimental manipulation, and this evaluation should always focus on the fundamental objective of conservation.

Threatened species face numerous threats, including future challenges triggered by global change. A possible way to cope with these challenges is through adaptive evolution, which requires adaptive potential. Adaptive potential is defined as the genetic variance needed to respond to selection and can be assessed either on adaptive traits or fitness [1]. However, a lack of high-quality data has made it difficult to rigorously test adaptive potential in threatened species, leading to controversy over its magnitude [1-3]. Here we assess the adaptive potential of a threatened New Zealand passerine (the hihi, Notiomystis cincta) based on two populations: (1) the sole remaining natural population, on the island of Te Hauturu-o-Toi, and (2) a reintroduced population with a long-term dataset (intensively monitored for 20 years) based on the island of Tiritiri Matangi. We use molecular information (reduced representation genome sequencing, on both populations), as well as long-term phenotypic and fitness data from the Tiritiri Matangi population, to find (1) a lack of molecular genetic diversity at a genome-wide level in both populations, (2) low heritability of traits under selection and (3) negligible additive genetic variance of fitness in the Tiritiri Matangi population. In combination, these results support a lack of adaptive potential in this threatened species. We discuss our findings within the context of other passerines and methods for assessing adaptive potential, as well as the impact of these results on conservation practice, for the hihi and species of conservation concern in general., (Copyright © 2019 Elsevier Ltd. All rights reserved.)

Many bird species have been observed shifting their laying date to earlier in the year in response to climate change. However, the vast majority of these studies were performed on non-threatened species, less impacted by reduced genetic diversity (which is expected to limit evolutionary response) as a consequence of genetic bottlenecks, drift and population isolation. Here, we study the relationship between lay date and fitness, as well as its genetic basis, to understand the evolutionary constraints on phenology faced by threatened species using a recently reintroduced population of the endangered New Zealand passerine, the hihi ( Notiomystis cincta ). A large discrepancy between the optimal laying date and the mode of laying date creates a strong selection differential of -11.24. The impact of this discrepancy on fitness is principally mediated through survival of offspring from hatchling to fledgling. This discrepancy does not seem to arise from a difference in female quality or a trade-off with lifetime breeding success. We find that start of breeding season depends on female age and average temperature prior to the breeding season. Laying date is not found to be significantly heritable. Overall, our research suggests that this discrepancy is a burden on hihi fitness, which will not be resolved through evolution or phenotypic plasticity. More generally, these results show that threatened species introduced to restored habitats might lack adaptive potential and plasticity to adjust their phenology to their new environment. This constraint is also likely to limit their ability to face future challenges, including climate change.

Coccidia are intracellular parasites of the phylum Apicomplexa that cause a range of pathologies collectively termed coccidiosis. Species of coccidia of commercial importance have been well studied, with the effect of other species on passerine birds receiving increasing attention. In this chapter, we review the literature on coccidia in passerines, with a particular focus on wild populations. The taxonomy and life cycle of passerine coccidia are covered, as is their impact on the health of passerines, their epidemiology and their role in parasite-mediated natural and sexual selection. Coccidia can pose a significant threat to the health of wild passerine populations, and high rates of mortality have been observed in some studies. We examine some of the genetic factors that influence host resistance to coccidia and discuss how these parasites may be important in relation to sexually selected traits. General patterns are beginning to emerge with regard to the epidemiology of the parasites, and the influence of different aspects of the host's ecology on the prevalence and intensity of coccidia is being revealed. We examine these, as well exceptions, in addition to the phenomenon of diurnal oocyst shedding that can bias studies if not accounted for. Finally, we discuss potential future directions for research on coccidia in passerines and the importance of understanding parasite ecology in the management of threatened species., (© 2018 Elsevier Ltd All rights reserved.)

Reintroduction biology is a field of scientific research that aims to inform translocations of endangered species. We review two decades of published literature to evaluate whether reintroduction science is evolving in its decision-support role, as called for by advocates of evidence-based conservation. Reintroduction research increasingly addresses a priori hypotheses, but remains largely focused on short-term population establishment. Similarly, studies that directly assist decisions by explicitly comparing alternative management actions remain a minority. A small set of case studies demonstrate full integration of research in the reintroduction decision process. We encourage the use of tools that embed research in decision-making, particularly the explicit consideration of multiple management alternatives because this is the crux of any management decisions., (Copyright © 2017 Elsevier Ltd. All rights reserved.)

Conservation translocations are increasingly used to manage threatened species and restore ecosystems. Translocations increase the risk of disease outbreaks in the translocated and recipient populations. Qualitative disease risk analyses have been used as a means of assessing the magnitude of any effect of disease and the probability of the disease occurring associated with a translocation. Currently multiple alternative qualitative disease risk analysis packages are available to practitioners. Here we compare the ease of use, expertise required, transparency, and results from, three different qualitative disease risk analyses using a translocation of the endangered New Zealand passerine, the hihi (Notiomystis cincta), as a model. We show that the three methods use fundamentally different approaches to define hazards. Different methods are used to produce estimations of the risk from disease, and the estimations are different for the same hazards. Transparency of the process varies between methods from no referencing, or explanations of evidence to justify decisions, through to full documentation of resources, decisions and assumptions made. Evidence to support decisions on estimation of risk from disease is important, to enable knowledge acquired in the future, for example, from translocation outcome, to be used to improve the risk estimation for future translocations. Information documenting each disease risk analysis differs along with variation in emphasis of the questions asked within each package. The expertise required to commence a disease risk analysis varies and an action flow chart tailored for the non-wildlife health specialist are included in one method but completion of the disease risk analysis requires wildlife health specialists with epidemiological and pathological knowledge in all three methods. We show that disease risk analysis package choice may play a greater role in the overall risk estimation of the effect of disease on animal populations involved in a translocation than might previously have been realised.

We provide an overview of the current state of knowledge of parasites in biological invasions by alien species. Parasites have frequently been invoked as drivers of invasions, but have received less attention as invasion passengers. The evidence to date that parasites drive invasions by hosts is weak: while there is abundant evidence that parasites have effects in the context of alien invasions, there is little evidence to suggest that parasites have differential effects on alien species that succeed versus fail in the invasion process. Particular case studies are suggestive but not yet informative about general effects. What evidence there is for parasites as aliens suggests that the same kind of factors determine their success as for non-parasites. Thus, availability is likely to be an important determinant of the probability of translocation. Establishment and spread are likely to depend on propagule pressure and on the environment being suitable (all necessary hosts and vectors are present); the likelihood of both of these dependencies being favourable will be affected by traits relating to parasite life history and demography. The added complication for the success of parasites as aliens is that often this will depend on the success of their hosts. We discuss how these conclusions help us to understand the likely effects of parasites on the success of establishing host populations (alien or native).

Through the exploration of disease risk analysis methods employed for four different UK herpetofauna translocations, we illustrate how disease hazards can be identified, and how the risk of disease can be analysed. Where ecological or geographical barriers between source and destination sites exist, parasite populations are likely to differ in identity or strain between the two sites, elevating the risk from disease and increasing the number and category of hazards requiring analysis. Simplification of the translocation pathway through the avoidance of these barriers reduces the risk from disease. The disease risk analysis tool is intended to aid conservation practitioners in decision making relating to disease hazards prior to implementation of a translocation.

Floating males are usually thought of as nonbreeders. However, some floating individuals are able to reproduce through extra-pair copulations. Floater reproductive success can impact breeders' sex ratio, reproductive variance, multiple paternity and inbreeding, particularly in small populations. Changes in reproductive variance alter the rate of genetic drift and loss of genetic diversity. Therefore, genetic management of threatened species requires an understanding of floater reproduction and determinants of floating behaviour to effectively conserve species. Here, we used a pedigreed, free-living population of the endangered New Zealand hihi (Notiomystis cincta) to assess variance in male reproductive success and test the genetic (inbreeding and heritability) and conditional (age and size) factors that influence floater behaviour and reproduction. Floater reproduction is common in this species. However, floater individuals have lower reproductive success and variance in reproductive success than territorial males (total and extra-pair fledglings), so their relative impact on the population's reproductive performance is low. Whether an individual becomes a floater, and if so then how successful they are, is determined mainly by individual age (young and old) and to lesser extents male size (small) and inbreeding level (inbred). Floating males have a small, but important role in population reproduction and persistence of threatened populations.

Supplementary feeding is often a knee-jerk reaction to population declines, and its application is not critically evaluated, leading to polarized views among managers on its usefulness. Here, we advocate a more strategic approach to supplementary feeding so that the choice to use it is clearly justified over, or in combination with, other management actions and the predicted consequences are then critically assessed following implementation. We propose combining methods from a set of specialist disciplines that will allow critical evaluation of the need, benefit, and risks of food supplementation. Through the use of nutritional ecology, population ecology, and structured decision making, conservation managers can make better choices about what and how to feed by estimating consequences on population recovery across a range of possible actions. This structured approach also informs targeted monitoring and more clearly allows supplementary feeding to be integrated in recovery plans and reduces the risk of inefficient decisions. In New Zealand, managers of the endangered Hihi (Notiomystis cincta) often rely on supplementary feeding to support reintroduced populations. On Kapiti island the reintroduced Hihi population has responded well to food supplementation, but the logistics of providing an increasing demand recently outstretched management capacity. To decide whether and how the feeding regime should be revised, managers used a structured decision making approach informed by population responses to alternative feeding regimes. The decision was made to reduce the spatial distribution of feeders and invest saved time in increasing volume of food delivered into a smaller core area. The approach used allowed a transparent and defendable management decision in regard to supplementary feeding, reflecting the multiple objectives of managers and their priorities., (© 2014 The Authors. Conservation Biology published by Wiley Periodicals, Inc., on behalf of Society for Conservation Biology.)

Dietary access to carotenoids is expected to determine the strength of carotenoid-based signal expression and potentially to maintain signal honesty. Species that display carotenoid-based yellow, orange, or red plumage are therefore expected to forage selectively for carotenoid-rich foods when they are depositing these pigments during molt, but whether they actually do so is unknown. We set out to address this in the hihi ( Notiomystis cincta ), a New Zealand passerine where males, but not females, display yellow carotenoid-based plumage. We measured circulating carotenoid concentrations in male and female hihi during breeding and molt, determined the nutritional content of common foods in the hihi diet, and conducted feeding observations of male and female hihi during molt. We found that although male and female hihi do not differ significantly in plasma carotenoid concentration, male hihi have a greater proportion of carotenoid-rich foods in their diet than do females. This is a consequence of a greater fruit and lower invertebrate intake than females and an avoidance of low-carotenoid content fruit. By combining behavioral observations with quantification of circulating carotenoids, we present evidence that colorful birds forage to maximize carotenoid intake, a conclusion we would not have drawn had we examined plasma carotenoids alone.

Why do some bird species show dramatic sexual dichromatism in their plumage? Sexual selection is the most common answer to this question. However, other competing explanations mean it is unwise to assume that all sexual dichromatism has evolved by this mechanism. Even if sexual selection is involved, further work is necessary to determine whether dichromatism results from competition amongst rival males, or by female choice for attractive traits, or both. Here, we test whether sexually dichromatic hihi (Notiomystis cincta) plumage is currently under sexual selection, with detailed behavioural and genetic analyses of a free-living island population. Bateman gradients measured for males and females reveal the potential for sexual selection, whilst selection gradients, relating reproductive success to specific colourful traits, show that there is stabilizing selection on white ear tuft length in males. By correlating colourful male plumage with different components of reproductive success, we show that properties of yellow plumage are most likely a product of male-male competition, whilst properties of the black and white plumage are an outcome of both male-male competition and female choice. Male plumage therefore potentially signals to multiple receivers (rival males and potential mates), and this may explain the multicoloured appearance of one of the most strikingly dichromatic species in New Zealand., (© 2014 The Authors. Journal of Evolutionary Biology published by John Wiley & Sons Ltd on behalf of European Society for Evolutionary Biology.)

The okapi is an endangered, evolutionarily distinctive even-toed ungulate classified within the giraffidae family that is endemic to the Democratic Republic of Congo. The okapi is currently under major anthropogenic threat, yet to date nothing is known about its genetic structure and evolutionary history, information important for conservation management given the species' current plight. The distribution of the okapi, being confined to the Congo Basin and yet spanning the Congo River, also makes it an important species for testing general biogeographic hypotheses for Congo Basin fauna, a currently understudied area of research. Here we describe the evolutionary history and genetic structure of okapi, in the context of other African ungulates including the giraffe, and use this information to shed light on the biogeographic history of Congo Basin fauna in general. Using nuclear and mitochondrial DNA sequence analysis of mainly non-invasively collected samples, we show that the okapi is both highly genetically distinct and highly genetically diverse, an unusual combination of genetic traits for an endangered species, and feature a complex evolutionary history. Genetic data are consistent with repeated climatic cycles leading to multiple Plio-Pleistocene refugia in isolated forests in the Congo catchment but also imply historic gene flow across the Congo River.

It is well established that the expression of many ornamental traits is dependent on the current condition of the bearer. However, conditions experienced in early life are also known to be important for an individual's subsequent fitness and therefore, directly or indirectly, for the fitness of their mate. Specifically, a recent hypothesis suggests that sexually selected traits might be sensitive to conditions experienced during early-life development and thereby function as honest indicators of developmental history. Whether this applies to colourful male plumage, however, is largely unknown. We tested this idea with a field experiment by manipulating neonatal nutrition in a sexually dichromatic passerine, the hihi (Notymystis cincta). We found that carotenoid supplementation increased nestling plasma carotenoid concentration, which was in turn correlated with increased yellow saturation in male breeding plumage after moulting. We also found that the post-moult luminance (lightness) of the white ear-tufts tended to be reduced in males that had received an all-round nutritional supplement as nestlings. Black breeding plumage was not affected by neonatal nutritional treatment. Although the mechanisms that generate colourful plumage are evidently diverse, our results show that at least some parts of this display are accurate indicators of environmental conditions during development.

Knowledge of the processes favouring the establishment of exotic parasites is poor. Herein, we test the characteristics of successful exotic parasites that have co-established in the remote island archipelago of New Zealand, due to the introduction of numerous avian host species. Our results show that avian malaria parasites (AM; parasites of the genus Plasmodium) that successfully invaded are more globally generalist (both geographically widespread and with a broad taxonomic range of hosts) than AM parasites not co-introduced to New Zealand. Furthermore, the successful AM parasites are presently more prevalent in their native range than AM parasites found in the same native range but not co-introduced to New Zealand. This has resulted in an increased number and greater taxonomic diversity of AM parasites now in New Zealand., (© 2012 Blackwell Publishing Ltd/CNRS.)

How sensitive should parents be to the demands of their young? Offspring are under selection to seek more investment than is optimal for parents to supply, which makes parents vulnerable to losing future fitness by responding to manipulative displays. Yet, parents cannot afford to ignore begging and risk allocating resources inefficiently. Here, we show that parents may solve this problem by adjusting their sensitivity to begging behaviour in relation to their own likelihood of breeding again, a factor largely neglected in previous analyses of parent-offspring interactions. In two carotenoid-supplementation experiments on a New Zealand passerine, the hihi Notiomystis cincta, we supplemented adults to enhance their propensity to breed again, and supplemented entire broods to increase their mouth colour, thus enhancing their solicitation display. We found that adults that attempted two breeding attempts a season were largely insensitive to the experimentally carotenoid-rich gapes of their brood, whereas those that bred just once responded by increasing their rate of provisioning at the nest. Our results show that parents can strategically vary their sensitivity to begging in relation to their future reproductive potential. By restricting opportunities for offspring to influence provisioning decisions, parents greatly limit the potential for offspring to win parent-offspring conflict.

1. Male-biased adult sex ratios are frequently observed in free-ranging populations and are known to cause changes in mating behaviours including increased male harassment of females, which can cause injury to females and/or alter female behaviour during breeding. 2. Although we can explain why such behaviours may evolve and have studied their impacts on individuals when it does, we know very little about the demographic consequences of harassment caused by changes in adult sex ratio. 3. Using a 12-year longitudinal data set of a free-living and endangered New Zealand passerine, the hihi (Notiomystis cincta), we show that a changing adult sex ratio has little or no effect on adult female survival or the number of fledglings produced per female. This is despite clear evidence of male harassment of breeding females when the sex ratio was male biased (up to three males per female). 4. The length of the study and major fluctuations in sex ratio observed made it possible to obtain narrow confidence or credible intervals for effect sizes, showing that any effect of sex ratio on demographic rates were small. 5. Our results provide rare empirical evidence for the demographic consequences of biased adult sex ratios in the wild and particularly in a conservation context., (© 2010 The Authors. Journal compilation © 2010 British Ecological Society.)