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SummaryCook’s Petrel Pterodroma cookii is an endemic New Zealand seabird that has experienced a large range decline since the arrival of humans and now only breeds on two offshore islands (Te Hauturu-o-Toi/Little Barrier Island and Whenua Hou/Codfish Island) at the extreme ends of its former distribution. Morphological, behavioural, and mitochondrial cytochrome oxidase 1 (CO1) sequence data led a previous study to recognise the two extant populations as distinct conservation management units. Here, we further examine the genetic relationship between the extant populations using two nuclear introns (β-fibint7 and PAX). Using one mitochondrial locus (CO1), we also investigate the past distribution of a single nucleotide polymorphism (SNP) that differentiates the modern populations using bone and museum skins sourced from within its former range across New Zealand’s North and South Islands. We found significant population genetic structure between the two extant Cook’s Petrel populations for one of the two nuclear introns (β-fibint7). The mitochondrial DNA CO1 analysis indicated that the SNP variant found in the Codfish Island population was formerly widely distributed across both the North and South Islands, whereas the Little Barrier Island variant was detected only in North Island samples. We argue that these combined data support the recognition of the extant populations as different subspecies. Previous names for these taxa exist, thus Cook’s Petrel from Little Barrier Island becomes Pterodroma cookii cookii and Cook’s Petrel from Codfish Island becomes P. c. orientalis. Furthermore, we suggest that both genetic and non-genetic data should be taken into consideration when planning future mainland translocations. Namely, any translocations on the South Island should be sourced from Codfish Island and future translocations on the North Island should continue to be sourced from Little Barrier Island only.

Imperfect detection of individuals in threatened wild populations is common and can obscure real population trends when it is unaccounted for in population monitoring, and therefore impede conservation decision making. For many threatened insects, there is a lack of biological information or available long-term data to inform how best to practice data collection and population monitoring. Here, we inform the design of a long-term population density monitoring protocol for Brachaspis robustus, a Nationally Endangered grasshopper endemic to the Mackenzie Basin of New Zealand. We use removal sampling (repeated visual searches of a predefined area where any individuals found are temporarily removed to achieve successive depletion) during a single austral summer season (November to March) to rapidly quantify seasonal and demographic visual detectability. Juvenile instars dominated population composition in all months except December and males represented > 50% of monthly captures. Adult females were 2–3 times larger than adult males, and 79% of those captured were found during the first search of an area compared to only 52% of adult males. The odds of detecting an individual increased by 6% per 1 mm of body length. Removal sampling was found to be an effective method for rapidly informing future long-term monitoring design for a visually cryptic, threatened insect. Recommendations include monitoring adult females as an index of population size, restricting monitoring to when adult abundance peaks (November and December), and conducting multiple monitoring events within peak months to counter the effects of daily and seasonal variation and imperfect detection.

We evaluate evidence that reducing mammalian predators benefits threatened and declining grasshoppers in the Mackenzie Basin, New Zealand. Long-term population trends of Sigaus minutus are investig...

Summary De-extinction sensu stricto is the resurrection of phenotypic traits once possessed by extinct species to create extant functional proxies. To realise the ecological benefit of de-extinction, self-sustaining (genetically viable) populations of functional proxies are required. It is often implied, yet rarely stated, that the genetic challenges associated with the survival and recovery of extant threatened species in an effort to conserve biodiversity are also relevant to the use of functional proxies of extinct species as a conversation tool. Here, we highlight the importance of prioritising evolutionary potential − the capacity to evolve (adapt) in response to environmental change − in populations of functional proxies. We use conservation genetic principles to describe impediments to the creation and maintenance of evolutionary potential as a series of potentially unavoidable genetic bottlenecks (pre-extinction, resurrection, captive, translocation). To give any successfully translocated populations of functional proxies the best chance to survive beyond the first few generations in the wild, we advocate the use of a holistic framework that includes the creation of sufficiently large, genetically diverse populations that harbour the ability to adapt to a changing environment. A lay summary is available for this article.

The Masked Booby is a highly vagile, pantropical seabird of which up to six subspecies have been recognised: S. d. dactylatra, S. d. californica, S. d. personata, S. d. melanops, S. d. bedouti and S. d. tasmani. The genetic distinction of several S. dactylatra colonies has been previously investigated, but this has not yet been conducted for the Bedout Island population in Western Australia, which has been considered by some to be part of a distinct subspecies. Suspected population decline on Bedout Island has renewed interest in determining the extent to which genetic novelty might be threatened. To answer this question, morphological and mitochondrial control region sequence variation were used to determine the distinction of the Bedout Island population. Whereas the morphological measures were equivocal, six haplotypes were identified from 31 individuals, none of which were shared by individuals previously sampled from the Indo-Pacific. The Bedout Island haplotypes were most closely related to other haplotypes found in a distinct Indian Ocean haplogroup, but haplotype frequencies at Bedout Island differed significantly from all other. This indicates that the Bedout Island population rarely exchanges mitochondrial genes with any of the other Masked Booby colonies presently studied, which may reflect dependence on local recruitment for its persistence.

Several reviews in the past decade have heralded the benefits of embracing high-throughput sequencing technologies to inform conservation policy and the management of threatened species, but few have offered practical advice on how to expedite the transition from conservation genetics to conservation genomics. Here, we argue that an effective and efficient way to navigate this transition is to capitalize on emerging synergies between conservation genetics and primary industry (e.g., agriculture, fisheries, forestry and horticulture). Here, we demonstrate how building strong relationships between conservation geneticists and primary industry scientists is leading to mutually-beneficial outcomes for both disciplines. Based on our collective experience as collaborative New Zealand-based scientists, we also provide insight for forging these cross-sector relationships.

Two captive-reared birds of wild origin presumed to be Kakī/Black Stilt (Himantopus novaezelandiae) were found to display plumage atypical of Kakī. We have combined genetic and non-genetic data to test the hypothesis that these birds are a product of brood parasitism by “non-kakī” [i.e. Poaka/Pied Stilt (Himantopus himantopus leucocephalus) or Kakī–Poaka hybrids]. We found that these atypically plumed birds have cytochrome b haplotypes and microsatellite alleles that could not be attributed to the putative Kakī parents associated with the nest, thus providing the first evidence for brood parasitism in Kakī.

Statistically robust monitoring of threatened populations is essential for effective conservation management because the population trend data that monitoring generates is often used to make decisions about when and how to take action. Despite representing the highest proportion of threatened animals globally, the development of best practice methods for monitoring populations of threatened insects is relatively uncommon. Traditionally, population trend data for the Nationally Endangered New Zealand grasshopper Brachaspis robustus has been determined by counting all adults and nymphs seen on a single ~1.5 km transect searched once annually. This method lacks spatial and temporal replication, both of which are essential to overcome detection errors in highly cryptic species like B. robustus. It also provides no information about changes in the grasshopper’s distribution throughout its range. Here, we design and test new population density and site occupancy monitoring protocols by comparing a) comprehensive plot and transect searches at one site and b) transect searches at two sites representing two different habitats (gravel road and natural riverbed) occupied by the species across its remaining range. Using power analyses, we determined a) the number of transects, b) the number of repeated visits and c) the grasshopper demographic to count to accurately detect long term change in relative population density. To inform a monitoring protocol design to track trends in grasshopper distribution, we estimated the probability of detecting an individual with respect to a) search area, b) weather and c) the grasshopper demographic counted at each of the two sites. Density estimates from plots and transects did not differ significantly. Population density monitoring was found to be most informative when large adult females present in early summer were used to index population size. To detect a significant change in relative density with power > 0.8 at the gravel road habitat, at least seventeen spatial replicates (transects) and four temporal replicates (visits) were required. Density estimates at the natural braided river site performed poorly and likely require a much higher survey effort. Detection of grasshopper presence was highest (pg > 0.6) using a 100 m x 1 m transect at both sites in February under optimal (no cloud) conditions. At least three visits to a transect should be conducted per season for distribution monitoring. Monitoring protocols that inform the management of threatened species are crucial for better understanding and mitigation of the current global trends of insect decline. This study provides an exemplar of how appropriate monitoring protocols can be developed for threatened insect species.

Males of many animal species fight to establish social dominance and control access to females so that they have more opportunities to reproduce than their competitors. Males with lower social status will struggle to directly compete for mates, thus they attempt to mate with females by stealth. This often leads to more than one male mating with the same female so that the sperm from each male end up competing to fertilise that female’s eggs, a phenomenon known as sperm competition. Males suspend their sperm in a fluid to make a mixture known as semen. It has been shown that, compared to high status males, low status males will produce higher quality semen that contains greater numbers of faster swimming sperm, giving them an advantage in sperm competition. Growing evidence from several species indicates that males can quickly adjust how fast their sperm swim in response to social cues that signal changing risks of sperm competition. However, how these rapid adjustments occur remains largely unknown, and whether they alter a male’s reproductive success against a competitor has seldom been examined. Chinook salmon usually live in the North Pacific Ocean but they swim up rivers in North America and Asia to reproduce. They have also been introduced to several other countries including New Zealand where they are farmed commercially. The fish are highly prized by sport fishermen and are also of cultural significance to certain groups of indigenous people in North America. Barlett et al. studied the semen of chinook salmon, undertaking a series of experiments in which males switched between high and low social status. The experiments show that, as predicted, the sperm of males that changed from high to low social status started to swim faster. These changes in speed were caused by the fluid in the semen and altered the number of eggs that the male’s sperm fertilised when competing against sperm from another male. In their natural range some populations of chinook salmon are declining due to overfishing combined with habitat loss and alteration. The findings of Barlett et al. contribute to a better understanding of how this fish species reproduces, which may lead to the introduction of measures that help natural populations to recover or help to improve commercial farming. Improved knowledge of how the fluid in semen affects sperm activity may also have important consequences for our wider understanding of male fertility in humans and other animals.

There is contentious debate surrounding the merits of de-extinction as a biodiversity conservation tool. Here, we use extant analogues to predict conservation actions for potential de-extinction candidate species from New Zealand and the Australian state of New South Wales, and use a prioritization protocol to predict the impacts of reintroducing and maintaining populations of these species on conservation of extant threatened species. Even using the optimistic assumptions that resurrection of species is externally sponsored, and that actions for resurrected species can share costs with extant analogue species, public funding for conservation of resurrected species would lead to fewer extant species that could be conserved, suggesting net biodiversity loss. If full costs of establishment and maintenance for resurrected species populations were publicly funded, there could be substantial sacrifices in extant species conservation. If conservation of resurrected species populations could be fully externally sponsored, there could be benefits to extant threatened species. However, such benefits would be outweighed by opportunity costs, assuming such discretionary money could directly fund conservation of extant species. Potential sacrifices in conservation of extant species should be a crucial consideration in deciding whether to invest in de-extinction or focus our efforts on extant species.

For threatened species with small captive populations, it is advisable to incorporate conservation management strategies that minimize inbreeding in an effort to avoid inbreeding depression. Using multilocus microsatellite genotype data, we found a significant negative relationship between genetic relatedness (inbreeding) and reproductive success (fitness) in a captive population of the critically endangered Black Stilt or KakīHimantopus novaezelandiae. In an effort to avoid inbreeding depression in this iconic New Zealand endemic, we recommend re-pairing closely related captive birds with less related individuals and pairing new captive birds with distantly related individuals.

Hybridization facilitated by human activities has dramatically altered the evolutionary trajectories of threatened taxa around the globe. Whereas introduced mammalian predators and widespread habitat loss and degradation clearly imperil the recovery and survival of the New Zealand endemic black stilt or kak o( Himantopus novaezelandiae), the risk associated with hybridization between this critically endangered endemic and its self-introduced congener, the pied stilt or poaka (Himantopus himantopus leucocephalus) is less clear. Here, we combine Bayesian admixture analyses of microsatellite data with mitochondrial DNA sequence data to assess the levels of hybridization and introgression between kak o and poaka. We show that birds classified as hybrids on the basis of adult plumage are indeed of hybrid origin and that hybridization between kak o and poaka is both extensive and bidirectional. Despite this, we found almost no evidence for introgression from poaka to kak o, thus negating the popular belief that kak o represent a hybrid swarm. To our knowledge, ours represents the first comprehensive study to document a lack of widespread introgression for a species at risk despite a recent history of extensive bidirectional human-induced hybridization. We attribute this rather surprising result, in part, to reduced reproductive success in female hybrids combined with a transient male-biased kak o sex ratio. To maximize the evolutionary potential of kak o, we use these data to recommend conservation management activities aimed to maintain the genetic integrity and to maximize the genetic diversity of this iconic rare bird.

To test the hypothesis that both physical and ecological barriers to gene flow drive population differentiation in tropical seabirds, we surveyed mitochondrial control region variation in 242 brown boobies (Sula leucogaster), which prefer inshore habitat, and 271 red-footed boobies (S. sula), which prefer pelagic habitat. To determine the relative influence of isolation and gene flow on population structure, we used both traditional methods and a recently developed statistical method based on coalescent theory and Bayesian inference (Isolation with Migration). We found that global population genetic structure was high in both species, and that female-mediated gene flow among ocean basins apparently has been restricted by major physical barriers including the Isthmus of Panama, and the periodic emergence of the Sunda and Sahul Shelves in Southeast Asia. In contrast, the evolutionary history of populations within ocean basins differed markedly between the two species. In brown boobies, we found high levels of population genetic differentiation and limited gene flow among colonies, even at spatial scales as small as 500 km. Although red-footed booby colonies were also genetically differentiated within ocean basins, coalescent analyses indicated that populations have either diverged in the face of ongoing gene flow, or diverged without gene flow but recently made secondary contact. Regardless, gene flow among red-footed booby populations was higher than among brown booby populations. We suggest that these contrasting patterns of gene flow within ocean basins may be explained by the different habitat preferences of brown and red-footed boobies.

Ancient DNA has revolutionized the way in which evolutionary biologists research both extinct and extant taxa, from the inference of evolutionary history to the resolution of taxonomy. Here, we present, to our knowledge, the first study to report the rediscovery of an ‘extinct’ avian taxon, the Tasman booby ( Sula tasmani ), using classical palaeontological data combined with ancient and modern DNA data. Contrary to earlier work, we show an overlap in size between fossil and modern birds in the North Tasman Sea (classified currently as S. tasmani and Sula dactylatra fullagari , respectively). In addition, we show that Holocene fossil birds have mitochondrial control region sequences that are identical to those found in modern birds. These results indicate that the Tasman booby is not an extinct taxon: S. dactylatra fullagari O'Brien & Davies, 1990 is therefore a junior synonym of Sula tasmani van Tets, Meredith, Fullagar & Davidson, 1988 and all North Tasman Sea boobies should be known as S. d. tasmani . In addition to reporting the rediscovery of an extinct avian taxon, our study highlights the need for researchers to be cognizant of multidisciplinary approaches to understanding taxonomy and past biodiversity.

Translocation of individuals among extant populations is an important tool in species conservation that allows managers to supplement dwindling populations and potentially alleviate the deleterious effects of inbreeding. Ideal translocation strategy should consider historical relationships among existing populations to avoid potential disruption of population subdivision and local adaptation. Here, we examine mitochondrial sequence variation in the endangered blue duck Hymenolaimus malacorhynchos, a New Zealand endemic riverine specialist, to facilitate informed decision making in future translocations. Behavioural observations suggest that blue duck dispersal is limited and may result in genetic structure within and between regional populations. We analysed 894 base pairs of mitochondrial control region in 78 adult blue ducks sampled from 11 river catchments across the species’ range (representing four regions in the North Island and three regions in the South Island) and found strong and significant genetic structure both within and among islands. These results, combined with a 2.0% sequence divergence between islands, indicates that North Island and South Island blue ducks should be treated as separate management units. The relationship between genetic differentiation and geographic distance for blue ducks on the South Island conformed to an “isolation by distance” pattern. Overall, we recommend that translocations of blue ducks should not be made between the North and the South Islands and those within each island should be restricted to neighbouring catchments.

To test the hypothesis that nonphysical barriers to gene flow play a role in the divergence of low-latitude seabird populations, we applied phylogeographic methods to mitochondrial control region sequence variation in a global sample of masked boobies ( Sula dactylatra ). In accord with previous studies, we found that Indo-Pacific and Atlantic haplotypes form two divergent lineages, excluding one haplotype previously attributed to secondary contact between the Indian Ocean and the Caribbean Sea. Within the Indo-Pacific and the Atlantic, we found a relatively large number of haplotypes, many of which were unique to a single population. Although haplotypes from most populations were found in more than one higher-level clade, nested clade analysis revealed a significant association between clades and geography for the majority of higher-level clades, most often interpreted as a consequence of isolation by distance. We found low levels of gene flow within Indo-Pacific and Atlantic populations, and a significant correlation between gene flow and geographical distance among Indo-Pacific populations. We estimate that Indo-Pacific masked boobies experienced rapid population growth ∼ 180 000 years ago and that the majority of Indo-Pacific and Atlantic populations diverged within the last ∼ ∼ ∼ 115 000 years. These combined data suggest that the predominant pattern between Indo-Pacific and Atlantic populations is long-term isolation by physical barriers to gene flow. In contrast, populations within these regions appear to have diverged despite few obvious physical barriers to gene flow, perhaps as a consequence of limited natal dispersal combined with local adaptation and/or genetic drift.

To further test the hypothesis that the Isthmus of Panama is a major barrier to gene flow in pantropical seabirds, we applied phylogeographic methods to mitochondrial control sequence variation in masked booby (Sula dactylatra) populations on either side of the Isthmus of Panama and the southern tip of Africa. In accord with Steeves et al. (2003), we found that all Caribbean masked boobies with the ‘secondary contact’ cytochrome b haplotype (m-B) shared a control region haplotype (Sd_100), which grouped with Indian‐ Pacific haplotypes and not Caribbean‐Atlantic haplotypes. In addition, Sd_100 was more closely related to control region haplotypes in the Indian Ocean than in the Pacific. We also found that the ‘secondary contact’ birds diverged more recently from extant populations in the Indian Ocean than in the Pacific. Thus, it appears that these masked boobies did not breach the Isthmus of Panama. Rather, birds likely dispersed around the southern tip of Africa during favourable oceanographic conditions in the Pleistocene.

We examined mitochondrial cytochrome b sequence variation in masked Sula dactylatra, red-footed S. sula, and brown S. leucogaster boobies sampled from islands in the central and eastern Pacific Ocean and in the Caribbean Sea. Each species showed a different phylogeographic pattern. Whereas haplotypes in masked and red-footed boobies were shared across the central and eastern Pacific (i.e., across the Eastern Pacific Basin), brown booby haplotypes were not shared across the Eastern Pacific Basin. Although most masked booby haplotypes from the Pacific were distinct from those in the Caribbean, one haplotype was shared across the Isthmus of Panama. Red-footed and brown boobies, however, did not share haplotypes across the Isthmus of Panama. We estimate that divergence of these regional populations occurred within the last 560,000 years. Thus, the Isthmus of Panama and the Eastern Pacific Basin (albeit to a lesser degree) appear to have played a role in the diversification of these species.

Although the majority of eastern North Pacific (ENP) gray whales migrate to feeding grounds in the Bering and Chukchi Seas, some terminate the migration in more southerly areas such as British Columbia (BC). Long-term sighting studies in Clayoquot Sound (CS), BC, indicate that approximately 35–50 individuals exhibit long-term fidelity to this site. To determine the sex composition (based on genetic sexing) of CS gray whales and to assess whether matrilineal site-fidelity occurs in CS, we collected skin biopsy samples from 16 CS individuals (‘residents’) and 41 samples from other areas (representative of the overall population in the ENP: ‘non-residents’). A total of 27 polymorphic sites defined 24 haploytpes among the 57 samples sequenced for HV1 of the mtDNA control region. The nucleotide and haplotype diversities of these samples were 0.017 (SE = 0.0012) and 0.94 (SE = 0.0019), respectively. Neighbor-joining analysis revealed five lineages each of which contained haplotypes that were observed in both residents and non-residents. Residents did not differ significantly from non-residents, and no significant sex-ratio bias was found. These data suggest a level of diversity that is inconsistent with a severe historical bottleneck, and given the available sample size, do not indicate matrilineally directed fidelity to Clayoquot Sound.

Pelagic seabirds are highly mobile, reducing the likelihood of allopatric speciation where disruption of gene flow between populations is caused by physically insurmountable, extrinsic barriers. Spatial segregation during the non-breeding season appears to provide an intrinsic barrier to gene flow among seabird populations that otherwise occupy nearby or overlapping regions during breeding, but how this is achieved remains unclear. Here we show that the two genetically distinct populations of Cook's petrel (Pterodroma cookii) exhibit transequatorial separation of non-breeding ranges at contemporary (ca. 2-3 yrs) and historical (ca. 100 yrs) time scales. Segregation during the non-breeding season per se appears as an unlikely barrier to gene flow. Instead we provide evidence that habitat specialization during the non-breeding season is associated with breeding asynchrony which, in conjunction with philopatry, restricts gene flow. Habitat specialization during breeding and non-breeding likely promotes evolutionary divergence between these two populations via local adaptation.

Pitman and Jehl (1998) recently argued that Masked Boobies (formerly Sula dactylatra granti) breeding on the Nazca Plate in the eastern Pacific Ocean are morphologically and ecologically distinct from other Masked Boobies and may represent a full species. The American Ornithologists' Union subsequently elevated that subspecies to a full species: the Nazca Booby (S. granti). To evaluate that change in classification, we compared sequence variation in the mitochondrial cytochrome-b gene among 75 Nazca Boobies and 37 Masked Boobies representing three subspecies from the central and eastern Pacific and Atlantic oceans. Results indicated strong differentiation of cytochrome-b variation among taxa. Sequences constituted three distinct groups: Nazca Boobies, Masked Boobies from the central and eastern Pacific (S. d. personata and S. d. californica), and Masked Boobies (S. d. dactylatra) from the Caribbean and Atlantic. Those three groups probably diverged within a very short period, 400,000–500,000 year...