Island radiations, such as those of the Australo-Pacific, offer unique insight into diversification, extinction, and early speciation processes. Yet, their speciation and colonization histories are often obscured by conflicting genomic signals from incomplete lineage sorting (ILS) or hybridization. Here, we integrated mitogenomes and genome-wide SNPs to unravel the evolutionary history of one of the world's most geographically widespread island radiations. The Australo-Pacific reed warblers ( Acrocephalus luscinius complex) are a speciose lineage including five species that have become extinct since the 19th century and ten additional species of conservation concern. The radiation spans over 10,000 km across Australo-Papua, Micronesia and Polynesia, including the Mariana, Hawaii and Pitcairn Island archipelagos. Earlier mtDNA studies suggested a stepping-stone colonization process, resulting in archipelago-level secondary sympatry of divergent mtDNA lineages in the Mariana Islands and Marquesas. These studies hypothesized that morphologically similar species on neighboring islands arose from ecological convergence. Using DNA from historical museum specimens and modern genetic samples, we show that ILS and/or gene flow have shaped the radiation of Australo-Pacific reed warblers rather than secondary sympatry. The nuclear genome reconstructs a simpler biogeographic history than mtDNA, showing close relationships between species in the Mariana Islands and Marquesas despite their paraphyletic mtDNA lineages. Gene flow likely involved early and late colonizing waves of the radiation before the loss of ancestral dispersive ability. Our results highlight how collection genomics can elucidate evolutionary history and inform conservation efforts for threatened species.

Effective species management and conservation benefit from knowledge of species distribution and status. Surveys to obtain that information often involve replicate sampling, which increases survey effort and costs. We simultaneously modeled species distribution, abundance and spatial correlation, and compared the uncertainty in replicate abundance estimates of the endangered palila (Loxioides bailleui) using hierarchical generalized additive models with a soap film smoother that incorporated random effects for visit. Based on survey coverage and detections, we selected the 2017 point-transect distance sampling survey on Mauna Kea, Hawai'i Island, for our modeling. Our modeling approach allowed us to account for imperfect detections, control the effects of boundary features, and generate visit-specific density surface maps. We found that visit-specific smooths were nearly identical, indicating that little information was gained from a subsequent visit, and that most of the estimator uncertainty was derived from within-visit variability. Scaling back the palila survey to a single visit would halve the survey effort and logistical costs and increase efficiencies in data management and processing. Changing the sampling protocol warrants careful consideration and our findings may help management and regulatory agencies by maximizing efficiency and minimizing costs of surveying protocols, while providing guidelines on how to best collect information critical to species' conservation.

Effective species management and conservation require knowledge of species distribution and status. We used point-transect distance sampling surveys of the endangered palila (Loxioides bailleui), a honeycreeper currently found only on the Island of Hawai'i, USA, to generate robust estimates of total abundance and simultaneously model the distribution, abundance, and spatial correlation of the species as a density surface model (DSM). Point-transect distance sampling is a widely applied method to estimate bird densities accounting for imperfect detection probability. For the DSM we used a generalized additive model framework and soap film smoothers to control the effects of boundary features. This modeling approach allowed us to account for imperfect detection and propagate detection probability uncertainty. We compared the uncertainty in palila abundance estimates using standard point-transect distance sampling to estimates from the DSM. The DSM, accounting for both distance-sampling-derived detection probability variance and the generalized additive model density estimate variance, did not improve population estimator precision; however, it provided insight into the species' distribution, density, and uncertainty. We also applied excursion sets analysis to objectively identify areas where the species occurs in high densities. The 2017 global population of <2,000 individuals was limited to an excursion area of 1,500 ha. Our findings can help management and regulatory agencies by simultaneously mapping a species' distribution and density, improving survey protocols, and providing information important to species conservation.

Birds can be unintentionally injured or killed by mammal traps. Unfortunately, some birds in Hawai' i, including puaiohi (Myadestes palmeri), and in New Zealand, have been killed by the widely used Goodnature (R) A24 rat-stoat self-resetting trap (A24s) during rodent control. To help address this problem, we conducted two sets of aviary trials using (1) barriers and (2) existing A24 excluders with red-winged blackbirds (Agelaius phoeniceus), European starlings (Sturnus vulgaris), and a single puaiohi. We conducted barrier trials to inform future bird excluder designs by establishing the minimum gap-height beneath a barrier that blackbirds and starlings successfully overcome. During barrier trials, starlings defeated barriers significantly lower (>= 1.9 cm) than blackbirds (>= 2.9 cm). We then presented disarmed A24s with no excluder or with one of two excluders (plastic Goodnature, 11 cm length; and metal mesh, 10 cm, or 15-17 cm length for puaiohi) to each bird species. We placed the A24s and excluders low (11- 25 cm trap height, 0-10 cm excluder height) and high (50-83 cm trap height, 37-72 cm excluder height) above ground to test bird entry abilities at trap heights used by land managers to control rodents. During the A24 excluder trials, all three bird species entered the trap at low or high heights with no excluder, confirming bird risk of injury when excluders aren't used. Excluders greatly decreased entry into A24s by blackbirds and puaiohi, but not by starlings. Plastic and metal excluders prevented puaiohi entry at low height only. Based on our trials and recent field uses, the plastic excluder performed best for excluding all three bird species if placed so the lower edge of the excluder is 0-2 cm above ground. However, plastic and metal excluders can clog with dead rodents when positioned low. Future trials aiming to exclude all small birds from A24s while maintaining trap efficacy against target rodents should consider new excluder designs incorporating the 1.9-2.9 cm gap-height thresholds. When deciding whether to use excluders and appropriate trap heights, managers need to consider both the risk of non-target injuries or deaths and the impact of potentially decreasing trap efficacy.

Many species around the world are declining precipitously as a result of multiple threats and changing climate. Managers tasked with protecting species often face difficult decisions in regard to identifying which threats should be addressed, given limited resources and uncertainty in the success of any identified management action. On Kaua'i Island, Hawai'i, USA, forest bird species have experienced accelerated declines over the last 20 years, and 2 species, the 'akikiki (Oreomystis bairdi) and 'akeke'e (Loxops caeruleirostris), are now at the brink of extinction. Both species face multiple threats, and managers face difficult decisions on whether to mitigate threats in the wild, establish a captive population as insurance against extinction, translocate birds to novel locations, or some combination of these actions. Each set of actions (alternatives) would require substantial resources with considerable uncertainty in success. In 2014, we brought together 14 experts representing biologists and managers familiar with the species and island to develop a conservation strategy under a structured decision making (SDM) framework, an approach for making complex decisions under uncertainty. The group's challenge was to identify a set of alternatives that reduces the risk of extinction, set the foundation for one or more genetically viable, reproducing, stable to increasing populations in 10 years, and promote conditions for long-term persistence in the wild. Multiple alternatives were evaluated, via expert judgement, in terms of the probability they would achieve the objectives concerning immediate extinction risk, near-term viability, and adequacy of habitat. Factors that might impede the success of each action were also evaluated. The process identified the establishment of a captive population and efforts to stabilize the existing wild population as the approach most likely to meet the objectives of preventing imminent extinction and ensuring long-term viability.

Conservation benefits from incorporating genomics to explore the impacts of population declines, inbreeding, loss of genetic variation and hybridization. Here we use the near-extinct Mariana Islands reedwarbler radiation to showcase how ancient DNA approaches can allow insights into the population dynamics of extinct species and threatened populations for which historical museum specimens or material with low DNA yield (e.g., scats, feathers) are the only sources for DNA. Despite their having paraphyletic mitochondrial DNA (mtDNA), nuclear single nucleotide polymorphisms (SNPs) support the distinctiveness of critically endangered Acrocephalus hiwae and the other three species in the radiation that went extinct between the 1960s and 1990s. Two extinct species, A. yamashinae and A. luscinius, were deeply divergent from each other and from a third less differentiated lineage containing A. hiwae and extinct A. nijoi. Both mtDNA and SNPs suggest that the two isolated populations of A. hiwae from Saipan and Alamagan Islands are sufficiently distinct to warrant subspecies recognition and separate conservation management. We detected no significant differences in genetic diversity or inbreeding between Saipan and Alamagan, nor strong signatures of geographical structuring within either island. However, the implications of possible signatures of inbreeding in both Saipan and Alamagan, and long-term population declines in A. hiwae that pre-date modern anthropogenic threats require further study with denser population sampling. Our study highlights the value that conservation genomics studies of island radiations have as windows onto the possible future for the world's biota as climate change and habitat destruction increasingly fragment their ranges and contribute to rapid declines in population abundances.

The Mariana Crow, or Åga (Corvus kubaryi), is a critically endangered species (IUCN -International Union for Conservation of Nature), endemic to the islands of Guam and Rota in the Mariana Archipelago. It is locally extinct on Guam, and numbers have declined dramatically on Rota to a historical low of less than 55 breeding pairs throughout the island in 2013. Because of its extirpation on Guam and population decline on Rota, it is of critical importance to assess the genetic variation among individuals to assist ongoing recovery efforts. We conducted a population genomics analysis comparing the Guam and Rota populations and studied the genetic structure of the Rota population. We used blood samples from five birds from Guam and 78 birds from Rota. We identified 145,552 candidate single nucleotide variants (SNVs) from a genome sequence of an individual from Rota and selected a subset of these to develop an oligonucleotide in-solution capture assay. The Guam and Rota populations were genetically differentiated from each other. Crow populations sampled broadly across their range on Rota showed significant genetic structuring – a surprising result given the small size of this island and the good flight capabilities of the species. Knowledge of its genetic structure will help improve management strategies to help with its recovery.

The Nightingale Reed-Warbler (Acrocephalus hiwae), a critically endangered songbird, is the last remaining of four reed-warbler species that once inhabited the Mariana Islands. The most recent population estimate for the species is 2915-3742 individuals distributed over the islands of Saipan (n = 2742, 95% CI = 1686-3956) and Alamagan (n = 946, 95% CI = 173-1000), which represents a significant decline for the species on Saipan. Though data on life history parameters such as survival rates are not widely available, other parameters such as clutch size and nest success have been studied. Given the extirpation of three of the four reed-warbler species from the Mariana Islands, the recent significant decline of the larger Saipan population, and the increasing threats faced by the species, it is critical to determine what additional life history information is needed to aid management decisions. Using Vortex, we developed stochastic population models to represent current reed-warbler population dynamics and used sensitivity analysis to identify the life history parameters to which the model was most sensitive. Baseline models without inbreeding indicated declines of the Nightingale Reed-Warbler populations on Saipan and Alamagan, as well as of the overall population. The inclusion of inbreeding further increases the modeled rate of population decline. Parameters such as initial population size, carrying capacity, and male survival have relatively little influence on reed-warbler population models, while female and juvenile survival and, to a lesser degree, fecundity measures, exhibit strong influences on the species' population dynamics. We recommend effort be placed on collecting updated survival data for all life stages, but particularly for females and juveniles. Given model predictions of vulnerability to extinction, we recommend management actions that may increase survival rates of juveniles and females.

Reasons for the decline of the Mariana Crow (Corms kubaryi) on the Western Pacific island of Rota are currently unknown, but a need to protect nesting habitat has been suggested. We examined 55 actual nest sites and 60 random sites from 1997 to 1999 to investigate habitat characteristics specific to crow nest sites. Both nests and random plots were predominantly in limestone forest habitat. Discriminant function analyses indicate actual nest sites were differentiated from random sites based on a higher percentage of canopy cover and mean DBH of papaya (Carica papaya) and woody vines, as well as a higher stem count of species associated with limestone forests. This resulted in correct classification of a potential site as nesting versus random in 92% of the cases. Actual nests were >300 m from buildings, while random sites averaged (+/- SE) 226.7 +/- 71.6 m from a building. Actual nest sites were about twice as far from a road as random nest sites. Twenty-eight of the 55 active nests fledged young. Nests in native forests were associated with higher reproductive success than nests in more disturbed areas. These findings suggest that damage to habitat from anthropogenic or natural causes may be limiting nesting success. Received 19 February 2010. Accepted 22 November 2010.

The Rota White-eye (Zosterops rotensis) is an endangered species endemic to the island of Rota in western Micronesia. We monitored eight nests from 2003 to 2005, four of which produced at least one fledgling. Clutch size was two in each of five nests that were counted the average number of fledglings from successful nests was 1.5 (n = 4). We filmed six nests and captured two nest Predation events on video. A Mariana Crow (Corvus kubaryi), which is also an endangered species, was filmed taking nestlings from one white-eye nest. Another nest containing eggs was depreciated by a rat (Rattus spp.) however, this may have occurred after the nest was abandoned due to the presence of the camera.