A recently published paper, titled “Coastal proximity of populations in 22 Pacific Island Countries and Territories” details the methodology used to undertake the analysis and presents the findings. Purpose * This analysis aims to estimate populations settled in coastal areas in 22 Pacific Island Countries and Territories (PICTS) using the data currently available. In addition to the coastal population estimates, the study compares the results obtained from the use of national population datasets (census) with those derived from the use of global population grids. * Accuracy and reliability from national and global datasets derived results have been evaluated to identify the most suitable options to estimate size and location of coastal populations in the region. A collaborative project between the Pacific Community (SPC), WorldFish and the University of Wollongong has produced the first detailed population estimates of people living close to the coast in the 22 Pacific Island Countries and Territories (PICTs).

description: The Pacific coast population of the western snowy plover (Charadrius alexandrinus nivosus) (western snowy plover) is federally listed as threatened. The current Pacific coast breeding population extends from Damon Point, Washington, south to Bahia Magdalena, Baja California, Mexico (including both Pacific and Gulf of California coasts). The western snowy plover winters mainly in coastal areas from southern Washington to Central America. The primary objective of this recovery plan is to remove the Pacific coast population of the western snowy plover from the List of Endangered and Threatened Wildlife and Plants by: (1) increasing population numbers distributed across the range of the Pacific coast population of the western snowy plover; (2) conducting intensive ongoing management for the species and its habitat and developing mechanisms to ensure management in perpetuity; and (3) monitoring western snowy plover populations and threats to determine success of recovery actions and refine management actions.; abstract: The Pacific coast population of the western snowy plover (Charadrius alexandrinus nivosus) (western snowy plover) is federally listed as threatened. The current Pacific coast breeding population extends from Damon Point, Washington, south to Bahia Magdalena, Baja California, Mexico (including both Pacific and Gulf of California coasts). The western snowy plover winters mainly in coastal areas from southern Washington to Central America. The primary objective of this recovery plan is to remove the Pacific coast population of the western snowy plover from the List of Endangered and Threatened Wildlife and Plants by: (1) increasing population numbers distributed across the range of the Pacific coast population of the western snowy plover; (2) conducting intensive ongoing management for the species and its habitat and developing mechanisms to ensure management in perpetuity; and (3) monitoring western snowy plover populations and threats to determine success of recovery actions and refine management actions.

Spatial datasets utilized to conduct the spatial analysis and additional information from the research article: Coastal proximity of populations in 22 Pacific Island Countries and Territories. https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0223249 https://sdd.spc.int/mapping-coastal

Figures and Supporting information included in the article Coastal proximity of populations in 22 Pacific Island Countries and Territories. https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0223249 https://sdd.spc.int/mapping-coastal

A growing body of evidence suggests that spatial population structure can develop in marine species despite large population sizes and high gene flow. Characterizing population structure is important for the effective management of exploited species, as it can be used to identify appropriate scales of management in fishery and aquaculture contexts. The California sea cucumber, Apostichopus californicus, is one such exploited species whose management could benefit from further characterization of population structure. Using restriction site-associated DNA (RAD) sequencing, we developed 2,075 single nucleotide polymorphisms (SNPs) to quantify genetic structure over a broad section of the species’ range along the North American west coast and within the Salish Sea, a region supporting the Washington State A. californicus fishery and developing aquaculture production of the species. We found evidence for population structure (global fixation index (FST) = 0.0068) with limited dispersal driving two patterns of differentiation: isolation-by-distance and a latitudinal gradient of differentiation. Notably, we found detectable population differences among collection sites within the Salish Sea (pairwise FST = 0.001–0.006). Using FST outlier detection and gene-environment association, we identified 10.2% of total SNPs as putatively adaptive. Environmental variables (e.g., temperature, salinity) from the sea surface were more correlated with genetic variation than those same variables measured near the benthos, suggesting that selection on pelagic larvae may drive adaptive differentiation to a greater degree than selection on adults. Our results were consistent with previous estimates of, and patterns in, population structure for this species in other extents of the range. Additionally, we found that patterns of neutral and adaptive differentiation co-varied, suggesting that adaptive barriers may limit dispersal. Our study provides guidance to decision-makers regarding the designation of management units for A. californicus and adds to the growing body of literature identifying genetic population differentiation in marine species despite large, nominally connected populations. Methods Approximately 50 adult A. californicus were collected by scuba divers from nine collection sites along the Pacific Coast of North America, ranging from Alaska to Oregon, including four collection sites within the southern Salish Sea. For each animal, a tissue sample was excised from a radial muscle band and stored in 100% ethanol. DNA was extracted from tissue samples using the EZNA Mollusc DNA Kit (OMEGA Bio-tek, Norcross, GA, USA) and the Qiagen DNeasy Kit (Qiagen, Germantown, MD, USA). DNA was quantified using the Quant-iT PicoGreen dsDNA Assay Kit (Thermo Fisher Scientific, Waltham, MA, USA) and DNA quality was checked by gel electrophoresis. DNA concentration was normalized to 500 ng in 20 μL of PCR-grade water. We selected samples with high DNA quality for restriction site associated DNA (RAD) sequencing and RAD libraries were prepared following standard protocols1. Briefly, DNA samples were barcoded with an individual six-base identifier sequence attached to an Illumina P1 adapter. Samples were then pooled into sub-libraries, containing approximately 12 individuals. Sub-libraries were sheared using a Bioruptor sonicator and size selected to 200-400 bp using a MinElute Gel Extraction Kit (Qiagen, Germantown, MD, USA). P2 adapters were ligated to DNA in sub-libraries and amplified with PCR using 12–18 cycles as in Etter et al. (2011). Finally, amplified sub-libraries were combined into pools of approximately 72 individuals. Paired-end 2 x 150-base pair sequencing was performed on an Illumina HiSeq4000 (San Diego, California, USA) at the Beijing Genomics Institute and the University of Oregon Genomics and Cell Characterization Core Facility. Only forward reads were used for analysis. To estimate genotyping error, 14 individuals were sequenced twice. Raw RAD sequencing data were demultiplexed using the process_radtags module in the pipeline STACKS v.1.442. A threshold of 800,000 reads was used to exclude poorly sequenced individuals. Because a genome was not available for A. californicus, we aligned individual sequences to the genome of a closely related species, A. parvimensis (GenBank accession number = GCA_000934455.1). The A. parvimensis genome was 760,654,621 bp, with 21,559 scaffolds and an N50 size of 9,587. We retained reads with a minimum mapping quality score of 20. Then, we used dDocent v.2.7.8 to perform a reference-guided locus assembly using the filtered reads and default parameters3. Additionally, a parallel de novo assembly was performed, which produced nearly identical results for population structure and 1.8–2.8% lower mean expected heterozygosity, 0.9–1.8% higher mean observed heterozygosity, and 1.2–3.3% higher proportions of polymorphic SNPs than in the with-reference assembly, although with similar patterns across collection sites. The reference-guided assembly was retained for further analyses due to decreased confidence in identifying genotyping errors in the de novo assembly4. We used vcftools v.0.1.165 to remove indels and to retain only single nucleotide polymorphisms (SNPs) with a minimum quality score of 20, minimum minor allele frequency of 0.05 and maximum missing data per locus of 30% across collection sites. Individuals with more than 30% missing data across SNPs were removed. In cases of multiple SNPs per RAD tag, we retained the SNP with the highest minor allele frequency6. SNPs that were not in Hardy Weinberg Equilibrium (HWE) were considered sequencing errors or poorly assembled loci and were removed from our data set, as selection and inbreeding are unlikely to cause significant deviations from HWE equilibrium at biallelic loci7. We tested SNPs for deviations from HWE using the R package genepop v.1.1.4 (Rousset, 2008). SNPs were identified as being out of HWE if they had a q-value below 0.05 in at least 2 of the collection sites after correcting for false discovery rate, following Waples (2015). We used a suite of R packages, stand-alone software, and custom scripts in the programming language R v.3.5.0 9 to quantify genetic diversity and population structure. Mean expected heterozygosity, observed heterozygosity, and the inbreeding coefficient (FIS) per SNP were calculated using the R package genepop. The proportion of polymorphic SNPs per collection site was calculated using a custom R script. To investigate population structure, we first calculated Weir-Cockerham fixation index (FST)10 to quantify population differentiation using the R packages genepop and hierfstat v.0.5.7. Exact G-tests11 were used to test for significant genic differentiation using the R package genepop. To investigate patterns of spatial differentiation among collection sites, the R package adegenet v.2.1.112 was used to conduct discriminant analyses of principal components (DAPC), a multivariate method that summarizes the between-group variation (i.e., population structure), while minimizing within-group variation13. The built-in optimization algorithm was used to retain the number of principal components that minimized over-fitting and under-fitting of the model. To determine the potential number of underlying populations, the program ADMIXTURE v.1.3.0 was used to conduct a clustering analysis14. Specifically, ADMIXTURE uses a maximum likelihood-based approach to estimate individual ancestries across different assumed numbers of populations, with the best fit selected using cross-validation. To examine the presence of hierarchical population structure, we conducted analyses of molecular variance (AMOVA) using the ade4 method of the R package poppr v.2.8.115. Significance of AMOVAs was determined using permutation tests with 1,000 iterations. Using AMOVA, we investigated whether the following oceanographic barriers limit dispersal: 1) the Victoria Sill (Victoria Sill grouping), 2) Admiralty Inlet (Admiralty Inlet grouping), and 3) the North Pacific Current (NPC grouping). Because AMOVAs for each oceanographic barrier include sites in an area with other potential oceanographic barriers, we added a fourth grouping of all three oceanographic barriers (All Barriers grouping) to investigate the relative role of oceanographic barriers compared to other factors. Additionally, we conducted an AMOVA by state or province (State grouping). Although not biologically meaningful, we included the State grouping to determine how much genetic variation is captured by regional management boundaries. Isolation-by-distance (IBD) was tested with Mantel tests16 in R as linear correlation between linearized FST17 using all SNPs and shortest Euclidean distance through water (in-water distance hereafter) approximated in Google Maps18 Following Xuereb et al (2018), we also tested IBD in the northern and southern population section separately. Following Buonaccorsi et al. (2005), we estimated mean dispersal distance from the slope of the regression of linearized FST and in-water distance. We used this 1-dimensional model because it is an appropriate approximation for coastal species with dispersal dimensions greater than one dimension of the habitat (e.g., dispersal distance likely greater than water depth for A. californicus). We estimated mean dispersal distance from a set of potential population density estimates as population density estimates were unavailable. We used two approaches to investigate putatively adaptive SNPs: FST outlier detection and gene-environment association. FST outlier detection is used to identify loci potentially under spatial selection20,21, although this method does not identify the potential cause of selection. Although gene-environment association does not explicitly test whether such associations are adaptive, this method is used to identify locus-environment associations as evidence for potential local

A memo on the initial phase of the bald eagle inventory from Cape Kubugaki to Chichagof Bay.

Proportion of population living in 1, 5 and 10km buffer zones for Pacific Island Countries and Territories, determined using most recent Population and Housing Census. Number of people living in 1,5 and 10km buffer zones determined by apportioning population projections.

Find more Pacific data on PDH.stat.

Spatial datasets utilized to conduct the spatial analysis and additional information from the research article: Coastal proximity of populations in 22 Pacific Island Countries and Territories. https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0223249 https://sdd.spc.int/mapping-coastal

Access this dataset from the Pacific Data Hub

Spatial datasets utilized to conduct the spatial analysis and additional information from the research article: Coastal proximity of populations in 22 Pacific Island Countries and Territories.

https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0223249 https://sdd.spc.int/mapping-coastal

Appendix M to the Recovery Plan. Detailed maps of each of these locations are given in Appendix L. Locations of current or historical Snowy Plover breeding and wintering areas. The following maps (Figures L-77 through L-149) show the general locations of current or historical western snowy plover breeding or wintering areas on the U.S. Pacific coast within each recovery unit. The breeding and wintering locations and recovery units include only the coastal beaches, estuaries, gravel bars and salt ponds that provide western snowy plover habitat; inland areas of counties are illustrated on Figures L-77 through L-149 solely for reference. Location numbers on the maps are referenced to the numbers in parentheses shown after the location names found in the left-hand column of Table B-1 (Appendix B) and Table C-1 (Appendix C).Appendix M. Agency and Public Comment on the Western Snowy Plover (Charadrius alexandrinus nivosus) Pacific Coast Population Draft Recovery Plan.

Spatial datasets utilized to conduct the spatial analysis and additional information from the research article: Coastal proximity of populations in 22 Pacific Island Countries and Territories. https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0223249 https://sdd.spc.int/mapping-coastal

Access this dataset from the Pacific Data Hub

Appendix L to the Recovery Plan. Detailed maps of each of these locations are given in Appendix L. Locations of current or historical Snowy Plover breeding and wintering areas. The following maps (Figures L-1 through L-76) show the general locations of current or historical western snowy plover breeding or wintering areas on the U.S. Pacific coast within each recovery unit. The breeding and wintering locations and recovery units include only the coastal beaches, estuaries, gravel bars and salt ponds that provide western snowy plover habitat; inland areas of counties are illustrated on Figures L-1 through L-76 solely for reference. Location numbers on the maps are referenced to the numbers in parentheses shown after the location names found in the left-hand column of Table B-1 (Appendix B) and Table C-1 (Appendix C).

This is a feature layer created from the Survey123 form to collect a baseline of data for the SNPL during annual window surveys. This data is designed for use across the entire west coast portion of the species range, in collaboration with partners and cooperators. The form was created based on an initial version that was field tested in Recovery Unit 2. This form will similarly be tested across the range for it's field usability and data format creation. The intent is to continue to take feedback and improve the form for use across all recovery units.Western Snowy Plover (Charadrius nivosus nivosus; plover) Census and Monitoring Surveys – United States Fish and Wildlife Service (Service). This project focuses on electronic data collection (using Survey123) for Western Snowy Plover annual monitoring surveys in all Recovery Units (1-6) which covers coastal California, Oregon and Washington.The plover was listed as a federally threatened species under the Endangered Species Act in 1993. The U.S. Fish and Wildlife Service’s Western Snowy Plover Pacific Coast Population Recovery Plan was published in 2007. The 2007 Recovery Plan provides reasonable actions believed to be required to recover and/or protect plovers. The first action needed from the Recovery Plan is to monitor breeding and wintering populations and habitats of the Pacific coast population of the western snowy plover to determine progress of recovery actions to maximize survival and productivity. The census and monitoring surveys are critical data for determining if the recovery criteria have been met. Recovery criteria for delisting the plover includes: 1) An average of 3,000 breeding adults has been maintained for 10 years and 2) A yearly average productivity of at least one (1.0) fledged chick per male has been maintained in each recovery unit in the last 5 years prior to delisting. The survey effort is a collaboration between multiple FWS Field Offices, contracted partners, and official volunteers.For more information:Here is a direct link to the Data Management Plan for this project, the ServCat reference page, the Survey123 link, and a link to the relevant program page for Arcata Fish & Wildlife Office.

Spatial datasets utilized to conduct the spatial analysis and additional information from the research article: Coastal proximity of populations in 22 Pacific Island Countries and Territories. https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0223249 https://sdd.spc.int/mapping-coastal

Spatial datasets utilized to conduct the spatial analysis and additional information from the research article: Coastal proximity of populations in 22 Pacific Island Countries and Territories. https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0223249 https://sdd.spc.int/mapping-coastal

Link to the ScienceBase Item Summary page for the item described by this metadata record. Service Protocol: Link to the ScienceBase Item Summary page for the item described by this metadata record. Application Profile: Web Browser. Link Function: information

This program captures the relative abundance and distribution of five common seabirds occurring in the waters of Pacific Rim National Park Reserve including the Marbled Murrelet (Brachyramphus marmoratus), Common Murre (Uria aalge), Rhinoceros Auklet (Cerorhinca monocerata), Pigeon Guillemot (Cepphus columba), and Pelagic Cormorant (Phalacrocorax pelagicus). The at-sea surveys are done approximately every two weeks from May to September and use standardized fixed-route strip transects to estimate annual variations in the population of seabirds using the near-shore waters of the park. Seabirds are prominent members of the inshore marine ecosystems and are considered to be sentinels of both local and broad environmental change. The demographic stability of seabird populations may serve as an integrated measure of health of the shoreline ecosystem.

Calibration of the molecular rate is one of the major challenges in marine population genetics. Although the use of an appropriate evolutionary rate is crucial in exploring population histories, calibration of the rate is always difficult because fossil records and geological events are rarely applicable for rate calibration. The acceleration of the evolutionary rate for recent coalescent events (or more simply, the time dependency of the molecular clock) is also a problem that can lead to overestimation of population parameters. Calibration of demographic transition (CDT) is a rate calibration technique that assumes a post-glacial demographic expansion, representing one of the most promising approaches for dealing with these potential problems in the rate calibration. Here, we demonstrate the importance of using an appropriate evolutionary rate, and the power of CDT, by using populations of the sandy beach amphipod Haustorioides japonicus along the Japanese coast of the northwestern Pacific Ocean. Analysis of mitochondrial sequences found that the most peripheral population in the Pacific coast of northeastern Honshu Island (Tohoku region) is genetically distinct from the other northwestern Pacific populations. By using the two-epoch demographic model and rate of temperature change, the evolutionary rate was modeled as a log-normal distribution with a median rate of 2.2%/My. The split-time of the Tohoku population was subsequently estimated to be during the previous interglacial period by using the rate distribution, which enables us to infer potential causes of the divergence between local populations along the continuous Pacific coast of Japan.

Colonial seabirds (murres, cormorants, gulls, puffins, and kittiwakes) were monitored along the Pacific Coast of the Becharof National Wildlife Refuge (NWR) to estimate population size, breeding chronology, and/or reproductive success during the 2001 breeding season. The target species monitored were common (Uria aalge) and thickbilled (U lomvia) murres; red-faced (Phalacrocorax urile) and double-crested (P. aurtitis) cormorants were also observed. These data were compared to wildlife damage assessment data collected in 1989-1992 as a result of the 1989 T/V Exxon Valdez oil spill. The primary colony surveyed was Puale Bay Colony. Both land-based and sea-based census data were collected for the Puale Bay colony. The mean population count was 2,197 murres for the sea-based count and 1,265 murres for the land-based counts. We found significant differences in the murre population for both sea-based and land-based surveys over the years (1989-92, 1999, 2001). Sea-based surveys of plots were also performed at Oil Creek and Cape Unalishagvak. Murre population counts for these two colonies declined from 35% to 54% from the period 1989 to 1992 to 2001. Similarly, the black-legged kittiwakes (Rissa tridactyla) count of 721 at Cape Unalishagvak was lower than counts from 1989 to 1992 by 35%. A small doublecrested cormorant colony was located at Portage Creek. At Puale Bay we monitored 701 common murre sites on 17 plots and 26 thick-billed murre sites on five plots for productivity measures. The mean hatch date for common murre was 8 August 2001 compared to a mean hatch date in 1992 of 17 August. Hatch date in 2001 was significantly earlier than the mean hatch date in 1992 (p < 0.001). We documented a fledging success of 0.92 (±0.04) and productivity ratio of 0.76 (±0.06) for common murres in 2001 that were significantly higher than the values documented in 1992. Similar improvements in reproductive parameters were noted for the 26 thickbilled murre sites monitored. We monitored 109 red-faced cormorant nests and seven double-crested cormorants nests. Mean hatch date for red-faced cormorants was 18 July 2001 and 1 August 2001 for double-crested cormorants. Red-faced cormorants productivity in 2001 was 1.7 (±0.2) chicks fledged / nest attempts.

This project aims to capture population trends by estimating absolute abundance of American Black Bears (Ursus americanus) every 2-3 years and relative abundance of three forest mammals (American Black Bear, Grey Wolf (Canis lupus) and Black-tailed Deer (Odocoileus hemionus ssp.)) annually. Forty two 6.8 km2 grid cell units on the landscape are surveyed for animal presence three times per season between May and September using remote wildlife cameras. Cameras are cycled through the 42 sites over the course of the sampling season with each survey lasting ca. 2 weeks within a 6 week period. At present 2 methods of abundance estimation are being considered and compared: (1) A DNA-based spatially explicit capture-recapture method that will allow for unbiased estimation of absolute abundance and (2) A wildlife camera trapping method that allows to estimate site occupancy on the landscape as a measure of relative abundance. Forest carnivores provide an excellent resource for long term ecological integrity monitoring and the analysis of population changes over time. Ecosystems with top carnivores are thought to have high biodiversity and be functioning well in terms of nutrient and energy cycling.