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Small, fragmented or isolated populations are at risk of population decline due to fitness costs associated with inbreeding and genetic drift. The King Island scrubtit Acanthornis magna greeniana is a critically endangered subspecies of the nominate Tasmanian scrubtit A. m. magna, with an estimated population of < 100 individuals persisting in three patches of swamp forest. The Tasmanian scrubtit is widespread in wet forests on mainland Tasmania. We sequenced the scrubtit genome using PacBio HiFi and undertook a population genomic study of the King Island and Tasmanian scrubtits using a double-digest restriction site-associated DNA (ddRAD) dataset of 5,239 SNP loci. The genome was 1.48 Gb long, comprising 1,518 contigs with an N50 of 7.715 Mb. King Island scrubtits formed one of four overall genetic clusters, but separated into three distinct subpopulations when analysed independently of the Tasmanian scrubtit. Pairwise FST values were greater among the King Island scrubtit subpopulations than among most Tasmanian scrubtit subpopulations. Genetic diversity was lower and inbreeding coefficients were higher in the King Island scrubtit than all except one of the Tasmanian scrubtit subpopulations. We observed crown baldness in 8/15 King Island scrubtits, but 0/55 Tasmanian scrubtits. Six loci were significantly associated with baldness, including one within the DOCK11 gene which is linked to early feather development. Contemporary gene flow between King Island scrubtit subpopulations is unlikely, with further field monitoring required to quantify the fitness consequences of its small population size, low genetic diversity and high inbreeding. Evidence-based conservation actions can then be implemented before the taxon goes extinct. Methods 2.1 Sample collection To obtain indicative genetic diversity metrics across mainland Tasmania, we sampled between five and eleven scrubtits from seven a-priori subpopulations on mainland Tasmania (including Bruny Island) during the non-breeding season (January – March 2021). Due to small population sizes and licensing restrictions on King Island, we sampled five individuals from each of the three locations during the same non-breeding season (Table 1, Figure 1). We trapped scrubtits using a single 6m mist net and one minute of scrubtit song broadcast using portable speakers (ANU animal ethics permit # A2021/33). We sampled blood (< 20 μl per individual) using the standard brachial venepuncture technique with a 0.7mm needle into 70% ethanol. For two individuals from whom we were unable to safely obtain blood, we collected feathers shed during handling. One male Tasmanian scrubtit was collected under licence (see acknowledgements) for genome sequencing, from which organ tissue samples (heart, spleen, kidney, gonads, brain, liver) were taken (Table S1). For each individual we took standard morphometric measurements and scanned for any unusual physical features such as feather abnormalities or skin lesions that may be indicators of poor health. A single observer (CY) sampled and measured all birds, and the maximum capture time was 35 minutes. No birds showed adverse reactions to sampling and all flew off strongly upon release. The fifteen individuals sampled on King Island was the maximum permissible sample size under licence conditions. 2.2 DNA extraction, sexing and sequencing High molecular weight DNA was extracted from flash frozen heart and kidney using the Nanobind Tissue Big DNA Kit v1.0 11/19 (Circulomics). A Qubit fluorometer (Thermo Fisher Scientific) was used to quantify DNA concentrations with the Qubit dsDNA BR assay kit (Thermo Fisher Scientific). RNA was extracted from heart, spleen, kidney, gonads, brain, and liver stored in RNA later using the RNeasy Plus mini Kit (Qiagen) with RNAse-free DNAse (Qiagen) digestion. RNA quality was assessed via Nanodrop (Thermo Fisher Scientific). We extracted DNA for population genomics from blood and feather samples using the Monarch® Genomic DNA Purification Kit (New England BioLabs, Victoria, Australia). We quantified DNA concentrations using a Qubit 3.0 fluorometer (yield range 10.3 – 209 ng μl-1, Table S1) and standardised the concentration of each sample to 10-30 ng µl-1 DNA for 20 – 25 μl and determined the sex of individuals using a polymerase chain reaction (PCR) protocol adapted from Fridolfsson and Ellegren (1999, Supplementary file S1). We arranged the samples on a single 96 well plate, containing five technical replicates of the samples with the highest DNA concentrations, an additional 21 non-technical replicates including all of the King Island samples, five extra samples from mainland Tasmania and one negative control. Double-digest restriction associated DNA (ddRAD) sequencing following Peterson et al. (2012) was undertaken at the Australian Genome Research Facility, Melbourne on an Illumina NovaSeq 6000 platform using 150bp paired-end reads. Samples were first quantified using Quantifluor and visualised on 1 % agarose e-gel to ensure all samples exceeded the minimum input DNA quantity of 50 ng. Three establishment samples with at least 250 ng DNA that were representative of the distribution of the samples (2 Tasmanian scrubtits, 1 King Island scrubtit) were used to determine the optimal combination of restriction enzymes, which were EcoRI and HpyCH4IV. Further details on the library preparation protocol are provided in Supplementary file S1. 2.3 Genome sequencing and assembly Full methodological details of the genome and transcriptome sequencing and assembly are provided in Supplementary file S2. In summary, high molecular weight DNA was sent for PacBio HiFi library preparation with Pippin Prep and sequencing on one single molecule real-time (SMRT) cell of the PacBio Sequel II (Australian Genome Research Facility, Brisbane, Australia). Total RNA was sequenced as 100 bp paired-end reads using Illumina NovaSeq 6000 with Illumina Stranded mRNA library preparation at the Ramaciotti Centre for Genomics (University of New South Wales, Sydney, Australia). Genome assembly was conducted on Galaxy Australia (The Galaxy Community, 2022) following the genome assembly guide (Price & Farquharson, 2022) using HiFiasm v0.16.1 with default parameters (Cheng et al., 2021; Cheng et al., 2022). Transcriptome assembly was conducted on the University of Sydney High Performance Computer, Artemis. Genome annotation was performed using FGENESH++ v7.2.2 (Softberry; (Solovyev et al., 2006)) on a Pawsey Supercomputing Centre Nimbus cloud machine (256 GB RAM, 64 vCPU, 3 TB storage) using the longest open reading frame predicted from the global transcriptome, non-mammalian settings, and optimised parameters supplied with the Corvus brachyrhynchos (American crow) gene-finding matrix. The mitochondrial genome was assembled using MitoHifi v3 (Uliano-Silva et al., 2023). Benchmarking universal single copy orthologs (BUSCO) was used to assess genome, transcriptome and annotation completeness (Manni et al., 2021). 2.4 Bioinformatics pipeline and SNP filtering Raw sequence data were processed using Stacks v2.62 (Catchen et al., 2013) and aligned to the genome with BWA v0.7.17-r1188 (Li & Durbin, 2009). Full details of the bioinformatics pipeline, which produced a variant call format (VCF) file containing 45,488 variants for SNP filtering in R v4.0.3 (R Core team 2020) are provided in Supplementary file S1. We filtered genotyped variants using the “SNPfiltR” v1.0.0 package (DeRaad, 2022) based on (i) minimum read depth (≥ 5), (ii) genotype quality (≥ 20), (iii) maximum read depth (≤ 137), and (iv) allele balance ratio (0.2 – 0.8). Then, using a custom R script, we filtered SNPs based on (i) the level of missing data (< 5%); (ii) minor allele count (MAC ≥ 3), (iii) observed heterozygosity (< 0.6), and (iv) linkage disequilibrium (correlation < 0.5 among loci within 500,000 bp). To ensure that relationships between individuals could be accurately inferred from the data, we used these SNPs and samples to construct a hierarchical clustering dendrogram based on genetic distance, with visual examination of the dendrogram confirming that all 24 replicates paired closely together on long branches (Figure S1). The percentage difference between called genotypes of technical replicates was also used to confirm that genotyping error rates were low after filtering (mean 99.91% ± 0.005% SE similarity between replicates). We therefore removed one of each replicate pair from all further analyses. We also made a higher-level bootstrapped dendrogram by using genetic distances among sampling localities instead of individuals (Figure S2). We used “tess3r” (Caye et al. 2016, 2018) to perform a genome scan for loci under selection, using the Bejamini-Hochberg algorithm (Benjamini & Hochberg, 1995), with a false discovery rate of 1 in 10,000 to correct for multiple testing. Because this method identified zero candidate loci under selection, we also used the gl.outflank function in “dartR” v2.0.4 to implement the OutFLANK method (Whitlock & Letterhos 2015) to infer the distribution of FST for loci unlikely to be strongly affected by spatially diversifying selection. This method also identified zero putatively adaptive loci, leaving a final dataset for formal population genetic analysis containing all 70 originally sampled individuals, 5,239 biallelic SNPs, and an overall missing data level of 0.98 %. The number of SNPs and samples removed from the dataset at each filtering step is provided in Table S2. See accompanying Supplementary File for further information on library preparation, molecular sexing, library preparation, bioinformatics, genome sequencing, assembly and annotation. References cited above are provided in the main document.
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Tarakihi (Nemadactylus macropterus) is a demersal fish that supports valuable commercial, recreational, and customary fisheries in New Zealand. However, little is known about its stock structure. The population genetic structure, genetic diversity, and demographic history of N. macropterus were investigated using the hypervariable region one of the mitochondrial control region. 370 samples from 14 locations around New Zealand were collected. While weak genetic breaks were detected between Hawke’s Bay and East Northland and between the west and east coasts of South Island, no clear genetic structure was detected for the overall New Zealand area (ФST = 0.002, P = 0.18), indicative of a panmictic genetic structure. N. macropterus display a high level of genetic diversity and appear to have a historically large and stable population with a long evolutionary history. Bayesian skyline analysis indicates that the historic population has gone through two expansions, likely caused by repeated glacial cycles during the second half of the Pleistocene. The addition of 15 king tarakihi samples (Nemadactylus n.sp.) collected from the Three Kings Islands showed a clear genetic differentiation between the two morphotypes. These findings can inform the future management of N. macropterus and N. n.sp. to ensure a sustainable harvest.
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Ground counts of King Penguin eggs, chicks, fledglings and adults at Gadget Gully on Macquarie Island (1993-2008 incomplete).
Counts were obtained in the field by observers at Gadget gully.
The data were also used in an online publication - the abstract is copied below:
During the late 19th and early 20th centuries, when blubber oil fuelled house lamps, the king penguin population at Macquarie Island was reduced from two very large (perhaps hundreds of thousands of birds) colonies to about 3000 birds. One colony, located on the isthmus when the island was discovered in 1810, was extinct by 1894 and it took about 100 years for king penguins to re-establish a viable breeding population there. Here we document this recovery. The first eggs laid at Gadget Gully on the isthmus were recorded in late February 1995 but in subsequent years egg laying took place earlier between November and February (this temporal discontinuity is a consequence of king penguin breeding behaviour). The first chick was hatched in April 1995 but the first fledgling was not raised until the following breeding season in October 1996. The colony increased on average 66% per annum in the five years between 1995 and 2000. King penguins appear resilient to catastrophic population reductions, and as the island's population increases, it is likely that other previously abandoned breeding sites will be reoccupied.
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Ground counts of King Penguin Aptenodytes patagonicuseggs, chicks, fledglings and adults at Gadget Gully on Macquarie Island (1993-2008 incomplete). Counts were obtained in the field by observers at Gadget gully. During the late 19th and early 20th centuries, when blubber oil fuelled house lamps, the king penguin population at Macquarie Island was reduced from two very large (perhaps hundreds of thousands of birds) colonies to about 3000 birds. One colony, located on the isthmus when the island was discovered in 1810, was extinct by 1894 and it took about 100 years for king penguins to re-establish a viable breeding population there. Here we document this recovery. The first eggs laid at Gadget Gully on the isthmus were recorded in late February 1995 but in subsequent years egg laying took place earlier between November and February (this temporal discontinuity is a consequence of king penguin breeding behaviour). The first chick was hatched in April 1995 but the first fledging was not raised until the following breeding season in October 1996. The colony increased on average 66% per annum in the five years between 1995 and 2000. King penguins appear resilient to catastrophic population reductions, and as the island’s population increases, it is likely that other previously abandoned breeding sites will be reoccupied.
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INDICATOR DEFINITION The size of the breeding population of King Penguins at Heard Island.
TYPE OF INDICATOR There are three types of indicators used in this report: 1. Describes the CONDITION of important elements of a system; 2. Show the extent of the major PRESSURES exerted on a system; 3. Determine RESPONSES to either condition or changes in the condition of a system.
This indicator is one of: CONDITION
RATIONALE FOR INDICATOR SELECTION The breeding population of King Penguins is related to resource availability (nesting space and food), behavioural mechanisms (immigration/emigration and breeding effort/success) in addition to climate change and human impacts such as fisheries. Monitoring breeding population and interpretation of the data provides information on changes in the Subantarctic ecosystem.
DESIGN AND STRATEGY FOR INDICATOR MONITORING PROGRAM Spatial scale: Heard Island (lat 53 deg 06' 00.0" S, long 73 deg 31' 59.9" E).
Frequency: 2-3 years. Access to remote colonies and other logistical constraints do not permit annual visits.
Measurement technique: Each colony is visited and individual birds are counted from the ground by two or three personnel performing replicate counts. Further counts are obtained by oblique ground and aerial photography. All breeding individuals in a colony are counted. Considerations regarding disturbance associated with census visits are also incorporated into monitoring strategies. The lack of annual census data does not reduce the value of these long-term monitoring programmes.
RESEARCH ISSUES The king penguin breeding population at Heard Island has increased at almost 20% per year since the late 1940s; other king penguin populations throughout the Southern Ocean have also increased, but not as rapidly. At present, there is no alternative hypothesis to that previously proposed, that these population increases are sustained by the enhanced availability of myctophids, the principal prey of king penguins (Woehler et al. 2001).
LINKS TO OTHER INDICATORS
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TwitterAustralia’s iconic emu (Dromaius novaehollandiae novaehollandiae) is the only living representative of its genus, but fossil evidence and reports from early European explorers suggest that three island forms (at least two of which were dwarfs) became extinct during the 19th century. While one of these - the King Island emu - has been found to be conspecific with Australian mainland emus, little is known about how the other two forms - Kangaroo Island and Tasmanian emus - relate to the others, or even the size of Tasmanian emus. We present a comprehensive genetic and morphological analysis of Dromaius diversity, including data from one of the few definitively genuine Tasmanian emu specimens known. Our genetic analyses suggest that all the island populations represent sub-populations of mainland D. novaehollandiae. Further, the size of island emus and those on the mainland appears to scale linearly with island size but not time since isolation, suggesting that island size—and presumably c...
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This data set describes the population dynamics of Wilson's Storm Petrels (Oceanites oceanicus) at King George Island (Isla 25 de Mayo, Antarctica) over a forty year period (1978 – 2020). It includes all available data on Wilson's Storm Petrels from two colonies: around the Argentinian Base Carlini (62°14′S, 58°40′W; CA, formerly called Base Jubany) and the Henryk Arctowski Polish Antarctic Station (62°09′S, 58°27′W; HA). Data on population productivity (number of nests, eggs, chicks and fledglings) was collected by regular visits to the colonies and searching for nest burrows, or monitoring of the egg or chick if found. Data on adult abundance and estimated age categories (i.e., presence of foot spots; Quillfeldt et al. (2000, doi:10.1007/s003000000167) were collected at CA by using the same size mistnet every study year in the same location within the breeding colony. Chicks were measured regularly (varying intervals depending on the study) at both CA and HA. Chick tarsus was measured using callipers (vernier or digital depending on the study year) to the nearest 0.1 mm, chick wing length was measured using wing rulers to the nearest 1 mm, and chick body mass was measured using mechanical or digital scales depending on the study year to the nearest 0.1 g. Chick growth rates were calculated based on the linear growth period following Ausems et al. (2020, doi:10.1016/j.scitotenv.2020.138768). Chick food loads (g) were recorded at CA and determined based on changes in chick body mass on consecutive days (Gladbach et al. (2009, doi:10.1007/s00300-009-0628-z); Kuepper et al. (2018, doi:10.1016/j.cbpa.2018.06.018).
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From 2007 to 2020, annual island-wide censuses of king penguin chicks were undertaken in the second week of August each year. This data was compared to environmental variables to understand what variables can be further explored to understand king penguin population changes. This data set contains chick count data, environmental parameters and R scripts used to investigate the current trajectory of the Macquarie Island king penguin population in relation to environmental variables. This data has been published in ICES Journal Of Marine Science (DOI to be provided).
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Graph and download economic data for Population Estimate, Total, Not Hispanic or Latino, Native Hawaiian and Other Pacific Islander Alone (5-year estimate) in King and Queen County, VA (B03002007E051097) from 2009 to 2023 about King and Queen County, VA; Pacific Islands; Richmond; non-hispanic; VA; estimate; 5-year; persons; population; and USA.
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This data set describes the population dynamics of Wilson's Storm Petrels (Oceanites oceanicus) at King George Island (Islas 25 de Mayo, Antarctica) over a forty year period (1978 - 2020). It includes all available data on Wilson's Storm Petrels from two colonies: around the Argentinian Base Carlini (62°14′S, 58°40′W; CA, formerly called Base Jubany) and the Henryk Arctowski Polish Antarctic Station (62°09′S, 58°27′W; HA). Data on population productivity (number of nests, eggs, chicks and fledglings) was collected by regular visits to the colonies and searching for nest burrows, or monitoring of the egg or chick if found.
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TwitterLions Rump is a headland on the western side of King George Island in the South Shetland Islands (Subarea 48.1). Research is conducted from the Polish Antarctic Station, Henryk Arctowski, to monitor to following parameters for each species:
Adelie penguins and Gentoo penguins:
Breeding population size
Breeding success
Chick weight at fledging
Chinstrap penguins:
Breeding population size
Breeding success
Purpose of CEMP: In order to provide information of the effects of fishing on dependent species, CCAMLR set up the CCAMLR Ecosystem Monitoring Program (CEMP) in 1989. The two aims of CEMP are to:
1) Detect and record significant changes in critical components of the marine ecosystem within the Convention Area, to serve as a basis for the conservation of Antarctic marine living resources.
2) Distinguish between changes due to harvesting of commercial species and changes due to environmental variability, both physical and biological.
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Access to different environments may lead to inter-population behavioural changes within a species that allow populations to exploit their immediate environments. Elephant seals from Marion Island (MI) and King George Island (KGI) (Isla 25 de Mayo) forage in different oceanic environments and evidently employ different foraging strategies. This study elucidates some of the factors influencing the diving behaviour of male southern elephant seals from these populations tracked between 1999 and 2002. Mixed-effects models were used to determine the influence of bathymetry, population of origin, body length (as a proxy for size) and individual variation on the diving behaviour of adult male elephant seals from the two populations. Males from KGI and MI showed differences in all dive parameters. MI males dived deeper and longer (median: 652.0 m and 34.00 min) than KGI males (median: 359.1 m and 25.50 min). KGI males appeared to forage both benthically and pelagically while MI males in this study rarely reached depths close to the seafloor and appeared to forage pelagically. Model outputs indicate that males from the two populations showed substantial differences in their dive depths, even when foraging in areas of similar water depth. Whereas dive depths were not significantly influenced by the size of the animals, size played a significant role in dive durations, though this was also influenced by the population that elephant seals originated from. This study provides some support for inter-population differences in dive behaviour of male southern elephant seals.
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TwitterMetadata record for data from ASAC Project 465 See the link below for public details on this project.
From the abstracts of the referenced papers:
The diet composition of King penguins Aptenodytes patagonicus at Heard Island (53deg 05S; 73 deg 30E) was determined from stomach contents of 98 adults captured as they returned to the island throughout 1992. During the two growth seasons, the diet was dominated by the myctophid fish Krefftichthys anderssoni (94 % by number, 48 % by mass). The paralepidid fish Magnisudis prionosa contributed less than 1 % by numbers but 17 % by mass. Mackerel icefish Champsocephalus gunnari accounted for 17 % by mass of chick diet in late winter, when chicks were malnourished and prone to starvation, although its annual contribution to the penguins diet was only 3 %. Squid was consumed only between April and August; Martialia hyadesi was the commonest squid taken, comprising 40 to 48 % of the winter diet. The remainder of the diet consisted of the squid Moroteuthis ingens and fish other than K. anderssoni. The energy content of the diet mix fed to the chicks varied seasonally being highest during the growth seasons (7.83 plus or minus 0.25 kJ.g-1) and lowest in winter (6.58 plus or minus 0.19 kJ.g-1). From energetic experiments we estimated that an adult penguin consumed 300 kg of food each of which its chick received 55 kg during the 1992 season. The chicks received large meals at the beginning of winter (1.2 plus or minus 0.3 kg) and during the middle of the second growth season (1.2 plus or minus 0.3 kg), and their smallest meals in late winter (0.4 plus or minus 0.1 kg). The gross energy required to rear a King penguin chick was estimated to be 724 MJ. The potential impact of commercial fisheries on the breeding activities of King penguins is discussed.
23 king penguins (Aptenodytes patagonicus) from Macquarie Island were tracked by satellite during the late incubation period in 1998-1999 to determine the overlap in the foraging zone of king penguins with an area to be declared a marine protected area (MPA) near the island. While all penguins left the colony in an easterly direction and travelled clockwise back to the island, three penguins foraged in the northern parts of the general foraging area and stayed north of 56 south. The remaining 20 penguins ventured south and most crossed 59 south before returning to the island. The total foraging area was estimated to be 156,000 square kilometres with 36,500 square kilometres being most important (where penguins spend greater than 150 hours in total). North-foraging penguins reached on average 331 plus or minus 24 kilometres from the colony compared to 530 plus or minus 76 kilometres for the south-foraging penguins. The latter travelled an average total distance of 1313 p lus or minus 176 kilometres, while the northern foragers averaged 963 plus or minus 166 kilometres. Not only did the penguins spend the majority of their foraging time within the boundaries of the proposed MPA, they also foraged chiefly within the boundaries of a highly protected zone. Thus, the MPA is likely to encompass the foraging zone of king penguins, at least during incubation.
The foraging strategies of king penguins from Heard and Macquarie islands were compared using satellite telemetry, time-depth recorders and diet samples. Trip durations were 16.8 plus or minus 3.6 days and 14.8 plus or minus 4.1 days at Macquarie and Heard islands, respectively. At Macquarie Island, total distances travelled were 1281 plus or minus 203 km compared to 1425 plus or minus 516 km at Heard Island. The total time the penguins spent at sea was 393 plus or minus 66 h at Macquarie Island and 369 plus or minus 108 h at Heard Island. The penguins from Macquarie Island performed more deep dives than those from Heard Island. King penguins from Macquarie Island travelled 1.5 plus or minus 0.2 km h-1 day-1 compared to 1.3 plus or minus 0.1 km h-1 day-1. At Macquarie Island, 19% of dives were up to 70-90 m depth compared to 35% at Heard Island. The main dietary prey species were the fish Krefftychthis anderssoni and the squid Moroteuthis ingens in both groups. The differences in the at-sea distribution and the foraging behaviour of the two groups of penguins were possibly related to differences in oceanography and bathymetric conditions around the two islands. Dietary differences may be due to interannual variability in prey availability since the two colonies were studied during incubation but in different years.
Nearly 36,000 vertical temperature profiles collected by 15 king penguins are used to map oceanographic fronts south of New Zealand. There is good correspondence between Antarctic Circumpolar Current (ACC) front locations derived from temperatures sampled in the upper 150m along the penguin tracks and front positions inferred using maps of sea surface height (SSH). Mesoscale features detected in the SSH maps from this eddy-rich region are also reproduced in the individual temperature sections based on dive data. The foraging strategy of Macquarie Island king penguins appears to be influenced strongly by oceanographic structure: almost all the penguin dives are confined to the region close to and between the northern and southern branches of the Polar Front. Surface chlorophyll distributions also reflect the influence of the ACC fronts, with the northern branch of the Polar Front marking a boundary between low surface chlorophyll to the north and elevated values to the south.
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The total population using the colony in a year is estimated by multiplying a count on any of the dates by the given factor. Credible intervals and a longer series of dates are provided the S1 Appendix. ANI = Año Nuevo Island, ANML = Año Nuevo Mainland, PR = Point Reyes, CI = Channel Islands, KR = King Range.
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A major goal of a research expedition by the Australian Antarctic Division over the summer of (2003/04) in the Southern Ocean off Heard Island was to answer some of the questions needed to determine what level of exploitation of Southern Ocean fisheries is sustainable. The use of novel equipment, cutting edge technology and some adept logistical co-ordination allowed the Aurora Australis, on the Southern Ocean, to catch the prey of the predators of Heard Island.
This work was accomplished by placing satellite trackers on animals at Heard Island, and then, using the ARGOS system, monitoring their activities in the Southern Ocean around the island. The Aurora Australis assisted in the monitoring and tracking of the animals by searching the areas the animals were foraging for prey species.
The animals tracked in this experiment were:
Light-mantled sooty albatrosses black-browed albatrosses king penguins macaroni penguins Antarctic fur seals
The columns in this data file are:
individual_id - the identifier of the individual animal species - the species name of that animal pttid - the identifier of the PTT tracker deployed on that animal deployment_longitude - the longitude at which the tracker was deployed deployment_latitude - the latitude at which the tracker was deployed observation_date - the date (ISO8601 format) of the position observation year, month, day, time, time_zone - as per the observation_date, but in separate columns locationclass - the ARGOS location class of the position (see http://www.argos-system.org/manual/3-location/34_location_classes.htm; value -3 corresponds to a "Z" class, value -2 to "B", value -1 to "A") latitude - the latitude of the position observation longitude - the longitude of the position observation
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TwitterData were collected from two penguin monitoring sites in the Antarctic peninsula region between 1977 and 2015 using traditional census methods. Seabirds observed in this study are Adélie (Pygoscelis adeliae), chinstrap (P. antarctica), and gentoo (P. papua) penguins. The two study sites are the US AMLR Program sites at Cape Shirreff (Livingston Island) and Copacabana (King George Island).
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This project empirically measures the effects of human activity on the behaviour of King penguins on Macquarie Island, under ASAC project 1148. This was achieved by collecting behavioural responses of individual penguins exposed to pedestrian approaches across the breeding stages of incubation and guard. Information produced includes minimum approach guidelines.
As of April 2003 all data are stored on Hi-8 digital tape, due to be transformed during 2003 - 2004 into a timecoded tab-delimited text format for analysis using the Observer (Noldus Information Technology 2002).
The fields in this dataset are:
Sample Date Breeding Phase Approach Colony Focal birds tape number Wide angle tape number Weather Time Windspeed Temperature Precipitation Cloud Pre-approach control Post-approach control Maximum approach distance
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This file contains 22 pages of scanned typewritten text, and 1 page of a sketched map. The document describes the establishment of Macquarie Island station in 1948, but the first ANARE (Australian National Antarctic Research Expeditions) party. It was written by Peter Wylie King on October 20, 1951.
The document details activities, living conditions, and other facets of life on Macquarie Island, including the construction of the early station, details about the sheep, goats and dog brought to the island, the rabbits already present on the island, exploration of the island, and the death of engineer Charlie Scoble.
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Small, fragmented or isolated populations are at risk of population decline due to fitness costs associated with inbreeding and genetic drift. The King Island scrubtit Acanthornis magna greeniana is a critically endangered subspecies of the nominate Tasmanian scrubtit A. m. magna, with an estimated population of < 100 individuals persisting in three patches of swamp forest. The Tasmanian scrubtit is widespread in wet forests on mainland Tasmania. We sequenced the scrubtit genome using PacBio HiFi and undertook a population genomic study of the King Island and Tasmanian scrubtits using a double-digest restriction site-associated DNA (ddRAD) dataset of 5,239 SNP loci. The genome was 1.48 Gb long, comprising 1,518 contigs with an N50 of 7.715 Mb. King Island scrubtits formed one of four overall genetic clusters, but separated into three distinct subpopulations when analysed independently of the Tasmanian scrubtit. Pairwise FST values were greater among the King Island scrubtit subpopulations than among most Tasmanian scrubtit subpopulations. Genetic diversity was lower and inbreeding coefficients were higher in the King Island scrubtit than all except one of the Tasmanian scrubtit subpopulations. We observed crown baldness in 8/15 King Island scrubtits, but 0/55 Tasmanian scrubtits. Six loci were significantly associated with baldness, including one within the DOCK11 gene which is linked to early feather development. Contemporary gene flow between King Island scrubtit subpopulations is unlikely, with further field monitoring required to quantify the fitness consequences of its small population size, low genetic diversity and high inbreeding. Evidence-based conservation actions can then be implemented before the taxon goes extinct. Methods 2.1 Sample collection To obtain indicative genetic diversity metrics across mainland Tasmania, we sampled between five and eleven scrubtits from seven a-priori subpopulations on mainland Tasmania (including Bruny Island) during the non-breeding season (January – March 2021). Due to small population sizes and licensing restrictions on King Island, we sampled five individuals from each of the three locations during the same non-breeding season (Table 1, Figure 1). We trapped scrubtits using a single 6m mist net and one minute of scrubtit song broadcast using portable speakers (ANU animal ethics permit # A2021/33). We sampled blood (< 20 μl per individual) using the standard brachial venepuncture technique with a 0.7mm needle into 70% ethanol. For two individuals from whom we were unable to safely obtain blood, we collected feathers shed during handling. One male Tasmanian scrubtit was collected under licence (see acknowledgements) for genome sequencing, from which organ tissue samples (heart, spleen, kidney, gonads, brain, liver) were taken (Table S1). For each individual we took standard morphometric measurements and scanned for any unusual physical features such as feather abnormalities or skin lesions that may be indicators of poor health. A single observer (CY) sampled and measured all birds, and the maximum capture time was 35 minutes. No birds showed adverse reactions to sampling and all flew off strongly upon release. The fifteen individuals sampled on King Island was the maximum permissible sample size under licence conditions. 2.2 DNA extraction, sexing and sequencing High molecular weight DNA was extracted from flash frozen heart and kidney using the Nanobind Tissue Big DNA Kit v1.0 11/19 (Circulomics). A Qubit fluorometer (Thermo Fisher Scientific) was used to quantify DNA concentrations with the Qubit dsDNA BR assay kit (Thermo Fisher Scientific). RNA was extracted from heart, spleen, kidney, gonads, brain, and liver stored in RNA later using the RNeasy Plus mini Kit (Qiagen) with RNAse-free DNAse (Qiagen) digestion. RNA quality was assessed via Nanodrop (Thermo Fisher Scientific). We extracted DNA for population genomics from blood and feather samples using the Monarch® Genomic DNA Purification Kit (New England BioLabs, Victoria, Australia). We quantified DNA concentrations using a Qubit 3.0 fluorometer (yield range 10.3 – 209 ng μl-1, Table S1) and standardised the concentration of each sample to 10-30 ng µl-1 DNA for 20 – 25 μl and determined the sex of individuals using a polymerase chain reaction (PCR) protocol adapted from Fridolfsson and Ellegren (1999, Supplementary file S1). We arranged the samples on a single 96 well plate, containing five technical replicates of the samples with the highest DNA concentrations, an additional 21 non-technical replicates including all of the King Island samples, five extra samples from mainland Tasmania and one negative control. Double-digest restriction associated DNA (ddRAD) sequencing following Peterson et al. (2012) was undertaken at the Australian Genome Research Facility, Melbourne on an Illumina NovaSeq 6000 platform using 150bp paired-end reads. Samples were first quantified using Quantifluor and visualised on 1 % agarose e-gel to ensure all samples exceeded the minimum input DNA quantity of 50 ng. Three establishment samples with at least 250 ng DNA that were representative of the distribution of the samples (2 Tasmanian scrubtits, 1 King Island scrubtit) were used to determine the optimal combination of restriction enzymes, which were EcoRI and HpyCH4IV. Further details on the library preparation protocol are provided in Supplementary file S1. 2.3 Genome sequencing and assembly Full methodological details of the genome and transcriptome sequencing and assembly are provided in Supplementary file S2. In summary, high molecular weight DNA was sent for PacBio HiFi library preparation with Pippin Prep and sequencing on one single molecule real-time (SMRT) cell of the PacBio Sequel II (Australian Genome Research Facility, Brisbane, Australia). Total RNA was sequenced as 100 bp paired-end reads using Illumina NovaSeq 6000 with Illumina Stranded mRNA library preparation at the Ramaciotti Centre for Genomics (University of New South Wales, Sydney, Australia). Genome assembly was conducted on Galaxy Australia (The Galaxy Community, 2022) following the genome assembly guide (Price & Farquharson, 2022) using HiFiasm v0.16.1 with default parameters (Cheng et al., 2021; Cheng et al., 2022). Transcriptome assembly was conducted on the University of Sydney High Performance Computer, Artemis. Genome annotation was performed using FGENESH++ v7.2.2 (Softberry; (Solovyev et al., 2006)) on a Pawsey Supercomputing Centre Nimbus cloud machine (256 GB RAM, 64 vCPU, 3 TB storage) using the longest open reading frame predicted from the global transcriptome, non-mammalian settings, and optimised parameters supplied with the Corvus brachyrhynchos (American crow) gene-finding matrix. The mitochondrial genome was assembled using MitoHifi v3 (Uliano-Silva et al., 2023). Benchmarking universal single copy orthologs (BUSCO) was used to assess genome, transcriptome and annotation completeness (Manni et al., 2021). 2.4 Bioinformatics pipeline and SNP filtering Raw sequence data were processed using Stacks v2.62 (Catchen et al., 2013) and aligned to the genome with BWA v0.7.17-r1188 (Li & Durbin, 2009). Full details of the bioinformatics pipeline, which produced a variant call format (VCF) file containing 45,488 variants for SNP filtering in R v4.0.3 (R Core team 2020) are provided in Supplementary file S1. We filtered genotyped variants using the “SNPfiltR” v1.0.0 package (DeRaad, 2022) based on (i) minimum read depth (≥ 5), (ii) genotype quality (≥ 20), (iii) maximum read depth (≤ 137), and (iv) allele balance ratio (0.2 – 0.8). Then, using a custom R script, we filtered SNPs based on (i) the level of missing data (< 5%); (ii) minor allele count (MAC ≥ 3), (iii) observed heterozygosity (< 0.6), and (iv) linkage disequilibrium (correlation < 0.5 among loci within 500,000 bp). To ensure that relationships between individuals could be accurately inferred from the data, we used these SNPs and samples to construct a hierarchical clustering dendrogram based on genetic distance, with visual examination of the dendrogram confirming that all 24 replicates paired closely together on long branches (Figure S1). The percentage difference between called genotypes of technical replicates was also used to confirm that genotyping error rates were low after filtering (mean 99.91% ± 0.005% SE similarity between replicates). We therefore removed one of each replicate pair from all further analyses. We also made a higher-level bootstrapped dendrogram by using genetic distances among sampling localities instead of individuals (Figure S2). We used “tess3r” (Caye et al. 2016, 2018) to perform a genome scan for loci under selection, using the Bejamini-Hochberg algorithm (Benjamini & Hochberg, 1995), with a false discovery rate of 1 in 10,000 to correct for multiple testing. Because this method identified zero candidate loci under selection, we also used the gl.outflank function in “dartR” v2.0.4 to implement the OutFLANK method (Whitlock & Letterhos 2015) to infer the distribution of FST for loci unlikely to be strongly affected by spatially diversifying selection. This method also identified zero putatively adaptive loci, leaving a final dataset for formal population genetic analysis containing all 70 originally sampled individuals, 5,239 biallelic SNPs, and an overall missing data level of 0.98 %. The number of SNPs and samples removed from the dataset at each filtering step is provided in Table S2. See accompanying Supplementary File for further information on library preparation, molecular sexing, library preparation, bioinformatics, genome sequencing, assembly and annotation. References cited above are provided in the main document.