13 datasets found
  1. Data from: Genomic insights into the critically endangered King Island...

    • data.niaid.nih.gov
    • search.dataone.org
    • +1more
    zip
    Updated Jun 3, 2024
    + more versions
    Share
    FacebookFacebook
    TwitterTwitter
    Email
    Click to copy link
    Link copied
    Close
    Cite
    Genomic insights into the critically endangered King Island scrubtit [Dataset]. https://data.niaid.nih.gov/resources?id=dryad_12jm63z66
    Explore at:
    zipAvailable download formats
    Dataset updated
    Jun 3, 2024
    Dataset provided by
    Australian National University
    Authors
    Ross Crates
    License

    https://spdx.org/licenses/CC0-1.0.htmlhttps://spdx.org/licenses/CC0-1.0.html

    Area covered
    King Island
    Description

    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.

  2. Data from: King penguin census data, Gadget Gully, Macquarie Island...

    • gbif.org
    • researchdata.edu.au
    • +1more
    Updated Jul 14, 2023
    Share
    FacebookFacebook
    TwitterTwitter
    Email
    Click to copy link
    Link copied
    Close
    Cite
    GBIF (2023). King penguin census data, Gadget Gully, Macquarie Island (1993-2008) [Dataset]. http://doi.org/10.15468/zj50ll
    Explore at:
    Dataset updated
    Jul 14, 2023
    Dataset provided by
    Global Biodiversity Information Facilityhttps://www.gbif.org/
    Australian Antarctic Data Centre
    License

    Attribution 4.0 (CC BY 4.0)https://creativecommons.org/licenses/by/4.0/
    License information was derived automatically

    Time period covered
    Sep 28, 1993 - Aug 1, 2008
    Area covered
    Description

    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.

  3. F

    Population Estimate, Total, Not Hispanic or Latino, Native Hawaiian and...

    • fred.stlouisfed.org
    json
    Updated Dec 12, 2024
    + more versions
    Share
    FacebookFacebook
    TwitterTwitter
    Email
    Click to copy link
    Link copied
    Close
    Cite
    (2024). Population Estimate, Total, Not Hispanic or Latino, Native Hawaiian and Other Pacific Islander Alone (5-year estimate) in Kings County, NY [Dataset]. https://fred.stlouisfed.org/series/B03002007E036047
    Explore at:
    jsonAvailable download formats
    Dataset updated
    Dec 12, 2024
    License

    https://fred.stlouisfed.org/legal/#copyright-public-domainhttps://fred.stlouisfed.org/legal/#copyright-public-domain

    Area covered
    Kings County, Brooklyn, New York, New York
    Description

    Graph and download economic data for Population Estimate, Total, Not Hispanic or Latino, Native Hawaiian and Other Pacific Islander Alone (5-year estimate) in Kings County, NY (B03002007E036047) from 2009 to 2023 about Kings County, NY; New York; Pacific Islands; NY; non-hispanic; estimate; persons; 5-year; population; and USA.

  4. The current trajectory of king penguin (Aptenodytes patagonicus) chick...

    • catalogue-temperatereefbase.imas.utas.edu.au
    • researchdata.edu.au
    • +1more
    Updated Jul 13, 2022
    Share
    FacebookFacebook
    TwitterTwitter
    Email
    Click to copy link
    Link copied
    Close
    Cite
    AU/AADC > Australian Antarctic Data Centre, Australia (2022). The current trajectory of king penguin (Aptenodytes patagonicus) chick numbers on Macquarie Island in relation to environmental conditions, 2007-2020 [Dataset]. https://catalogue-temperatereefbase.imas.utas.edu.au/geonetwork/srv/api/records/King_Penguin_census_Macquarie_Island
    Explore at:
    www:link-1.0-http--linkAvailable download formats
    Dataset updated
    Jul 13, 2022
    Dataset provided by
    Australian Antarctic Divisionhttps://www.antarctica.gov.au/
    Australian Antarctic Data Centre
    Time period covered
    Aug 1, 2007 - Aug 31, 2020
    Area covered
    Description

    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).

  5. n

    King Penguin breeding population at Heard Island.

    • cmr.earthdata.nasa.gov
    • catalogue-temperatereefbase.imas.utas.edu.au
    • +1more
    Updated Apr 10, 2019
    Share
    FacebookFacebook
    TwitterTwitter
    Email
    Click to copy link
    Link copied
    Close
    Cite
    (2019). King Penguin breeding population at Heard Island. [Dataset]. https://cmr.earthdata.nasa.gov/search/concepts/C1214311342-AU_AADC
    Explore at:
    Dataset updated
    Apr 10, 2019
    Time period covered
    Jan 1, 1948 - Dec 31, 2004
    Area covered
    Description

    This indicator is no longer maintained, and is considered OBSOLETE.

    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

  6. F

    Population Estimate, Total, Hispanic or Latino, Native Hawaiian and Other...

    • fred.stlouisfed.org
    json
    Updated Dec 12, 2024
    + more versions
    Share
    FacebookFacebook
    TwitterTwitter
    Email
    Click to copy link
    Link copied
    Close
    Cite
    (2024). Population Estimate, Total, Hispanic or Latino, Native Hawaiian and Other Pacific Islander Alone (5-year estimate) in King William County, VA [Dataset]. https://fred.stlouisfed.org/series/B03002017E051101
    Explore at:
    jsonAvailable download formats
    Dataset updated
    Dec 12, 2024
    License

    https://fred.stlouisfed.org/legal/#copyright-public-domainhttps://fred.stlouisfed.org/legal/#copyright-public-domain

    Area covered
    King William County, Virginia
    Description

    Graph and download economic data for Population Estimate, Total, Hispanic or Latino, Native Hawaiian and Other Pacific Islander Alone (5-year estimate) in King William County, VA (B03002017E051101) from 2009 to 2023 about King William County, VA; Richmond; Pacific Islands; VA; latino; hispanic; estimate; persons; 5-year; population; and USA.

  7. F

    Population Estimate, Total, Hispanic or Latino, Native Hawaiian and Other...

    • fred.stlouisfed.org
    json
    Updated Dec 12, 2024
    + more versions
    Share
    FacebookFacebook
    TwitterTwitter
    Email
    Click to copy link
    Link copied
    Close
    Cite
    (2024). Population Estimate, Total, Hispanic or Latino, Native Hawaiian and Other Pacific Islander Alone (5-year estimate) in King George County, VA [Dataset]. https://fred.stlouisfed.org/series/B03002017E051099
    Explore at:
    jsonAvailable download formats
    Dataset updated
    Dec 12, 2024
    License

    https://fred.stlouisfed.org/legal/#copyright-public-domainhttps://fred.stlouisfed.org/legal/#copyright-public-domain

    Area covered
    King George County, Virginia
    Description

    Graph and download economic data for Population Estimate, Total, Hispanic or Latino, Native Hawaiian and Other Pacific Islander Alone (5-year estimate) in King George County, VA (B03002017E051099) from 2009 to 2023 about King George County, VA; Pacific Islands; VA; latino; hispanic; estimate; persons; 5-year; population; and USA.

  8. Effects of human activity on King penguins on Macquarie Island

    • data.aad.gov.au
    • researchdata.edu.au
    • +1more
    Updated May 22, 2003
    + more versions
    Share
    FacebookFacebook
    TwitterTwitter
    Email
    Click to copy link
    Link copied
    Close
    Cite
    GIESE, MELISSA (2003). Effects of human activity on King penguins on Macquarie Island [Dataset]. http://doi.org/10.26179/5c9b0945b3957
    Explore at:
    Dataset updated
    May 22, 2003
    Dataset provided by
    Australian Antarctic Divisionhttps://www.antarctica.gov.au/
    Australian Antarctic Data Centre
    Authors
    GIESE, MELISSA
    License

    Attribution 4.0 (CC BY 4.0)https://creativecommons.org/licenses/by/4.0/
    License information was derived automatically

    Time period covered
    Oct 20, 2002 - Mar 20, 2003
    Area covered
    Description

    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

  9. n

    Animal Tracking at Heard Island 2003/2004 - ARGOS data

    • cmr.earthdata.nasa.gov
    • data.aad.gov.au
    • +2more
    cfm
    Updated Apr 26, 2017
    Share
    FacebookFacebook
    TwitterTwitter
    Email
    Click to copy link
    Link copied
    Close
    Cite
    (2017). Animal Tracking at Heard Island 2003/2004 - ARGOS data [Dataset]. http://doi.org/10.4225/15/55C9581205236
    Explore at:
    cfmAvailable download formats
    Dataset updated
    Apr 26, 2017
    Time period covered
    Dec 15, 2003 - Feb 13, 2004
    Area covered
    Description

    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

  10. d

    Annual Penguin Census 1977-2015 v1.0

    • catalog.data.gov
    • datasets.ai
    Updated Oct 19, 2024
    + more versions
    Share
    FacebookFacebook
    TwitterTwitter
    Email
    Click to copy link
    Link copied
    Close
    Cite
    (Point of Contact, Custodian) (2024). Annual Penguin Census 1977-2015 v1.0 [Dataset]. https://catalog.data.gov/dataset/annual-penguin-census-1977-2015-v1-02
    Explore at:
    Dataset updated
    Oct 19, 2024
    Dataset provided by
    (Point of Contact, Custodian)
    Description

    Data 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).

  11. n

    The 1987/1988 Field Season at Heard Island

    • cmr.earthdata.nasa.gov
    • researchdata.edu.au
    • +2more
    Updated Feb 13, 2018
    Share
    FacebookFacebook
    TwitterTwitter
    Email
    Click to copy link
    Link copied
    Close
    Cite
    (2018). The 1987/1988 Field Season at Heard Island [Dataset]. http://doi.org/10.4225/15/5a82602ff3e92
    Explore at:
    Dataset updated
    Feb 13, 2018
    Time period covered
    Sep 18, 1987 - Mar 2, 1988
    Area covered
    Description

    1987/88 Field Season at Heard Island.

    Harry R. Burton. Field Leader, Antarctic Division. The 1987/88 ANARE to Heard Island was the last of a series of three summer programs there (1985 and 1986/87); and with five and a half months on the Island. It was also the longest. Earth science had been the primary focus of the 1986/87 program. In 1987/88 the focus of the work was again biology, as it had been in 1985; and island transport (other than pedestrian) was by LARC.

    Nella Dan delivered the party of 17 from September 18 to 20 1987, with four at Spit Bay and the remainder at Atlas Cove. About a month later, on October 18 and 19 she returned: four of the party left and there were two new arrivals, so that 15 people were on the Island until Lady Franklin picked up the party and left on March 2 1988.

    A major task of the Expedition was to carry out a complete census of Heard Island's breeding population of Southern Elephant Seals. This task was done in the middle of October, when the numbers of cows hauled out to pup on the beaches were at a maximum and counts made at that time were sensibly referable to other years and other islands. It was the first total census ever completed on Heard Island although one made in 1985 was nearly so. The party was able to walk to Long Beach and census that area. and the availab1l1ty of a helicopter for two days allowed the total photographic coverage of Spit Island, a sedimentary island little more than a metre above sea level and about a kilometre to the east. This island is home to several thousand seals. The one photographic run over this island on October 18 produced a 70mm film record. and thus the whole Island census was completed. Although strong winds during the photography prevented complete overlap of all the aerial photographs. allowance for the small proportion of missed ground was made in censusing. The final total for Spit Island was 3,200 plus or minus 150 cows.

    A number of other whole Island Southern Elephant Seal counts (excluding Spit Island) were made at intervals of approximately a month so that seal numbers at particular sites and dates could be compared to historical records for these same places at equivalent seasonal times. These counts also gave quantitative measures of 'seal abuse' to coastal vegetation.

    A daily count of all Southern Elephant Seals in the Four Bays area was maintained for two months. This work enabled the day of maximum numbers to be calculated with precision, as well as providing a detailed record of the haul-out pattern for comparison with other years and islands.

    The day of maximum numbers, 17 October, was two days later in 1987 than in 1985. The results also indicated a further small reduction in the pup production of the Four Bays area, compared to 1985. However a complete enumeration of the seals on all island beaches still waits on a careful checking of all data.

    Another Southern Elephant Seal study was the weighing of weaned pups. About 400 pups were weighed at each end of the Island. The total (821) is a considerable data set and it demonstrated the variation in sex ratio and weight through the weaning period. Male pups had a mean weight of 116.5kg (408 animals), and female pups had a mean weight of 111.6kg (413 animals). These data allow real comparison with weaned weights from other islands and thus may provide insights into the reasons for the decline of seal numbers on some islands (the Indian Ocean Sector) and not others (South Georgia). Sixty Southern Elephant Seals. newly arrived at the beach to moult, were anaesthetised, measured and weighed before having their stomach contents flushed out by water through a soft rubber hose. These collections contained obvious examples of squid beaks and stomach worms but await analysis. This will provide the first detailed information on the diet of these seals in the Heard Island area.

    Leopard Seals were counted whenever they were seen, and at times (late February) they out numbered Southern Elephant Seals on some beaches. Thirty five animals were anaesthetised. measured and weighed before being tagged and their blood sampled.

    A surprise was the discovery of two Subantarctic Fur Seals bearing tags from Marion Island. This was the first record of this species on the island. Also surprising was the very large number (in excess of 10,000) of Antarctic Fur Seals hauling out in late February. They are not a rare Sight on the Island any more! A detailed study of the attendance patterns of lactating cows and the corresponding weight gains of their pups was carried out.

    An archaeological survey of the Corinthian Bay sealer's shanty and a botanical study of pool complexes in the north west of the Island were studies undertaken in the first month on the Island.

    A great deal of effort was also put into censusing birds. A thorough survey of the distribution of all burrow nesting seabirds was completed for the Island and the population of Gentoo Penguins was counted (16,500 pairs in 60 colonies) as well as having the breeding success of their chicks recorded.

    The colonies of King Penguins were recorded regularly, and appear to be continuing to increase in numbers. 1987/88 was a good season for the Heard Island Cormorant too, as 94 chicks were fledged, compared to six in 1986/87.

    A large number of banded seabirds were resighted. These Included Subantarctic and Antarctic Skuas, Wandering and Black-browed Albatrosses and a Cape Petrel. Many of these birds had been banded on other islands, away from Heard Island.

    Nearly all colonies of Southern Giant Petrels were visited and the counts of these colonies showed a near 50% decline compared to 1963. However, 19 breeding birds, banded as chicks in 1963, were resighted. These 25 year old birds give evidence of the long life capabilities of this species. The breeding success of a colony of Black-browed Albatrosses was also recorded.

    The vegetation of the Island was mapped in detail, and growth studies carried out at a number of dispersed sites. The recognition of another possible species of grass in some newly exposed morainal areas suggests that the retreat of glaciers on the Island is creating new areas suitable for colonisation. Comparison of the vegetation of Heard Island with that of climatically less rigorous Macquarie Island promises to throw up a number of ecologically interesting insights.

    Many minor projects were also completed (particularly in view of the extra month on the island due to the loss of the Nella Dan) and these included a tethered kelp experiment to discover the plants capabilities as platforms for long distance transport of marine invertebrates.

    A comparison of the Collembollan (insect) populations in different habitats and the collection of funnel extracted invertebrates in some quantity may extend the species list for the Island.

    Five more sealers' shanties were discovered around the Island and the artefacts in their vicinity were recorded. A detailed study of casks remaining from sealing days was undertaken, and showed that most originated from the period (1881) when the shipwrecked sailors of the Trinity were living on the island. A windlass was uncovered at low tide, after a storm on Spit Bay Beach, and was returned to Australia.

    The lengthy period on the Island and enthusiastic assistance from the passengers of relief ships enabled a significant volume of debris from the old station to be picked up for return to Australia for disposal.

    The tide gauge lost in 1985 was washed up on the beach and was recovered still in a watertight condition. Twelve oceanographic drift cards were found on the beaches and a complete collection of all ocean debris (other than wood) was made from the beaches. East European fishing floats were still dominant items, and indicate the fishing effort in the area up-current from Heard Island.

    The 1987/88 ANARE was a long expedition for 'a summer', as nearly six months were spent on the island. But this considerable period allowed a very thorough and unusually comprehensive assessment of the status of vertebrate populations and of the distribution of plants.

  12. n

    Macquarie Island Penguin Colonies, 1911-1980

    • cmr.earthdata.nasa.gov
    • catalogue-temperatereefbase.imas.utas.edu.au
    • +2more
    Updated Jan 25, 2019
    + more versions
    Share
    FacebookFacebook
    TwitterTwitter
    Email
    Click to copy link
    Link copied
    Close
    Cite
    (2019). Macquarie Island Penguin Colonies, 1911-1980 [Dataset]. http://doi.org/10.26179/5c4a470f42e40
    Explore at:
    Dataset updated
    Jan 25, 2019
    Time period covered
    Jan 1, 1911 - Aug 8, 1980
    Area covered
    Description

    This dataset contains information on the distribution of Penguins and their breeding colonies in the Australian Antarctic sector, as of 1983. It forms Australia's contribution to the International Survey of Antarctic Seabirds (ISAS). The results are listed in the documentation. These include counts of chicks, adults and nests, as well as colony distribution maps. The survey includes Emperor Penguins, Adelie Penguins, King Penguins, Gentoo Penguins, Macaroni Penguins, Rockhopper Penguins, Chinstrap Penguins and Royal Penguins.

    Original data were taken from ANARE Research Notes 9.

    Only data from the Australian Antarctic Territory is described in this metadata record.

    Images of rough maps detailing the locations of each of the colonies are available for download from the url given below. Observation and count data have been incorporated into the Australian Antarctic Data Centre's Biodiversity Database.

    The data are presented in the format of Croxall and Kirkwood (1979) as recommended by the Report of the Subcommittee on Bird Biology held in Pretoria. In the tables all counts are estimates of the number of breeding pairs except where otherwise indicated. The numerical estimates and counts are of three kinds, indicated by the coded N, C or A:

    NESTS (N = count of NESTS or breeding/incubating pairs) The most accurate count of breeding pairs is that derived from a count of nests. This is usually carried out during incubation, but may also be made while chicks are still in the nest, before creches are formed. Such counts are only underestimates of breeding pairs by the number of breeding failures sustained between egg laying and the date of the count.

    CHICKS (C = count of CHICKS) Late in the breeding season the only counts possible are those of chicks. In general most pygosceild penguins raise one chick per pair per season, so a count of chicks gives a reasonable approximation of the original number of breeding pairs. However, season to season variation in breeding success can often be considerable. For example Yeates (1968) reports breeding success in Adelie Penguins at Cape Royds of twenty-six per cent, forty-seven per cent and sixty-eight per cent ever three seasons. Also, Macaroni Penguins only raise approximately 0.5 chicks per pair per season, so that chick counts of this species may be a considerable underestimate of the true breeding population.

    ADULTS (A = count of ADULTS) Many colony counts and estimates were expressed as total number of birds or adults. These figures are difficult to interpret as they depend on the time during the breeding season at which they were made. For some days prior to and until laying is finished, both birds of a pair will be present at the nest site while during incubation it is more likely that only one bird will be present. A further problem with counts of 'birds' is that they may include individuals who are not breeding and this gives an overestimate of the true breeding population. The counts of 'birds' or 'adults' which appear unqualified in log books have been divided by two to give an estimate of the number of breeding pairs. It must be stressed therefore that these counts are the least accurate.

    The degree of accuracy of these counts is inevitably highly variable and it is often difficult to ascertain on what basis a figure was arrived at. For the present survey counts have been allocated to one of five degrees of accuracy.

    1. Pairs/nests essentially individually counted. The count is probably accurate to better than + 5 per cent.

    2. Numbers of pairs in a known area counted individually and knowing the total area of the colony, the overall total calculated. This technique is useful for very large colonies.

    3. Accurate estimates; + 10-15 per cent accuracy.

    4. Rough estimate; accurate to 25-50 per cent.

    5. Guesstimate; to nearest order of magnitude.

    Many references are in the form ANARE (Johnstone) or simply ANARE. These refer to unpublished reports extracted from ANARE station biology logs. Those in the form Budd (1961) refer to published records and are listed in the references at the end of this publication.

    The locations of some colonies are indicated on maps. Place names that (as of 1983) have not yet been approved are shown in the tables and on the maps in parentheses, for example: (ROCKERY ISLAND).

  13. n

    An account of the establishment of Macquarie Island Station in 1948-1949 by...

    • cmr.earthdata.nasa.gov
    • data.aad.gov.au
    • +1more
    Updated Jan 25, 2019
    Share
    FacebookFacebook
    TwitterTwitter
    Email
    Click to copy link
    Link copied
    Close
    Cite
    (2019). An account of the establishment of Macquarie Island Station in 1948-1949 by Peter Wylie King [Dataset]. http://doi.org/10.4225/15/5345F40695753
    Explore at:
    Dataset updated
    Jan 25, 2019
    Time period covered
    Feb 28, 1948 - Apr 14, 1949
    Area covered
    Description

    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.

  14. Not seeing a result you expected?
    Learn how you can add new datasets to our index.

Share
FacebookFacebook
TwitterTwitter
Email
Click to copy link
Link copied
Close
Cite
Genomic insights into the critically endangered King Island scrubtit [Dataset]. https://data.niaid.nih.gov/resources?id=dryad_12jm63z66
Organization logo

Data from: Genomic insights into the critically endangered King Island scrubtit

Related Article
Explore at:
zipAvailable download formats
Dataset updated
Jun 3, 2024
Dataset provided by
Australian National University
Authors
Ross Crates
License

https://spdx.org/licenses/CC0-1.0.htmlhttps://spdx.org/licenses/CC0-1.0.html

Area covered
King Island
Description

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.

Search
Clear search
Close search
Google apps
Main menu