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).

Like many polar animals, emperor penguin populations are challenging to monitor because of the species’ life history and remoteness. Consequently, it has been difficult to establish its global status, a subject important to resolve as polar environments change. To advance our understanding of emperor penguins, we combined remote sensing, validation surveys, and using Bayesian modeling we estimated a comprehensive population trajectory over a recent 10-year period, encompassing the entirety of the species’ range. Reported as indices of abundance, our study indicates with 81% probability that the global population of adult emperor penguins declined between 2009 and 2018, with a posterior median decrease of 9.6% (95% credible interval (CI) -26.4% to +9.4%). The global population trend was -1.3% per year over this period (95% CI = -3.3% to +1.0%) and declines likely occurred in four of eight fast ice regions, irrespective of habitat conditions. Thus far, explanations have yet to be identifi..., During the 2018 Antarctic field season, under permit #2019-006 granted by the National Science Foundation, our US-based team conducted aerial photography at emperor penguin colonies in the Ross Sea to add to robust validation of imagery. Our efforts included one flight via fixed wing aircraft over colonies distant from McMurdo Station and five flights via helicopter to a single colony (Cape Crozier) near the station. The five flights to Cape Crozier, 24 October to 15 November, were used to better understand population fluctuation through a single season. Our fixed wing survey took place on 31 October 2018, flying in the vicinity of Beaufort Island (ASPA 105), Franklin Island, Cape Washington (ASPA 173), Coulman Island, and Cape Roget. At each location (both by fixed wing and helicopter), we circled the colony 1-4 times, maintaining a minimum of 500 m horizontal distance from the periphery of the colony and a minimum altitude of 500 m. No behavioral disturbance to birds (e.g., rapid move..., , # LaRue et al. (2024): Advances in remote sensing of emperor penguins: first multi-year time series documenting global population change

10.5061/dryad.m63xsj48v

Overview

This repository contains data, code, and model output associated with the global-scale analysis of Emperor penguin population dynamics described in LaRue et al. (2024), based on integrating raw data from aerial surveys with time series of circumpolar satellite surveys of known emperor penguin colonies.

The model is used to estimate an annual index of abundance at every known Emperor penguin colony in Antarctica (as of 2018), for every year between 2008 and 2018. Regional and global population indices are then calculated by summing colony-level estimates, according to regional colony membership.

Simulations are also performed to evaluate the ability of the model to accurately detect population trends, if they exist.

File structure and code description

• analysis/
  • **ou...

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.

The fundamental long-term objective of the seabird component of the Palmer LTER (PAL) has been to identify and understand the mechanistic processes that regulate the mean fitness (population growth rate) of regional penguin populations. Two hypotheses have guided this research, with one suggesting that population mean fitness is best explained by changes in regional krill biomass, and the other proposing that long-term changes in sea ice affects mean fitness by tipping the balance in favor of one species over another in accordance with species-specific evolved life history affinities to sea ice. Although these hypotheses are not mutually exclusive, current evidence in the PAL region tends to favor the latter over the former. Since the inception of PAL, Adélie penguin populations have effectively collapsed, while those of gentoo and chinstrap penguins have increased dramatically, trends that are spatially and temporally coherent with decreasing regional sea ice duration. Adélie penguins are an ice-obligate polar species whose life history is intimately linked to the presence of sea ice, while chinstrap and gentoo penguins are ice-intolerant species whose life histories evolved in the sub-Antarctic, where sea ice is a less permanent feature of the marine ecosystem. In contrast, although krill constitute the most important component of the summer diets by mass of these three penguin species, changes in PAL krill abundances have exhibited no long-term trends, and thus fail to explain the divergent patterns in penguin populations evident in our time series. The arrival chronology of adult Adélie penguins on Humble Island is documented annually through island-wide censuses performed as ice and weather conditions permit. Recorded data (numbers of adults present) provide a measure of the number of adults arriving daily at the breeding colonies, a metric that is sensitive to environmental conditions such as sea ice extent during late winter and early spring. These data are also used in combination with other metrics to determine the optimal window for other, more extensive area-wide breeding population censuses (see CENSUS). Dr. Megan Cimino took over as PI of the LTER seabird project in 2020 from Dr. William Fraser. Field data collection between 2020-2022 has remained consistent with previous years. No data collected during the 2021-2022 season due to the Palmer Station Pier Build.

We hypothesized that regional spatial organization of Antarctic penguin breeding populations was affected by social factors, i.e., proximity and size of adjacent colonies, and by physical factors, i.e., availability of breeding habitat and proximity of polynyas and submarine canyons where prey is abundant. The hypothesis of Furness & Birkhead (1984), that forage competition and density-dependence affect geographic structure of seabird populations, was tested previously for Antarctic penguins when biologging to quantify colony foraging areas was less common and when assessments of colony size reflected a compendium of historical counts. These data on foraging areas and colony size are now available following 20 years of frequent biologging and real-time satellite data on colony locations and sizes. We prepared a literature summary on the basis of biologging studies to improve assessment of foraging ranges. We collated colony sizes from recent sources and integrated them with data on submarine canyon systems and polynyas. We used geospatial models to assess the relations of the latter features to colony size, clustering, and distribution around Antarctica. The equal spacing of emperor penguin colonies was constant, with spacing a function of foraging range. In contrast, colonies of other penguin species were clustered, with small colonies adjacent to one another and within outer edge of the foraging area of large colonies. Colonies and especially clusters occurred near polynyas and canyons around Antarctica. Density-dependent processes and geography explained penguin colony distribution. We conclude that inter- and intraspecific trophic competition affects a geographic structuring of colony distribution and size, although not necessarily in the same way among species. Results are relevant to assessing effects of climate and other factors on penguin population trends at regional scales. We suggest that considering penguin colony distribution and abundance at the regional or cluster level is necessary to understand changes in these attributes Methods See Methods and Supplemental Materials for description of data summary and processing.

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

INDICATOR DEFINITION
Demographic parameters for the Adelie penguin at Bechervaise Island near Mawson.

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 Adelie penguin is a relatively long lived sea bird dependent on krill. It is expected that major changes in the availability of food (krill) to sea birds will be reflected ultimately in recruitment into the breeding population. Causes of changes in the availability of krill relate directly to changes in both the biological and physical environment brought about by man made or natural means. Ageing populations may give an outward appearance of stability in terms of numbers at a breeding colony but such a condition may mask a decline in recruitment. To determine whether there are environmental influences on the population it is necessary to undertake detailed demographic studies.

Demographic studies carried out over many years on animal populations comprising known age cohorts are required to determine those factors responsible for any observed changes in recruitment and/or mortality. Population reconstruction techniques provide estimates of recruitment and mortality and relate these functions to population size and/or population trends. These studies may alert us to possible changes in the ecosystem particularly related to the availability of food to the penguins or changes to the physical environment. The identification of the cause of changes must come from detailed investigations of food availability and the environment carried out at the same time.

Annual breeding success at Bechervaise Island (eggs laid to chicks fledged) varies enormously from 0 in catastrophic years to above 1 for good seasons. The population at Bechervaise Island near Mawson has been monitored since 1990 as part of the CCAMLR Ecosystem Monitoring Program. Chicks and adults have been tagged annually. The number of breeding pairs has increased slightly between 1990-2001, but changes in the non -breeding population are unknown. Demographic studies based on the return rate of birds tagged as chicks provide information on trends in the overall population and the net rate of recruitment. Since it is intended that this program be undertaken indefinitely it makes this population an excellent subject for monitoring in the context of the SOE.

DESIGN AND STRATEGY FOR INDICATOR MONITORING PROGRAM
Spatial Scale: Restricted to the Mawson region. Similar studies are carried out by other national research programs at Terra Nova Bay (Italy) and on the Antarctic Peninsula (USA).

Frequency: Annual

Measurement Technique: The Adelie penguin population at Bechervaise Island consists of approximately 1800 breeding pairs. Each breeding season since 1990/91 in excess of 250 chicks have been given implanted electronic identification tags. The return of birds to their natal colony has been detected automatically by the Automated Penguin Monitoring System (APMS)or by checking all birds with a hand held tag reader. Additional and associated biological data as prescribed by CCAMLR (1997 are collected to aid interpretation of demographic and other trends. To detect trends in the population size and in demographic parameters, particularly of recruitment, it will be necessary to maintain an annual tagging program of chicks and recording of all tagged birds.

RESEARCH ISSUES
comprehensive analysis of the data collected over the duration of this study is required to determine natural variation and potential anthropogenic influences affecting Adelie penguin population dynamics.

LINKS TO OTHER INDICATORS
Sea-ice extent and concentration.

Understanding the boundaries of breeding populations is of great importance for conservation efforts and estimates of extinction risk for threatened species. However, determining these boundaries can be difficult when population structure is subtle. Emperor penguins are highly reliant on sea ice, and some populations may be in jeopardy as climate change alters sea-ice extent and quality. An understanding of emperor penguin population structure is therefore urgently needed. Two previous studies have differed in their conclusions, particularly whether the Ross Sea, a major stronghold for the species, is isolated or not. We assessed emperor penguin population structure using 4,596 genome-wide single nucleotide polymorphisms (SNPs), characterized in 110 individuals (10–16 per colony) from eight colonies around Antarctica. In contrast to a previous conclusion that emperor penguins are panmictic around the entire continent, we find that emperor penguins comprise at least four metapopulations,...

Individuals and pairs of Adelie and Emperor penguins were counted at the breeding colonies near Syowa Station. Their numbers are recorded in this data set.

The fundamental long-term objective of the seabird component of the Palmer LTER (PAL) has been to identify and understand the mechanistic processes that regulate the mean fitness (population growth rate) of regional penguin populations. Two hypotheses have guided this research, with one suggesting that population mean fitness is best explained by changes in regional krill biomass, and the other proposing that long-term changes in sea ice affects mean fitness by tipping the balance in favor of one species over another in accordance with species-specific evolved life history affinities to sea ice. Although these hypotheses are not mutually exclusive, current evidence in the PAL region tends to favor the latter over the former. Since the inception of PAL, Adélie penguin populations have effectively collapsed, while those of gentoo and chinstrap penguins have increased dramatically, trends that are spatially and temporally coherent with decreasing regional sea ice duration. Adélie penguins are an ice-obligate polar species whose life history is intimately linked to the presence of sea ice, while chinstrap and gentoo penguins are ice-intolerant species whose life histories evolved in the sub-Antarctic, where sea ice is a less permanent feature of the marine ecosystem. In contrast, although krill constitute the most important component of the summer diets by mass of these three penguin species, changes in PAL krill abundances have exhibited no long-term trends, and thus fail to explain the divergent patterns in penguin populations evident in our time series.

   No lay dates were recorded during the 2020-2021 season due to a late start to the field season due to COVID. No data collected during the 2021-2022 season due to the Palmer Station Pier Build.

Intermittent Adelie penguin population counts for Bechervaise, Verner and Petersen Islands, Mawson since 1971. Data include counts of occupied nests for the post 1990/91 data conducted on or about 2nd December. Data collected prior to this were obtained from ANARE Research Notes or field note books. These counts may not have been performed at the 'optimal' time for occupied nests counts, and when this is the case have been adjusted according to a 'correction' factor.

The post 1990/91 data were completed as part of ASAC Project 2205, Adelie penguin research and monitoring in support of the CCAMLR Ecosystem Monitoring Project.

The fields in this dataset are:

Year Bechervaise Island Counts Verner Island Counts Petersen Island Counts Date Season occ nests (occupied nests)

This indicator is no longer maintained, and is considered OBSOLETE. INDICATOR DEFINITION Breeding populations of Adelie penguins at Davis, Mawson and Casey (including Shirley Island and Whitney Point). 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 Adelie 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 (fisheries, tourism, pollution, disturbance). Monitoring these colonies and interpretation of the data provides information on changes in the Antarctic ecosystem. DESIGN AND STRATEGY FOR INDICATOR MONITORING PROGRAM Spatial scale: Colonies near Australian Stations - Casey (lat 66 deg 16' 54.5" S, long 110 deg 31' 39.4" E) Davis (lat 68 deg 34' 35.8" S, long 77 deg 58' 02.6" E) Mawson (lat 67 deg 36' 09.7" S, long 62 deg 52' 25.7" E) All colonies on - Shirley Island (lat 66 deg 16' 55.9" S, long 110 deg 29' 17.9" E) and Whitney Point (lat 66 deg 15' 08.6" S, long 110 deg 31' 40.1" E) Frequency: Annual surveys at Shirley Island and Whitney Point. Other colonies every 2-3 years, depending on logistical constraints. Measurement technique: Each colony is visited and all breeding birds are counted from the ground by two or three personnel performing replicate counts. Supplementary census data are obtained from oblique ground and aerial photographs. All breeding adults in a colony are counted. Considerations regarding disturbance associated with census visits are also incorporated into monitoring strategies. The lack of annual census data for some colonies does not reduce the value of these long-term monitoring programmes. RESEARCH ISSUES Adelie Penguin populations throughout East Antarctica have shown sustained, long-term increases for the past 30 or more years; in contrast, populations elsewhere around the Antarctic and on the Antarctic Peninsula have exhibited decreases or no clear long-term trends (Woehler et al. 2001). Greater coverage of colonies throughout the AAT would provide a more accurate estimate of the total annual breeding population in East Antarctica. In addition to basic inventory requirements, data on the population trends would contribute to a better understanding of the role of Adelie penguins in the Antarctic ecosystem, and provide managers with feedback or management strategies. LINKS TO OTHER INDICATORS

Ecologists are increasingly turning to historical abundance data to understand past changes in animal abundance and more broadly the ecosystems in which animals occur. However, developing reliable ecological or management interpretations from temporal abundance data can be difficult because most population counts are subject to measurement or estimation error.

There is now widespread recognition that counts of animal populations are often subject to detection bias. This recognition has led to the development of a general framework for abundance estimation that explicitly accounts for detection bias and its uncertainty, new methods for estimating detection bias, and calls for ecologists to estimate and account for bias and uncertainty when estimating animal abundance. While these methodological developments are now being increasingly accepted and used, there is a wealth of historical population count data in the literature that were collected before these developments. These historical abundance data may, in their original published form, have inherent unrecognised and therefore unaccounted biases and uncertainties that could confound reliable interpretation. Developing approaches to improve interpretation of historical data may therefore allow a more reliable assessment of extremely valuable long-term abundance data.

This dataset contains details of over 200 historical estimates of Adelie penguin breeding populations across the Australian Antarctic Territory (AAT) that have been published in the scientific literature. The details include attributes of the population count (date and year of count, count value, count object, count precision) and the published estimate of the breeding population derived from those attributes, expressed as the number of breeding pairs. In addition, the dataset contains revised population estimates that have been re-constructed using new estimation methods to account for detection bias as described in the associated publication. All population data used in this study were sourced from existing publications.

The Adélie penguin is the most important animal currently used for ecosystem monitoring in the Southern Ocean. The diet of this species is generally studied by visual analysis of stomach contents; or ratios of isotopes of carbon and nitrogen incorporated into the penguin from its food. There are significant limitations to the information that can be gained from these methods. We evaluated population diet assessment by analysis of food DNA in scats as an alternative method for ecosystem monitoring with Adélie penguins as an indicator species. Scats were collected at four locations, three phases of the breeding cycle, and in four different years. A novel molecular diet assay and bioinformatics pipeline based on nuclear small subunit ribosomal RNA gene (SSU rDNA) sequencing was used to identify prey DNA in 389 scats. Analysis of the twelve population sample sets identified spatial and temporal dietary change in Adélie penguin population diet. Prey diversity was found to be greater than pre...

The fundamental long-term objective of the seabird component of the Palmer LTER (PAL) has been to identify and understand the mechanistic processes that regulate the mean fitness (population growth rate) of regional penguin populations. Two hypotheses have guided this research, with one suggesting that population mean fitness is best explained by changes in regional krill biomass, and the other proposing that long-term changes in sea ice affects mean fitness by tipping the balance in favor of one species over another in accordance with species-specific evolved life history affinities to sea ice. Although these hypotheses are not mutually exclusive, current evidence in the PAL region tends to favor the latter over the former. Since the inception of PAL, Adélie penguin populations have effectively collapsed, while those of gentoo and chinstrap penguins have increased dramatically, trends that are spatially and temporally coherent with decreasing regional sea ice duration. Adélie penguins are an ice-obligate polar species whose life history is intimately linked to the presence of sea ice, while chinstrap and gentoo penguins are ice-intolerant species whose life histories evolved in the sub-Antarctic, where sea ice is a less permanent feature of the marine ecosystem. In contrast, although krill constitute the most important component of the summer diets by mass of these three penguin species, changes in PAL krill abundances have exhibited no long-term trends, and thus fail to explain the divergent patterns in penguin populations evident in our time series. Adélie penguin chick fledging weights are obtained every two days (or as ice and weather conditions permit) at three beaches on Humble Island beginning when the first fledglings appear on any one of these beaches, and continuing until the last fledglings depart. These data are generally collected during the first three weeks of February by first censusing the total number of chicks present on each beach, and then sub-sampling 30% of the censused population. The metric of interest is the weight (in grams) of individual chicks, which is an important predictor of overwinter survival and thus future recruitment into the population as breeding adults. Dr. Megan Cimino took over as PI of the LTER seabird project in 2020 from Dr. William Fraser. Field data collection between 2020-2022 has remained consistent with previous years. No data collected during the 2021-2022 season due to the Palmer Station Pier Build.

The fundamental long-term objective of the seabird component of the Palmer LTER (PAL) has been to identify and understand the mechanistic processes that regulate the mean fitness (population growth rate) of regional penguin populations. Since the inception of PAL, Adélie penguin populations have effectively collapsed, gentoo penguin populations have increased dramatically and chinstrap penguin populations have remained relatively stable. These trends are spatially and temporally coherent with regional warming and decreasing sea ice duration. Adélie penguins are an ice-obligate polar species whose life history is intimately linked to the presence of sea ice, while chinstrap and gentoo penguins are ice-intolerant species whose life histories evolved in the sub-Antarctic, where sea ice is a less permanent feature of the marine ecosystem. The PAL study region includes five main islands on which Adélie penguin colonies have historically occurred, with each island containing a different number of spatially segregated sub-colonies. These colonies are censused to determine the total number of nests and chicks produced each year, and breeding success. Diet samples are acquired to understand diet composition (e.g., krill, fish) and krill length-frequencies. In general, krill constitute the most important component of the summer diets by mass of these three penguin species, but changes in PAL krill abundances have exhibited no long-term trends and thus far, have failed to explain the divergent patterns in penguin populations evident in our time series. Chick fledging masses are recorded as a cumulative measure of climate, weather, diet, and parental influences on chick health at the end of the breeding season. These data have provided valuable insights into the marine and terrestrial factors that influence Adélie penguin population fitness. No data were collected during the 2021-2022 season due to the Palmer Station pier rebuild.

Understanding changes in abundance is crucial for conservation, but population growth rates often vary over space and time. We use 40 years of count data (1979–2019) and Bayesian state-space models to assess the African penguin Spheniscus demersus population under IUCN Red List Criterion A. We deconstruct the overall decline in time and space to identify where urgent conservation action is needed. The global African penguin population met the threshold for Endangered with a high probability (97%), having declined by almost 65% since 1989. An historical low of ~17,700 pairs bred in 2019. Annual changes were faster in the South African population (−4.2%, highest posterior density interval, HPDI: −7.8 to −0.6%) than the Namibian one (−0.3%, HPDI: −3.3 to +2.6%), and since 1999 were almost −10% at South African colonies north of Cape Town. Over the 40-year period, the Eastern Cape colonies went from holding ~25% of the total penguin population to ~40% as numbers decreased more rapidly elsew...

Population reference: CHI (Chiloé), PUP (Pupuya), ALG (Algarrobo), CAC (Cachagua), TIL (Tilgo), PAJ (Pajaros), CHO (Choros), CHA (Chañaral), GRA (Isla Grande), AZU (Pan de Azucar), and PSJ (Punta San Juan).

This dataset contains data on the habitats, distribution and numbers of Adelie Penguins (Pygoscellis adeliae) along the Vestfold Hills coast (including colonies on the mainland and offshore islands) during November 1973. The data are obtained from counts at the colonies and black and white photographs. Some aerial photographs were taken at Davis in 1981-82 and 1987-88, and will be compared to the results of this survey. The results are listed in the documentation. A total of 174178 26127 breeding pairs were counted. An increase in Adelie penguin population was found at most locations in East Antarctica.

Data from this record has been incorporated into a larger Adelie penguin dataset described by the metadata record - Annual population counts at selected Adelie Penguin colonies within the AAT (SOE_seabird_candidate_sp_AP). It also falls under ASAC project 1219 (ASAC_1219).

Data can be accessed via that metadata record.

Aerial reconnaissance and photography are used in the Ross Sea sector of Antarctica to determine the breeding locations of Adélie penguins and to count the numbers of nests occupied during the early incubation period. From 1981 to present (two-year embargo), all islands and sea coasts between 158°E and 175°E have been searched, and 11 previously unreported breeding colonies discovered.

The aim is to census Adélie (Pygoscelis adeliae) populations to provide basic data against which future population levels can be compared in order to monitor environmental change of the Antarctic Ocean ecosystem, both natural and man-induced.