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...

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).

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. A sample of Adélie penguin nests from colonies on Humble Island is randomly selected annually and checked daily (or as ice and weather conditions permit) throughout the breeding season from the time adults arrive until the chick crèche phase of the reproductive cycle. Recorded data (the timing of egg laying, hatching and crèching) provide a measure of annual breeding chronology, and the number of chicks crèched, an estimate of reproductive success (chicks crèched/breeding pair). 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 lay dates were recorded during the 2020-2021 season due to a late start to the field season. 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 See Methods and Supplemental Materials for description of data summary and processing. A ReadMe file is included in the data package describing the various data layers.

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

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 …Show full descriptionThis 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.

MAPPPD ((Mapping Application for Penguin Populations and Projected Dynamics) is a project funded by the National Aeronautics and Space Administration (NASA) in partnership with Oceanites and the Lab of Dr. Heather Lynch at Stony Brook University.

Penguins are some of the most charismatic animals in the world and have captured the imaginations of news-makers, scientists, film producers and the general public. Beyond their general intrinsic value, they are considered important ecosystem indicators. That is to say, monitoring these beautiful species can tell us a lot about the general health of the Antarctic. This is because penguins are top predators, and changes (natural or anthropogenic) which influence the oceanography of the region or prey abundance, will ultimately be detected through changes in distribution or population size.

The Antarctic is currently governed by nations which make up the Antarctic Treaty System (ATS). Management strategies designed by the ATS rely on accurate and citable penguin population data in order to mitigate any anthropogenic impacts in the region. However, data on penguin populations are limited primarily due to the fact that most monitored colonies are nearby permanent research stations. This means that any remote populations are essentially ignored during planning processes. Due to advances in remote sensing, modeling and aerial imagery, it is now possible to obtain population estimates for these hard-to-reach sites.

MAPPPD aims to deliver population data from four species of penguin to any interested party with the goal of helping support conservation decisions in the Antarctic. We use a combination of highly advanced remote sensing technologies, aerial imagery and field counts to estimate penguin abundance across the entire continent.

All of the data in MAPPPD are open access to the general public, and the process is well documented in our white paper report. (http://www.penguinmap.com)

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...

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.

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, and that the Ross Sea is clearly a distinct metapopulation. Using larger sample sizes and a thorough assessment of the limitations of different analytical methods, we have shown that population structure within emperor penguins does exist and argue that its recognition is vital for the effective conservation of the species. We discuss the many difficulties that molecular ecologists and managers face in the detection and interpretation of subtle population structure using large SNP data sets, and argue that subtle structure should be taken into account when determining management strategies for threatened species, until accurate estimates of demographic connectivity among populations can be made.,Emperor penguin neutral SNP datasetEP_final.vcf

Metadata record for data from ASAC Project 484 See the link below for public details on this project. ---- Public Summary from Project ---- Emperor penguins are the only birds that breed in the …Show full descriptionMetadata record for data from ASAC Project 484 See the link below for public details on this project. ---- Public Summary from Project ---- Emperor penguins are the only birds that breed in the Antarctic winter. They feed mainly on fish and squid but also ingest krill. Changes in food availability due to oceanographic or climatic factors, or to the extent of sea ice (through the processes of global warming) will have a direct impact on the breeding success and population size of the penguins. By counting the number of males that incubate at mid-winter each year, we can monitor trends in their population size. Counts of fledglings in spring (November) tell us how successful the penguins bred. The download file contains an excel spreadsheet which presents a summary of known Emperor Penguin colonies in the area of the Australian Antarctic Territory (AAT), and a file which details counts of male emperor penguins at the Taylor Glacier colony. A description of the column headings used in the spreadsheet is below. Colony: Colony name lat, long: latitude and longitude of colony discovered: date colony was discovered current est pop (BP): Current estimated population size in breeding pairs - current as at date the colony was last seen last seen: date the colony was last seen counting method: method used to count the breeding pairs in the colony comments: any applicable comments reference: references relating to the colony Taken from the 2009-2010 Progress Report: Public summary of the season progress: Population size of colonies fluctuates which is why long term monitoring studies are necessary to detect trends. At the emperor penguin colony at Taylor Glacier, monitored continuously since 1988, a slight downward trend is apparent but is not (yet?) statistically significant. The colony was visited three times: once in winter to obtain an estimate of the number of adults in the colony (roughly equivalent to the number of breeding pairs), and twice during the late chick rearing season to estimate breeding success. The count of adults in 2009 was the lowest on record. Reasons for this are still unknown.

The emperor penguin, an iconic species threatened by projected sea-ice loss in Antarctica, has long been considered to forage at the fast ice edge, presumably relying on large/yearly-persistent polynyas as their main foraging habitat during the breeding season. Using newly developed fine-scale sea-icescape data and historical penguin tracking data, this study for the first time suggests the importance of less-recognized small openings, including cracks, flaw leads and ephemeral short-term polynyas, as foraging habitats for emperor penguins. The tracking data retrieved from 47 emperor penguins in two different colonies in East Antarctica suggest that those penguins spent 23% of their time in ephemeral polynyas and did not use the large/yearly-persistent, well-studied polynyas, even they occur much more regularly with predictable locations. These findings challenge our previous understanding of emperor penguin breeding habitats, highlighting the need for incorporating fine-scale seascape features when assessing the population persistence in a rapidly changing polar environment.

Seabirds are considered to be useful and practical indicators of the state of marine ecosystems because they integrate across changes in the lower trophic levels and the physical environment. Signals from this key group of species can indicate broad scale impacts or response to environmental change. Recent studies of penguin populations, the most commonly abundant Antarctic seabirds in the west Antarctic Peninsula and western Ross Sea, have demonstrated that physical changes in Antarctic marine environments have profound effects on biota at high trophic levels. Large populations of the circumpolar-breeding Adélie penguin occur in East Antarctica, but direct, standardized population data across much of this vast coastline have been more limited than in other Antarctic regions. We combine extensive new population survey data, new population estimation methods, and re-interpreted historical survey data to assess decadal-scale change in East Antarctic Adélie penguin breeding populations. We show that, in contrast to the west Antarctic Peninsula and western Ross Sea where breeding populations have decreased or shown variable trends over the last 30 years, East Antarctic regional populations have almost doubled in abundance since the 1980's and have been increasing since the earliest counts in the 1960's. The population changes are associated with five-year lagged changes in the physical environment, suggesting that the changing environment impacts primarily on the pre-breeding age classes. East Antarctic marine ecosystems have been subject to a number of changes over the last 50 years which may have influenced Adélie penguin population growth, including decadal-scale climate variation, an inferred mid-20th century sea-ice contraction, and early-to-mid 20th century exploitation of fish and whale populations.

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)

The Commission for the Conservation of Antarctic Marine Living Resources (CCAMLR) and the Antarctic Treaty System (ATS) have committed to using ecosystem-based management approaches in Antarctica. The Mapping Application for Penguin Populations and Projected Dynamics (MAPPPD) is a web-based, open access, decision support tool designed to assist scientists, non-governmental organizations, and policymakers working to meet the management objectives as set forth by CCAMLR and other components of the ATS (i.e., Consultative Meetings and the ATS Committee on Environmental Protection). MAPPPD was designed specifically to complement existing efforts such as the CCAMLR Ecosystem Monitoring Program (CEMP) and the ATS's Visitor Site Guidelines. The database underlying MAPPPD includes all available (published and unpublished) data on the four penguin species (Emperor, Gentoo, Ad�lie, and Chinstrap) with significant breeding populations south of 60� S. Population models can then be used to assimilate available data into estimates of abundance for each site and for each year; estimates are easily aggregated across multiple sites to obtain abundance estimates over any user-defined area of interest. A front-end web interface located at www.penguinmap.com provides free and ready access to the most recent count and modeled data, and can act as a facilitator for data transfer between scientists and Antarctic stakeholders to help inform management decisions for the continent.

Emperor penguin colonies 2009. Size of circle relates to estimated number of pairs in each colony. (EPS)

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.

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) …Show full descriptionThis 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).

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.