Geology topics

Dennis Jongsomjit

Publications and source records attributed to Dennis Jongsomjit.

11 recordsLinked to original sources

USGS2026

Novel avian papillomaviruses identified in a south polar skua sampled on Ross Island, Antarctica

Papillomaviruses are small circular DNA viruses that infect epithelial cells of their hosts. Avian papillomaviruses are poorly sampled/documented compared to those infecting humans. We used a viral metagenomic approach to identify viruses from the oral swab taken from a deceased south polar skua ( Stercorarius maccormicki ) found at Cape Royds, Ross Island, Antarctica in late 2024. We identified three papillomaviruses and determined their complete genomes, Stercorarius maccormicki papillomavirus (SmacPV) 1-3. SmacPV1 is the most divergent of the three SmacPVs, sharing 62% genome-wide pairwise identity to SmacPV2 and SmacPV3 and <63.5% to other avian papillomaviruses. The genomes of SmacPV2 and SmacPV3 represent two new papillomavirus types sharing 82.4% genome-wide pairwise identity with each other and <72% to other papillomaviruses. SmacPV2 and SmacPV3 phylogenetically cluster with sequences of the Rissa tridactyla papillomavirus 1 from black-legged kittiwake ( Rissa tridactyla ), Larus smithsonianus papillomavirus 1 from American herring gull ( Larus smithsonianus ) and Fratercula arctica papillomavirus 1 from Atlantic puffin ( Fratercula arctica ), and they collectively represent a new papillomavirus species. These are the first papillomaviruses to be identified in Stercorarius spp . and add to the handful of known papillomaviruses in identified avian species. We also expand the known host range of papillomaviruses in Antarctic animals, which previously included Adélie penguins ( Pygoscelis adeliae ), Weddell seals ( Leptonychotes weddellii ), Antarctic fur seals ( Arctocephalus gazella ), leopard seals ( Hydrurga leptonyx ) and emerald notothen ( Trematomus bernacchii ).

Archives of Virology↗

USGS2025

Diversity of polyomaviruses and papillomaviruses in penguins from eastern and western Antarctica

Polyomaviruses and papillomaviruses are icosahedral viruses with small circular dsDNA genomes. Limited information on their diversity and evolution in avian hosts is available, with even less known regarding Antarctic penguins. Prior to this study, only one polyomavirus and two papillomaviruses had been identified in Adélie penguins ( Pygoscelis adeliae ). To expand our knowledge of these viruses in Antarctic penguins, we collected faecal and cloacal swab samples from 246 Adélie penguins over 3 breeding seasons (2021–2024) and 10 emperor penguins ( Aptenodytes forsteri ) during the 2023–2024 season on Ross Island (Ross Sea). Additionally, we sampled 66 Adélie, 40 chinstrap ( Pygoscelis antarcticus ) and 71 gentoo ( Pygoscelis papua ) penguins during the 2022–2023 season across various sites on the Antarctic Peninsula. All samples were screened for papillomaviruses and polyomaviruses. We identified 31 polyomaviruses in Adélie, gentoo and chinstrap penguins and 4 papillomaviruses in Adélie penguins sampled in both eastern and western Antarctica. The 31 penguin polyomaviruses belong to a single species but form four distinct variants that are host species specific with strong geographic clustering. The four papillomaviruses represent three different types, of which two are new types from Adélie penguins sampled on Yalour Island in the West Antarctic Peninsula. Co-occurrence of two polyomavirus variants was identified in two individual gentoo penguins. Both of these variants appear to be circulating in gentoo penguins at Cierva Cove, Hope Bay in Trinity Peninsula along the Antarctic Peninsula, and at Hannah Point on Livingstone Island and Stranger Point on King George Island in the South Shetland Islands. Here, we expand the known diversity, host and geographical ranges of penguin polyomaviruses and, together with a previously identified polyomavirus on Ross Island from 2012 to 2013, show that they form five distinct lineages. The four papillomaviruses identified in this study, together with two previously identified from Ross Island in 2012 and 2013 breeding seasons, show substantial diversity reflecting four papillomavirus types across three viral species and two distinct genera. Continued surveillance and viral genomic analysis across a larger geographical framework will help understand the evolution, transmission and incidence rates of these viruses.

Microbial Genomics↗

USGS2024

Going with the floe: Sea-ice movement affects distance and destination during Adélie penguin winter movements

Seasonal migration, driven by shifts in annual climate cycles and resources, is a key part of the life history and ecology of species across taxonomic groups. By influencing the amount of energy needed to move, external forces such as wind and ocean currents are often key drivers of migratory pathways exposing individuals to varying resources, environmental conditions, and competition pressures impacting individual fitness and population dynamics. Although wildlife movements in connection with wind and ocean currents are relatively well understood, movements within sea-ice fields have been much less studied, despite sea ice being an integral part of polar ecology. Adélie penguins ( Pygoscelis adeliae ) in the southern Ross Sea, Antarctica, currently exist at the southernmost edge of their range and undergo the longest (~12,000 km) winter migration known for the species. Within and north of the Ross Sea, the Ross Gyre drives ocean circulation and the large-scale movement of sea ice. We used remotely sensed sea-ice movement data together with geolocation-based penguin movement data to test the hypothesis that penguins use gyre-driven sea-ice movement to aid their migration. We found that penguins traveled greater distances when their movement vectors were aligned with those of sea ice (i.e., ice support) and the amount of ice support received depended on which route a penguin took. We also found that birds that took an eastern route traveled significantly further north in two of the 3 years we examined, coinciding with higher velocities of sea ice in those years. We compare our findings to patterns observed in migrating species that utilize air or water currents for their travel and with other studies showing the importance of ocean/sea-ice circulation patterns to wildlife movement and life history patterns within the Ross Sea. Changes in sea ice may have consequences not only for energy expenditure but, by altering migration and movement pathways, to the ecological interactions that exist in this region.

Ecology↗

USGS2023

Sea ice concentration decline in an important Adélie penguin molt area

Unlike in many polar regions, the spatial extent and duration of the sea ice season have increased in the Ross Sea sector of the Southern Ocean during the satellite era. Simultaneously, populations of Adélie penguins, a sea ice obligate, have been stable or increasing in the region. Relationships between Adélie penguin population growth and sea ice concentration are complex, with sea ice driving different, sometimes contrasting, demographic patterns. Adélie penguins undergo a complete molt annually, replacing all their feathers while fasting shortly after the breeding season. Unlike most penguin species, a majority of Adélies are thought to molt on sea ice, away from the breeding colonies, which makes this period particularly difficult to study. Here, we evaluate the hypothesis that persistent areas of high sea ice concentration provide important molting habitat for Adélie penguins. We analyzed data from geolocating dive recorders deployed year-round on 195 adult penguins at two colonies in the Ross Sea from 2017-2019. We identified molt by detecting extended gaps in post-breeding diving activity and used associated locations to define two key molting areas. Remotely sensed data indicated that sea ice concentration during molt was anomalously low during the study and has declined in the primary molt area since 1980. Further, annual return rates of penguins to breeding colonies were positively correlated with sea ice concentration in the molt areas over 20 years. Together these results suggest that sea ice conditions during Adélie penguin molt may represent a previously underappreciated annual bottleneck for adult survival.

PNAS↗

USGS2023

High-resolution recording of foraging behaviour over multiple annual cycles shows decline in old Adélie penguins’ performance

Age-related variation in foraging performance can result from both within-individual change and selection processes. These mechanisms can only be disentangled by using logistically challenging long-term, longitudinal studies. Coupling a long-term demographic data set with high-temporal-resolution tracking of 18 Adélie penguins ( Pygoscelis adeliae , age 4–15 yrs old) over three consecutive annual cycles, we examined how foraging behaviour changed within individuals of different age classes. Evidence indicated within-individual improvement in young and middle-age classes, but a significant decrease in foraging dive frequency within old individuals, associated with a decrease in the dive descent rate. Decreases in foraging performance occurred at a later age (from 12–15 yrs old to 15–18 yrs old) than the onset of senescence predicted for this species (9–11 yrs old). Foraging dive frequency was most affected by the interaction between breeding status and annual life-cycle periods, with frequency being highest during returning migration and breeding season and was highest overall for successful breeders during the chick-rearing period. Females performed more foraging dives per hour than males. This longitudinal, full annual cycle study allowed us to shed light on the changes in foraging performance occurring among individuals of different age classes and highlighted the complex interactions among drivers of individual foraging behaviour.

Proceedings of the Royal Society B↗

USGS2021

The influence of subcolony-scale nesting habitat on the reproductive success of Adélie penguins

Group-size variation is common in colonially breeding species, including seabirds, whose breeding colonies can vary in size by several orders of magnitude. Seabirds are some of the most threatened marine taxa and understanding the drivers of colony size variation is more important than ever. Reproductive success is an important demographic parameter that can impact colony size, and it varies in association with a number of factors, including nesting habitat quality. Within colonies, seabirds often aggregate into distinct groups or subcolonies that may vary in quality. We used data from two colonies of Adélie penguins 73 km apart on Ross Island, Antarctica, one large and one small to investigate (1) How subcolony habitat characteristics influence reproductive success and (2) How these relationships differ at a small (Cape Royds) and large (Cape Crozier) colony with different terrain characteristics. Subcolonies were characterized using terrain attributes (elevation, slope aspect, slope steepness, wind shelter, flow accumulation), as well group characteristics (area/size, perimeter-to-area ratio, and proximity to nest predators). Reproductive success was higher and less variable at the larger colony while subcolony characteristics explained more of the variance in reproductive success at the small colony. The most important variable influencing subcolony quality at both colonies was perimeter-to-area ratio, likely reflecting the importance of nest predation by south polar skuas along subcolony edges. The small colony contained a higher proportion of edge nests thus higher potential impact from skua nest predation. Stochastic environmental events may facilitate smaller colonies becoming “trapped” by nest predation: a rapid decline in the number of breeding individuals may increase the proportion of edge nests, leading to higher relative nest predation and hindering population recovery. Several terrain covariates were retained in the final models but which variables, the shapes of the relationships, and importance varied between colonies.

Scientific Reports↗

USGS2021

Using high resolution satellite and telemetry data to track flooded habitats, their use by waterfowl, and evaluate effects of drought on waterfowl and shorebird bioenergetics in California

Wetland managers in the Central Valley of California, a dynamic hydrological landscape, require information regarding the amount and location of existing wetland habitat to make decisions on how to best use water resources to support multiple wildlife objectives, particularly during drought. Scientists from the U.S. Geological Survey Western Ecological Research Center (WERC), Point Blue Conservation Science (Point Blue), and the U.S. Fish and Wildlife Service (USFWS) partnered to learn how wetland and flooded agricultural habitats used by waterfowl and shorebirds change during the non-breeding season (July–April) particularly during drought. During extreme drought conditions, the ability to provide sufficient water for wildlife often depends on the timing of water deliveries to managed wetlands and winter-flooded crop fields and decisions on whether to fallow croplands. Waterfowl and shorebirds could be particularly affected by these decisions because they typically rest and feed in flooded habitats. Poor habitat conditions resulting from spatially or temporally suboptimal water deliveries (that is, mismatch between waterfowl habitat needs and timing and location of flooded habitats) could reduce waterfowl hunting opportunities and body condition. Point Blue scientists developed a system for near real-time tracking of habitats used by waterfowl, shorebirds, and some other wetland-dependent “waterbirds” ( www.pointblue.org/watertracker ) and to assess the impacts of drought on habitat availability and on waterfowl and shorebird bioenergetics. The WERC researchers linked these data with near real-time tracking (telemetry) data of duck locations throughout the Valley. The team used these two datasets to relate duck locations to open-water characteristics and to learn how waterfowl use habitats under spatially and temporally changing conditions during drought and non-drought periods. We found that recent extreme drought (2013–15) significantly changed the timing and magnitude of flooding and consequently reduced the availability of habitats used by waterfowl and shorebirds more than other recent historic droughts 2000–11. Drought reduced irrigations of moist soil seed plants and thus there was lower food energy available for waterfowl. Analyses using bioenergetics models indicated that, overall, extreme drought increased food energy deficits (total number of deficit days) for shorebirds and waterfowl. Our analysis indicated a strong direct relationship between duck locations and classified habitat derived from open-water data during the wintering period (October–March). This result helps confirm the application of dynamic water data to identify flooded areas that provide waterfowl habitat. Presence of open water at a 1-hectare resolution can be used effectively to identify flooded landscape areas available as habitat for ducks. Our discoveries from evaluating use of space by ducks also indicated that nighttime feeding locations of ducks were concentrated nearby primary roosts and that foraging distances could depend on hydrologic dynamics of location (Suisun Marsh versus California excluding Suisun Marsh) and time of season (early, middle, late). Other results indicated that some areas on the California landscape with extremely reliable water supplies could receive consistent use by ducks year after year (in essence, almost drought proof). The Water Tracker is set up to automatically track wetland habitat and food availability each year and is making these data available to water and wetland managers. Results from this research are a significant step toward understanding how waterfowl and shorebird habitats can be optimally managed on the landscape to support desired populations of these migratory birds during extreme drought.

California↗

USGS2020

Inter-individual differences in the foraging behavior of breeding Adélie penguins are driven by individual quality and sex

Inter-individual differences in demographic traits of iteroparous species can arise through learning and maturation, as well as from permanent differences in individual ‘quality’ and sex-specific constraints. As the ability to acquire energy determines the resources an individual can allocate to reproduction and self-maintenance, foraging behavior is a key trait to study to better understand the mechanisms underlying these differences. So far, most seabird studies have focused on the effect of maturation and learning processes on foraging performance, while only a few have included measures of individual quality. Here, we investigated the effects of age, breeding experience, sex, and individual breeding quality on the foraging behavior and location of 83 known-age Adélie penguins at Cape Bird, Ross Sea, Antarctica. Over a 2 yr period, we showed that (1) high-quality birds dived deeper than lower quality ones, apparently catching a higher number of prey per dive and targeting different foraging locations; (2) females performed longer foraging trips and a higher number of dives compared to males; (3) there were no significant age-related differences in foraging behavior; and (4) breeding experience had a weak influence on foraging behavior. We suggest that high-quality individuals have higher physiological ability, enabling them to dive deeper and forage more effectively. Further inquiry should focus on determining the physiological differences among penguins of different quality.

MEPS↗

USGS2019

Identification of a novel Adélie penguin circovirus at Cape Crozier (Ross Island, Antarctica)

Understanding the causes of disease in Antarctic wildlife is crucial as many of these species are already threatened by environmental changes brought about by climate change. In recent years, Antarctic penguins have been showing signs of an unknown pathology: a feather disorder characterised by missing feathers resulting in exposed skin. During the 2018-19 austral summer breeding season at Cape Crozier colony on Ross Island, Antarctica, for the first time we observed an Adlie penguin chick missing down over most of its body. A guano sample was collected from the nest of the featherless chick and, using high throughput sequencing we identified a novel circovirus. Using abutting primers, we amplified the full genome, which we cloned, and Sanger sequenced to determine the complete genome of the circovirus. The Adlie penguin guano-associated circovirus genome shares <67% genome-wide nucleotide identity to other circoviruses, representing a new species of circovirus, therefore we named it penguin circovirus (PenCV). Using the same primer pair, we screened 25 previously collected cloacal swabs taken at Cape Crozier from known-age adult Adlie penguins during the 2014-15 season displaying no clinical signs of feather-loss disorder. Three of the 25 samples (12%) were positive for a PenCV, whose genome shared >99% pairwise identity to the one identified in 2018-19. This is the first report of a circovirus associated with a penguin species and could be a possible etiological agent of the feather-loss disorder in Antarctic penguins.

Viruses↗

USGS2019

Prevalence of three-chick nests in Adelie Penguins Pygoscelis adeliae at Cape Crozier, Ross Island

In 2017/18, we recorded multiple instances of Adelie Penguin Pygoscelis adeliae nests containing three chicks at Cape Crozier, Ross Island, Antarctica. In one sub-colony, 0.67 % of nests had three chicks, or two chicks and one egg. We found that some Adelie Penguin pairs were willing to brood three chicks, as well as chicks that were not their own. Many factors could lead to supra-normal clutches and broods, including foreign eggs added to a nest, adoption of chicks belonging to other parents, and double-yolked eggs. In order to understand the true cost of colonial breeding in large Adelie Penguin colonies and to assess the source of chicks or eggs in supra-normal clutches and broods, we conclude that future studies should examine the frequency of supra-normal clutches and broods and analyze the genetics of chicks within sub-colonies.

Marine Ornithology: Journal of Seabird Research an↗

USGS2017

Unique genome organization of non-mammalian papillomaviruses provides insights into the evolution of viral early proteins

The family Papillomaviridae contains more than 320 papillomavirus types, with most having been identified as infecting skin and mucosal epithelium in mammalian hosts. To date, only nine non-mammalian papillomaviruses have been described from birds ( n = 5), a fish ( n = 1), a snake ( n = 1), and turtles ( n = 2). The identification of papillomaviruses in sauropsids and a sparid fish suggests that early ancestors of papillomaviruses were already infecting the earliest Euteleostomi. The Euteleostomi clade includes more than 90 per cent of the living vertebrate species, and progeny virus could have been passed on to all members of this clade, inhabiting virtually every habitat on the planet. As part of this study, we isolated a novel papillomavirus from a 16-year-old female Adélie penguin ( Pygoscelis adeliae ) from Cape Crozier, Ross Island (Antarctica). The new papillomavirus shares ∼64 per cent genome-wide identity to a previously described Adélie penguin papillomavirus. Phylogenetic analyses show that the non-mammalian viruses (expect the python, Morelia spilota , associated papillomavirus) cluster near the base of the papillomavirus evolutionary tree. A papillomavirus isolated from an avian host (Northern fulmar; Fulmarus glacialis ), like the two turtle papillomaviruses, lacks a putative E9 protein that is found in all other avian papillomaviruses. Furthermore, the Northern fulmar papillomavirus has an E7 more similar to the mammalian viruses than the other avian papillomaviruses. Typical E6 proteins of mammalian papillomaviruses have two Zinc finger motifs, whereas the sauropsid papillomaviruses only have one such motif. Furthermore, this motif is absent in the fish papillomavirus. Thus, it is highly likely that the most recent common ancestor of the mammalian and sauropsid papillomaviruses had a single motif E6. It appears that a motif duplication resulted in mammalian papillomaviruses having a double Zinc finger motif in E6. We estimated the divergence time between Northern fulmar-associated papillomavirus and the other Sauropsid papillomaviruses be to around 250 million years ago, during the Paleozoic-Mesozoic transition and our analysis dates the root of the papillomavirus tree between 400 and 600 million years ago. Our analysis shows evidence for niche adaptation and that these non-mammalian viruses have highly divergent E6 and E7 proteins, providing insights into the evolution of the early viral (onco-)proteins.

Virus Evolution↗