C. Scott Baker

Author Correction: Universal DNA methylation age across mammalian tissues

Publisher: Springer Science and Business Media LLC

Date: 06-09-2023

DOI: 10.1038/S43587-023-00499-7

Long-term stability in the circumpolar foraging range of a Southern Ocean predator between the eras of whaling and rapid climate change

Publisher: Proceedings of the National Academy of Sciences

Date: 27-02-2023

DOI: 10.1073/PNAS.2214035120

Abstract: Assessing environmental changes in Southern Ocean ecosystems is difficult due to its remoteness and data sparsity. Monitoring marine predators that respond rapidly to environmental variation may enable us to track anthropogenic effects on ecosystems. Yet, many long-term datasets of marine predators are incomplete because they are spatially constrained and/or track ecosystems already modified by industrial fishing and whaling in the latter half of the 20th century. Here, we assess the contemporary offshore distribution of a wide-ranging marine predator, the southern right whale (SRW, Eubalaena australis ), that forages on copepods and krill from ~30°S to the Antarctic ice edge ( °S). We analyzed carbon and nitrogen isotope values of 1,002 skin s les from six genetically distinct SRW populations using a customized assignment approach that accounts for temporal and spatial variation in the Southern Ocean phytoplankton isoscape. Over the past three decades, SRWs increased their use of mid-latitude foraging grounds in the south Atlantic and southwest (SW) Indian oceans in the late austral summer and autumn and slightly increased their use of high-latitude ( °S) foraging grounds in the SW Pacific, coincident with observed changes in prey distribution and abundance on a circumpolar scale. Comparing foraging assignments with whaling records since the 18th century showed remarkable stability in use of mid-latitude foraging areas. We attribute this consistency across four centuries to the physical stability of ocean fronts and resulting productivity in mid-latitude ecosystems of the Southern Ocean compared with polar regions that may be more influenced by recent climate change.

An epigenetic clock to estimate the age of living beluga whales

Publisher: Wiley

Date: 03-02-2021

DOI: 10.1111/EVA.13195

Abstract: DNA methylation data facilitate the development of accurate molecular estimators of chronological age or “epigenetic clocks.” We present a robust epigenetic clock for the beluga whale, Delphinapterus leucas , developed for an endangered population in Cook Inlet, Alaska, USA. We used a custom methylation array to measure methylation levels at 37,491 cytosine–guanine sites (CpGs) from skin s les of dead whales ( n = 67) whose chronological ages were estimated based on tooth growth layer groups. Using these calibration data, a penalized regression model selected 23 CpGs, providing an R 2 = 0.92 for the training data and an R 2 = 0.74 and median absolute age error = 2.9 years for the leave one out cross‐validation. We applied the epigenetic clock to an independent dataset of 38 skin s les collected with a biopsy dart from living whales between 2016 and 2018. Age estimates ranged from 11 to 27 years. We also report sex correlations in CpG data and describe an approach of identifying the sex of an animal using DNA methylation. The epigenetic estimators of age and sex presented here have broad applications for conservation and management of Cook Inlet beluga whales and potentially other cetaceans.

A surplus no more? Variation in krill availability impacts reproductive rates of Antarctic baleen whales

Publisher: Wiley

Date: 15-01-2023

DOI: 10.1111/GCB.16559

Abstract: The krill surplus hypothesis of unlimited prey resources available for Antarctic predators due to commercial whaling in the 20th century has remained largely untested since the 1970s. Rapid warming of the Western Antarctic Peninsula (WAP) over the past 50 years has resulted in decreased seasonal ice cover and a reduction of krill. The latter is being exacerbated by a commercial krill fishery in the region. Despite this, humpback whale populations have increased but may be at a threshold for growth based on these human‐induced changes. Understanding how climate‐mediated variation in prey availability influences humpback whale population dynamics is critical for focused management and conservation actions. Using an 8‐year dataset (2013–2020), we show that inter‐annual humpback whale pregnancy rates, as determined from skin‐blubber biopsy s les ( n = 616), are positively correlated with krill availability and fluctuations in ice cover in the previous year. Pregnancy rates showed significant inter‐annual variability, between 29% and 86%. Our results indicate that krill availability is in fact limiting and affecting reproductive rates, in contrast to the krill surplus hypothesis. This suggests that this population of humpback whales may be at a threshold for population growth due to prey limitations. As a result, continued warming and increased fishing along the WAP, which continue to reduce krill stocks, will likely impact this humpback whale population and other krill predators in the region. Humpback whales are sentinel species of ecosystem health, and changes in pregnancy rates can provide quantifiable signals of the impact of environmental change at the population level. Our findings must be considered paramount in developing new and more restrictive conservation and management plans for the Antarctic marine ecosystem and minimizing the negative impacts of human activities in the region.

New Zealand southern right whale (Eubalaena australis; Tohorā nō Aotearoa) behavioural phenology, demographic composition, and habitat use in Port Ross, Auckland Islands over three decades: 1998–2021

Publisher: Springer Science and Business Media LLC

Date: 08-2022

DOI: 10.1007/S00300-022-03076-7

Abstract: Changes in habitat availability and prey abundance are predicted to adversely influence survival and reproduction of wildlife in the Southern Ocean. Some populations of southern right whale (SRW Eubalaena australis ) are showing dramatic changes in habitat use. Surveys were undertaken in the austral winters of 2020 and 2021 at the key nursery and socialising ground for New Zealand SRWs: Port Ross, Auckland Islands, with 548 encounters and 599 skin biopsy s les collected. Data from these two surveys spanned peak periods of use and were used to test the hypothesis there have been shifts in the phenology, demographic composition and behaviour of SRWs using the Auckland Islands over the past three decades. The behavioural phenology and demographic composition of SRW resembles that observed in the 1990s. In contrast, the proportion of groups containing cow-calf pairs increased from 20% in the 1998 survey to 50% in 2020/21. These changes are consistent with a growing population undergoing strong recruitment, not limited by food resources. Continued use of Port Ross by all SRW demographic classes confirms this as key habitat for SRW in New Zealand waters, and we support increased enforcement of existing management measures to reduce whale-vessel interactions in this remote subantarctic archipelago.

DNA methylation networks underlying mammalian traits

Publisher: American Association for the Advancement of Science (AAAS)

Date: 11-08-2023

DOI: 10.1126/SCIENCE.ABQ5693

Abstract: Using DNA methylation profiles ( n = 15,456) from 348 mammalian species, we constructed phyloepigenetic trees that bear marked similarities to traditional phylogenetic ones. Using unsupervised clustering across all s les, we identified 55 distinct cytosine modules, of which 30 are related to traits such as maximum life span, adult weight, age, sex, and human mortality risk. Maximum life span is associated with methylation levels in HOXL subclass homeobox genes and developmental processes and is potentially regulated by pluripotency transcription factors. The methylation state of some modules responds to perturbations such as caloric restriction, ablation of growth hormone receptors, consumption of high-fat diets, and expression of Yamanaka factors. This study reveals an intertwined evolution of the genome and epigenome that mediates the biological characteristics and traits of different mammalian species.

Universal DNA methylation age across mammalian tissues

Publisher: Springer Science and Business Media LLC

Date: 10-08-2023

DOI: 10.1038/S43587-023-00462-6

Abstract: Aging, often considered a result of random cellular damage, can be accurately estimated using DNA methylation profiles, the foundation of pan-tissue epigenetic clocks. Here, we demonstrate the development of universal pan-mammalian clocks, using 11,754 methylation arrays from our Mammalian Methylation Consortium, which encompass 59 tissue types across 185 mammalian species. These predictive models estimate mammalian tissue age with high accuracy ( r 0.96). Age deviations correlate with human mortality risk, mouse somatotropic axis mutations and caloric restriction. We identified specific cytosines with methylation levels that change with age across numerous species. These sites, highly enriched in polycomb repressive complex 2-binding locations, are near genes implicated in mammalian development, cancer, obesity and longevity. Our findings offer new evidence suggesting that aging is evolutionarily conserved and intertwined with developmental processes across all mammals.

University Of Hawaii System

Location: United States of America

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Oregon State University

Location: United States of America

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Linkage Projects - Grant ID: LP0562517

Start Date: 11-2005

End Date: 12-2008

Amount: $288,000.00

Funder: Australian Research Council

Linkage Projects - Grant ID: LP0348721

Start Date: 08-2003

End Date: 12-2006

Amount: $82,000.00

Funder: Australian Research Council