Biology subjects

Ferguson, S. H.

Publications and source records attributed to Ferguson, S. H..

7 recordsLinked to original sources

bioRxiv2024

Unraveling the genetic legacy of commercial whaling in bowhead whales and narwhals

Commercial whaling decimated many whale populations over several centuries. Bowhead whales (Balaena mysticetus) and narwhal (Monodon monoceros) have similar habitat requirements and are often seen together in the Canadian Arctic. Although their ranges overlap extensively, bowhead whales experienced significantly greater whaling pressure than narwhals. The different harvest histories but similar habitat requirements of these two species provide an opportunity to examine the demographic and genetic consequences of commercial whaling. We whole-genome resequenced Canadian Arctic bowhead whales and narwhals to delineate population structure and reconstruct demographic history. Bowhead whale effective population size sharply declined contemporaneously with the intense commercial whaling period. Narwhals instead exhibited recent growth in effective population size, reflecting limited opportunistic commercial harvest. Although the genetic diversity of bowhead whales and narwhals was similar, bowhead whales had more genetic diversity prior to commercial whaling and will likely continue to experience significant genetic drift in the future. In contrast, narwhals appear to have had long-term low genetic diversity and may not be at imminent risk of the consequences of the erosion of genetic diversity. This work highlights the importance of considering population trajectories in addition to genetic diversity when assessing the genetics of populations for conservation and management purposes.

genomics↗

bioRxiv2023

The dynamic interaction between predator and prey drives mesopredator movement and foraging ecology

Prey availability and predation risk drive animal distribution, movement, and foraging ecology, yet studies rarely analyze multiple predator-prey levels together. Understanding how predators optimize risk-reward tradeoffs is important for species conservation and management, especially in systems facing extreme ecosystem change. We examined how top-down (modelled polar bear habitat selection) and bottom-up (modeled fish diversity) processes influence the habitat selection, movement, and foraging behavior of 26 ringed seals (greater than 70,000 dives and 10,000 locations over 877 seal days). Our results suggest that polar bears spatially restrict seal movements and reduce the time seals spend foraging, potentially decreasing foraging success. Seals were more likely to be present and dive longer in high-predation risk areas when prey diversity was high. Further, seal habitat selection models excluding polar bears overestimated core space use. These findings illustrate the dynamic tradeoffs that mesopredators make when balancing predation risk and resource acquisition.

ecology↗

bioRxiv2021

Epigenetic predictors of maximum lifespan and other life history traits in mammals

Maximum lifespan of a species is the oldest that individuals can survive, reflecting the genetic limit of longevity in an ideal environment. Here we report methylation-based models that accurately predict maximum lifespan (r=0.89), gestational time (r=0.96), and age at sexual maturity (r=0.87), using cytosine methylation patterns collected from over 12,000 samples derived from 192 mammalian species. Our epigenetic maximum lifespan predictor corroborated the extended lifespan in growth hormone receptor knockout mice and rapamycin treated mice. Across dog breeds, epigenetic maximum lifespan correlates positively with breed lifespan but negatively with breed size. Lifespan-related cytosines are located in transcriptional regulatory regions, such as bivalent chromatin promoters and polycomb-repressed regions, which were hypomethylated in long-lived species. The epigenetic estimators of maximum lifespan and other life history traits will be useful for characterizing understudied species and for identifying interventions that extend lifespan.

evolutionary biology↗

bioRxiv2021

DNA Methylation Networks Underlying Mammalian Traits

Epigenetics has hitherto been studied and understood largely at the level of individual organisms. Here, we report a multi-faceted investigation of DNA methylation across 11,117 samples from 176 different species. We performed an unbiased clustering of individual cytosines into 55 modules and identified 31 modules related to primary traits including age, species lifespan, sex, adult species weight, tissue type and phylogenetic order. Analysis of the correlation between DNA methylation and species allowed us to construct phyloepigenetic trees for different tissues that parallel the phylogenetic tree. In addition, while some stable cytosines reflect phylogenetic signatures, others relate to age and lifespan, and in many cases responding to anti-aging interventions in mice such as caloric restriction and ablation of growth hormone receptors. Insights uncovered by this investigation have important implications for our understanding of the role of epigenetics in mammalian evolution, aging and lifespan.

evolutionary biology↗

bioRxiv2021

Universal DNA methylation age across mammalian tissues

Aging is often perceived as a degenerative process resulting from random accrual of cellular damage over time. Despite this, age can be accurately estimated by epigenetic clocks based on DNA methylation profiles from almost any tissue of the body. Since such pan-tissue epigenetic clocks have been successfully developed for several different species, we hypothesized that one can build pan-mammalian clocks that measure age in all mammalian species. To address this, we generated data using 11,754 methylation arrays, each profiling up to 36 thousand cytosines in highly-conserved stretches of DNA, from 59 tissue-types derived from 185 mammalian species. From these methylation profiles, we constructed three age predictors, each with a single mathematical formula, termed universal pan-mammalian clocks that are accurate in estimating the age (r>0.96) of any mammalian tissue. Deviations between epigenetic age and chronological age relate to mortality risk in humans, mutations that affect the somatotropic axis in mice, and caloric restriction. We characterized specific cytosines, whose methylation levels change with age across most mammalian species. These cytosines are greatly enriched in polycomb repressive complex 2-binding sites, are located in regions that gradually lose chromatin accessibility with age and are proximal to genes that play a role in mammalian development, cancer, human obesity, and human longevity. Collectively, these results support the notion that aging is indeed evolutionarily conserved and coupled to developmental processes across all mammalian species - a notion that was long-debated without the benefit of this new compelling evidence. SUMMARYThis study identifies and characterizes evolutionarily conserved cytosines implicated in the aging process across mammals and establishes pan mammalian epigenetic clocks.

developmental biology↗

bioRxiv2019

Sex identification of ancient pinnipeds using the dog genome

Determining the male and female representation in zooarchaeological material from hunted animal species is essential, to fully investigate the effects and means of prehistoric hunting practices, and may further provide valuable biological information on past animal life-history, behaviour and demography. However, the fragmented nature of the zooarchaeological record and a lack of clear diagnostic skeletal markers, often prevents such inference. Here, we test the usability of the dog nuclear genome (CanFam3.1) for sex identification of pinnipeds. First, a contemporary sample set (n=72) of ringed seals (Pusa hispida), with known sex was used to test the genetic sex identification method. By quantifying the proportion of X chromosome reads, as the chrX/chr1 ratio, the ratios clustered in two clearly distinguishable sex groups. Of the 72 individuals, 69 were identified to the accurate sex, which proves a high reliability of the genetic method. Second, random down sampling of a subset of the ringed seal samples to different read number, suggests at least 5000 DNA sequence reads mapped to the reference genome as the lower limit for which this method is applicable. Finally, applying this standard, sex identification was successfully carried out on a broad set of ancient pinniped samples, including walruses (Odobenus rosmarus), grey seals (Halichoerus grypus) and harp seals (Pagophilus groenlandicus), which all showed clearly distinct male and female chrX/chr1 ratio groups.

genomics↗

bioRxiv2019

Bayesian abundance estimation from genetic mark-recapture data when not all sites are sampled: an example with the bowhead whale

Estimating abundance is one of the most fundamental and important aspects of population biology, with major implications on how the status of a population is perceived and thus on conservation and management efforts. Although typically based on one of two methods (distance sampling or mark-recapture), there are many individual identification methods that can be used for mark-recapture purposes. In recent years, the use of genetic data for individual identification and abundance estimation through mark-recapture analyses have increased, and in some situations such genetic identifications are more efficient than their field-based counterparts for population monitoring. One issue with mark-recapture analyses, regardless of which method of individual identification is used, is that the study area must provide adequate opportunities for "capturing" all individuals within a population. However, many populations are unevenly and widely distributed, making it unfeasible to adequately sample all necessary areas. Here we develop an analytical technique that accounts for unsampled locations, and provides a means to infer "missing" individuals from unsampled locations, and therefore obtain more accurate abundance estimates when it is not possible to sample all sites. This method is validated using simulations, and is used to estimate abundance of the Eastern Canada-West Greenland (EC-WG) bowhead whale population. Based on these analyses, the estimated size of this population is 9,089 individuals, with a 95% highest density interval of 5,107-17,079.

zoology↗