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Museum epigenomics: characterizing cytosine methylation in historic museum specimens
Rubi, Tricia; Knowles, L. Lacey; Dantzer, Ben — 2020-08-14 <p>Museum genomics has transformed the field of collections-based research, opening up a range of new research directions for paleontological specimens as well as natural history specimens collected over the past few centuries. Recent work demonstrates that it is possible to characterize epigenetic markers such as DNA methylation in well preserved ancient tissues. This approach has not yet been tested in traditionally prepared natural history specimens such as dried bones and skins, the most common specimen types in vertebrate collections. In this study, we developed and tested methods to characterize cytosine methylation in dried skulls up to 76 years old. Using a combination of ddRAD and bisulphite treatment, we characterized patterns of cytosine methylation in two species of deer mouse (Peromyscus spp.) collected in the same region in Michigan in 1940, 2003, and 2013–2016. We successfully estimated methylation in specimens of all age groups, although older specimens yielded less data and showed greater interindividual variation in data yield than newer specimens. Global methylation estimates were reduced in the oldest specimens (76 years old) relative to the newest specimens (1–3 years old), which may reflect post-mortem hydrolytic deamination. Methylation was reduced in promoter regions relative to gene bodies and showed greater bimodality in autosomes relative to female X chromosomes, consistent with expectations for methylation in mammalian somatic cells. Our work demonstrates the utility of historic specimens for methylation analyses, as with genomic analyses; however, studies will need to accommodate the large variance in the quantity of data produced by older specimens.</p>
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Territory acquisition mediates the influence of predators and climate on juvenile red squirrel survival
Hendrix, Jack G; Fisher, David; Martinig, April; Boutin, Stan; Dantzer, Ben; Lane, Jeffrey; McAdam, Andrew — 2021-03-06 <p>1) Juvenile survival to first breeding is a key life history stage for all taxa. Survival through this period can be particularly challenging when it can coincide with harsh environmental conditions such as a winter climate or food scarcity, leading to highly variable cohort survival. However, the small size and dispersive nature of juveniles generally makes studying their survival more difficult. 2) In territorial species, a key life history event is the acquisition of a territory. A territory is expected to enhance survival, but how it does so is not often identified. We tested how the timing of territory acquisition influenced the winter survival of juvenile North American red squirrels Tamiasciurus hudsonicus, hereafter red squirrels, and how the timing of this event mediated sources of mortality. We hypothesized that securing a territory prior to when food resources become available would reduce juvenile susceptibility to predation and climatic factors over winter. 3) Using 27 years of data on the survival of individually-marked juvenile red squirrels, we tested how the timing of territory acquisition influenced survival, whether the population density of red squirrel predators and mean temperature over winter were related to individual survival probability, and if territory ownership mediated these effects. 4) Juvenile red squirrel survival was lower in years of high predator abundance and in colder winters. Autumn territory owners were less susceptible to lynx Lynx canadensis, and possibly mustelid Mustela and Martes spp., predation. Autumn territory owners had lower survival in colder winters, but surprisingly non-owners had higher survival in cold winters. 5) Our results show how the timing of a life history event like territory acquisition can directly affect survival and also mediate the effects of biotic and abiotic factors later in life. This engenders a better understanding of the fitness consequences of the timing of key life history events.</p>
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Data from: Multilevel and sex-specific selection on competitive traits in North American red squirrels.
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Fisher, David N.; Boutin, Stan; Dantzer, Ben; Humphries, Murray M.; Lane, Jeffrey E.; McAdam, Andrew G. — 2022-04-26 Individuals often interact more closely with some members of the population (e.g. offspring, siblings or group members) than they do with other individuals. This structuring of interactions can lead to multilevel natural selection, where traits expressed at the group-level influence fitness alongside individual-level traits. Such multilevel selection can alter evolutionary trajectories, yet is rarely quantified in the wild, especially for species that do not interact in clearly demarcated groups. We quantified multilevel natural selection on two traits, postnatal growth rate and birth date, in a population of North American red squirrels (Tamiasciurus hudsonicus). The strongest level of selection was typically within-acoustic social neighbourhoods (within 130m of the nest), where growing faster and being born earlier than nearby litters was key, while selection on growth rate was also apparent both within-litters and within-study areas. Higher population densities increased the strength of selection for earlier breeding, but did not influence selection on growth rates. Females experienced especially strong selection on growth rate at the within-litter level, possibly linked to the biased bequeathal of the maternal territory to daughters. Our results demonstrate the importance of considering multilevel and sex-specific selection in wild species, including those that are territorial and sexually monomorphic.
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Data from: Body temperature, heart rate, and activity patterns of two boreal homeotherms in winter: homeostasis, allostasis, and ecological coexistence
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Menzies, Allyson; Studd, Emily; Majchrzak, Yasmine; Peers, Michael; Boutin, Stan; Dantzer, Ben; Lane, Jeffrey; McAdam, Andrew; Humphries, Murray — 2020-07-31 <ol> <li style="margin-bottom:12px;">Organisms survive environmental variation by combining homeostatic regulation of critical states with allostatic variation of other traits, and species differences in these responses can contribute to coexistence in temporally-variable environments.</li> <li style="margin-bottom:12px;">In this paper, we simultaneously record variation in three functional traits – body temperature (Tb), heart rate, and activity - in relation to three forms of environmental variation – air temperature (Ta), photoperiod, and experimentally-manipulated resource levels – in free-ranging snowshoe hares and North American red squirrels to characterize distinctions in homeotherm responses to the extreme conditions of northern boreal winters.</li> <li style="margin-bottom:12px;">Hares and squirrels differed in the level and precision of Tb regulation, but also in the allostatic pathways necessary to maintain thermal homeostasis. Hares demonstrated a stronger metabolic pathway (through heart rate variation reflective of the thermogenesis), while squirrels demonstrated a stronger behavioral pathway (through activity variation that minimizes cold exposure).</li> <li style="margin-bottom:12px;">As intermediate-sized, winter-active homeotherms, hares and squirrels share many functional attributes, yet, through the integrated monitoring of multiple functional traits in response to shared environmental variation, our study reveals many pairwise species differences in homeostatic and allostatic traits, that both define and are defined by the natural history, functional niches, and coexistence of sympatric species.</li> </ol> https://creativecommons.org/publicdomain/zero/1.0/
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Phenotype-environment mismatch errors enhance lifetime fitness in wild red squirrels
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Petrullo, Lauren; Dantzer, Ben; McAdam, Andrew; Boutin, Stan; Lane, Jeffrey E. — 2023 Included in this repository are three (3) dataset .csv files. The first is the main dataset for all females included in the study (emt_data_pub.csv). The second is the main dataset for all offspring/pups born to the females from Dataset 1 included in the study (emt_offspring_dataset.csv). The third is a subset of the first dataset including only females for who we had total cache size estimates for (cache_size_pub.csv). Please see the Materials and Methods section of the supplementary material for this manuscript for detail on statistical methods and variable descriptions. Additionally included in this repository is a single R script (emt_code.R) containing the necessary code and calls to the relevant tables in order to generate the data presented in the manuscript. https://creativecommons.org/licenses/by/4.0/legalcode

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(Author: Dantzer, Ben)

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