Landscape of stress: Tree mortality influences physiological stress and survival in a native mesocarnivore

Climate change and anthropogenic modifications to the landscape can have both positive and negative effects on an animal. Linking landscape change to physiological stress and fitness of an animal is a fundamental tenet to be examined in applied ecology. Cortisol is a glucocorticoid hormone that can be used to indicate an animal’s physiological stress response. In the Sierra Nevada Mountains of California, fishers (Pekania pennanti) are a threatened mesocarnivore that have been subjected to rapid landscape changes due to anthropogenic modifications and tree mortality related to a 4-year drought. We measured cortisol concentrations in the hair of 64 fishers (41 females, 23 males) captured and radio-collared in the Sierra National Forest, California. We addressed two main questions: (1) Is the physiological stress response of fishers influenced by anthropogenic factors, habitat type, canopy cover, and tree mortality due to drought in their home range? (2) Does the physiological stress response influence survival, reproduction, or body condition? We examined these factors within a fisher home range at 3 scales (30, 60, 95% isopleths). Using model selection, we found that tree mortality was the principle driver influencing stress levels among individual fishers with female and male fishers having increasing cortisol levels in home ranges with increasing tree mortality. Most importantly, we also found a link between physiological stress and demography where female fishers with low cortisol levels had the highest annual survival rate (0.94), whereas females with medium and high cortisol had lower annual survival rates, 0.78 and 0.81, respectively. We found no significant relationships between cortisol levels and body condition, male survival, or litter size. We concluded that tree mortality related to a 4-year drought has created a “landscape of stress” for this small, isolated fisher population

Landscape of Stress: Does Drought Prevail Over Anthropogenic Activity in Influencing Cortisol Levels and Fitness in the Pacific Fisher?

Fishers (Pekania pennanti) are a species of concern in the Sierra Nevada Mountains of California. Cortisol is a glucocorticoid hormone released to mobilize energy in response to stress and has been used as an indication of an individual’s physiological response to its environment. By collecting samples of fisher hair and measuring an individual’s cortisol, we examined the physiological stress response of the animals to human disturbances (housing density, road density, habitat type, and silvicultural treatements) and drought (tree mortality) in their home ranges. Using AICc model selection, we found that levels of tree mortality within a fisher’s home range significantly influenced cortisol levels. Various human disturbances had a smaller effect on cortisol levels. Furthermore, we examined the relationship between cortisol and fitness through the metrics of body condition, female kit counts, and survival. We found that females with low cortisol had significantly higher survival rates than females with medium and high cortisol. With the recent drought, bark beetle infestation and subsequent tree mortality being \u3e80% in some areas of our study, cortisol levels could continue to increase, potentially leading to further decreased fitness within this fisher population. We also examined the difference in habitat selection between the core and entirety of the home ranges and found that fishers prefer late-successional forest in the core of their home ranges

Landscape use by fishers (\u3ci\u3ePekania pennanti\u3c/i\u3e): core areas differ in habitat than the entire home range

Home ranges have long been studied in animal ecology. Core areas may be used at a greater proportion than the rest of the home range, implying the core contains dependable resources. The Pacific fisher (Pekania pennanti (Erxleben, 1777)) is a rare mesocarnivore occupying a small area in the Sierra Nevada Mountains, California, USA. Once statewide, fishers declined in the 1900s due to trapping, habitat fragmentation, and development. Recently, drought induced by climate change may be affecting this population. We examined space use of fishers in their core versus their home range for levels of anthropogenic modifications (housing density, road density, silvicultural treatments), habitat types, and tree mortality. We found core areas contained more late-successional forest and minimal human activity compared with their territory. Their core had higher levels of dense canopy and higher amounts of conifer cover, while minimizing the amount of buildings, developed habitat, and low canopy cover. Fishers may in effect be seeking refugia by minimizing their exposure to these elements in their core. Conserving landscape components used by fishers in their core areas will be important for the persistence of this isolated population. Les domaines vitaux sont étudiés depuis longtemps en écologie animale. Les aires principales pourraient être utilisées en plus grande proportion que le reste du domaine vital, ce qui sous-entend qu’elles renferment des ressources fiables. Le pékan (Pekania pennanti (Erxleben, 1777)) est un mésocarnivore rare qui occupe une petite région de la chaîne des Sierra Nevada, en Californie (États-Unis). Autrefois présents dans l’ensemble de l’État, les pékans ont connu un déclin au 20e siècle causé par le piégeage, la fragmentation de leurs habitats et l’aménagement du territoire. Des sécheresses récentes induites par les changements climatiques pourraient avoir une incidence sur cette population. Nous avons comparé l’utilisation de l’espace par les pékans dans leurs aires principales et dans leurs domaines vitaux pour différents degrés de modifications d’origine humaine (densité de logement, densité de routes, traitements sylvicoles), types d’habitats et taux de mortalité des arbres. Nous avons constaté que les aires principales des pékans renferment plus de forêts en fin de succession et très peu d’activités humaines comparativement à l’ensemble de leur territoire. Les aires principales présentent de plus grandes proportions de canopée dense et de plus grandes quantités de couvert de conifères, alors que la quantité de bâtiments, les habitats aménagés et le couvert forestier bas y sont très limités. Les pékans pourraient en fait chercher des refuges en minimisant leur exposition à ces éléments dans leur aire principale. La conservation d’éléments du paysage utilisés par les pékans dans leurs aires principales sera importante pour la persistance de cette population isolée

Landscape use by fishers: core areas differ in habitat than the entire home range

Home ranges have long been studied in animal ecology. Core areas may be used at a greater proportion than the rest of the home range, implying the core contains dependable resources. The Pacific fisher (Pekania pennanti Erxleben, 1777) is a rare mesocarnivore occupying a small area in the Sierra Nevada Mountains, California. Once statewide, fishers declined in the 1900s due to trapping, habitat fragmentation, and development. Recently, drought induced by climate change may be affecting this population. We examined space use of fishers in their core versus their home range for levels of anthropogenic modifications (housing density, road density, silvicultural treatments), habitat types, and tree mortality. We found core areas contained more late-successional forest and minimal human activity compared to their territory. Their core had higher levels of dense canopy and higher amounts of conifer cover, while minimizing the amount of buildings, developed habitat, and low canopy cover. Fishers may in effect be seeking refugia by minimizing their exposure to these elements in their core. Conserving landscape components fishers’ use in their core will be important for the persistence of this isolated population.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

A draft human pangenome reference

Here the Human Pangenome Reference Consortium presents a first draft of the human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals1. These assemblies cover more than 99% of the expected sequence in each genome and are more than 99% accurate at the structural and base pair levels. Based on alignments of the assemblies, we generate a draft pangenome that captures known variants and haplotypes and reveals new alleles at structurally complex loci. We also add 119 million base pairs of euchromatic polymorphic sequences and 1,115 gene duplications relative to the existing reference GRCh38. Roughly 90 million of the additional base pairs are derived from structural variation. Using our draft pangenome to analyse short-read data reduced small variant discovery errors by 34% and increased the number of structural variants detected per haplotype by 104% compared with GRCh38-based workflows, which enabled the typing of the vast majority of structural variant alleles per sample

Assembly of 43 human Y chromosomes reveals extensive complexity and variation.

The prevalence of highly repetitive sequences within the human Y chromosome has prevented its complete assembly to date1 and led to its systematic omission from genomic analyses. Here we present de novo assemblies of 43 Y chromosomes spanning 182,900 years of human evolution and report considerable diversity in size and structure. Half of the male-specific euchromatic region is subject to large inversions with a greater than twofold higher recurrence rate compared with all other chromosomes2. Ampliconic sequences associated with these inversions show differing mutation rates that are sequence context dependent, and some ampliconic genes exhibit evidence for concerted evolution with the acquisition and purging of lineage-specific pseudogenes. The largest heterochromatic region in the human genome, Yq12, is composed of alternating repeat arrays that show extensive variation in the number, size and distribution, but retain a 1:1 copy-number ratio. Finally, our data suggest that the boundary between the recombining pseudoautosomal region 1 and the non-recombining portions of the X and Y chromosomes lies 500 kb away from the currently established1 boundary. The availability of fully sequence-resolved Y chromosomes from multiple individuals provides a unique opportunity for identifying new associations of traits with specific Y-chromosomal variants and garnering insights into the evolution and function of complex regions of the human genome

Assembly of 43 human Y chromosomes reveals extensive complexity and variation

The uploaded file contains Supplementary Tables S1-S61 for the manuscript "Assembly of 43 human Y chromosomes reveals extensive complexity and variation

Assembly of 43 human Y chromosomes reveals extensive complexity and variation

The uploaded file contains Supplementary Tables S1-S61 for the manuscript "Assembly of 43 human Y chromosomes reveals extensive complexity and variation

A draft human pangenome reference.

Here the Human Pangenome Reference Consortium presents a first draft of the human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals1. These assemblies cover more than 99% of the expected sequence in each genome and are more than 99% accurate at the structural and base pair levels. Based on alignments of the assemblies, we generate a draft pangenome that captures known variants and haplotypes and reveals new alleles at structurally complex loci. We also add 119 million base pairs of euchromatic polymorphic sequences and 1,115 gene duplications relative to the existing reference GRCh38. Roughly 90 million of the additional base pairs are derived from structural variation. Using our draft pangenome to analyse short-read data reduced small variant discovery errors by 34% and increased the number of structural variants detected per haplotype by 104% compared with GRCh38-based workflows, which enabled the typing of the vast majority of structural variant alleles per sample