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Polar bear evolution is marked by rapid changes in gene copy number in response to dietary shift.

ABSTRACT: Polar bear (Ursus maritimus) and brown bear (Ursus arctos) are recently diverged species that inhabit vastly differing habitats. Thus, analysis of the polar bear and brown bear genomes represents a unique opportunity to investigate the evolutionary mechanisms and genetic underpinnings of rapid ecological adaptation in mammals. Copy number (CN) differences in genomic regions between closely related species can underlie adaptive phenotypes and this form of genetic variation has not been explored in the context of polar bear evolution. Here, we analyzed the CN profiles of 17 polar bears, 9 brown bears, and 2 black bears (Ursus americanus). We identified an average of 318 genes per individual that showed evidence of CN variation (CNV). Nearly 200 genes displayed species-specific CN differences between polar bear and brown bear species. Principal component analysis of gene CN provides strong evidence that CNV evolved rapidly in the polar bear lineage and mainly resulted in CN loss. Olfactory receptors composed 47% of CN differentiated genes, with the majority of these genes being at lower CN in the polar bear. Additionally, we found significantly fewer copies of several genes involved in fatty acid metabolism as well as AMY1B, the salivary amylase-encoding gene in the polar bear. These results suggest that natural selection shaped patterns of CNV in response to the transition from an omnivorous to primarily carnivorous diet during polar bear evolution. Our analyses of CNV shed light on the genomic underpinnings of ecological adaptation during polar bear evolution.

SUBMITTER: Rinker DC

PROVIDER: S-EPMC6613075 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature

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Polar bear evolution is marked by rapid changes in gene copy number in response to dietary shift.

Rinker David C DC Specian Natalya K NK Zhao Shu S Gibbons John G JG

Proceedings of the National Academy of Sciences of the United States of America 20190617 27

Polar bear (<i>Ursus maritimus</i>) and brown bear (<i>Ursus arctos</i>) are recently diverged species that inhabit vastly differing habitats. Thus, analysis of the polar bear and brown bear genomes represents a unique opportunity to investigate the evolutionary mechanisms and genetic underpinnings of rapid ecological adaptation in mammals. Copy number (CN) differences in genomic regions between closely related species can underlie adaptive phenotypes and this form of genetic variation has not b ...[more]

PMID: 31209046

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Project description:Polar bears in captivity can be exposed to opportunistic pathogens not present in their natural environments. A 4-month-old polar bear (Ursus maritimus) living in an isolated enclosure with his mother in the Tierpark Berlin, Berlin, Germany, was suffering from severe abdominal pain, mild diarrhea, and loss of appetite and died in early 2017. Histopathology revealed severe hepatic degeneration and necrosis without evidence of inflammation or inclusion bodies, although a viral infection had been suspected on the basis of the clinical signs. We searched for nucleic acids of pathogens by shotgun high-throughput sequencing (HTS) from genomic DNA and cDNA extracted from tissue and blood. We identified a novel Mastadenovirus and assembled a nearly complete genome from the shotgun sequences. Quantitative PCR (qPCR) revealed that viral DNA was present in various concentrations in all tissues examined and that the highest concentrations were found in blood. Viral culture did not yield cytopathic effects, but qPCR suggested that virus replication was sustained for up to three passages. Positive immunofluorescence staining confirmed that the virus was able to replicate in the cells during early passage. Phylogenetic analysis demonstrated that the virus is highly divergent compared to other previously identified Mastadenovirus members and basal to most known viral clades. The virus was found only in the 4-month-old bear and not in other captive polar bears tested. We surmised, therefore, that the polar bear was infected from an unknown reservoir, illustrating that adenoviral diversity remains underestimated and that cross-species transmission of viruses can occur even under conditions of relative isolation.IMPORTANCE Cross-species transmission of viral pathogens is becoming an increasing problem for captive-animal facilities. This study highlights how animals in captivity are vulnerable to novel opportunistic pathogens, many of which do not result in straightforward diagnosis from symptoms and histopathology. In this study, a novel pathogen was suspected to have contributed to the death of a juvenile polar bear. HTS techniques were employed, and a novel Mastadenovirus was isolated. The virus was present in both the tissue and blood samples. Phylogenetic analysis of the virus at both the gene and genome levels revealed that it is highly divergent to other known mastadenoviruses. Overall, this study shows that animals in isolated conditions still come into contact with novel pathogens, and for many of these pathogens, the host reservoir and mode of transmission are yet to be determined.

Project description:BackgroundFlexible foraging strategies, such as prey switching, omnivory and food mixing, are key to surviving in a labile and changing environment. Polar bears (Ursus maritimus) in western Hudson Bay are versatile predators that use all of these strategies as they seasonally exploit resources across trophic levels. Climate warming is reducing availability of their ice habitat, especially in spring when polar bears gain most of their annual fat reserves by consuming seal pups before coming ashore in summer. How polar bears combine these flexible foraging strategies to obtain and utilize terrestrial food will become increasingly important in compensating for energy deficits from lost seal hunting opportunities. We evaluated patterns in the composition of foods in scat to characterize the foraging behaviors that underpin the diet mixing and omnivory observed in polar bears on land in western Hudson Bay. Specifically, we measured diet richness, proportions of plant and animal foods, patterns in co-occurrence of foods, spatial composition and an index of temporal composition.ResultsScats contained between 1 and 6 foods, with an average of 2.11 (SE = 0.04). Most scats (84.9%) contained at least one type of plant, but animals (35.4% of scats) and both plants and animals occurring together (34.4% of scats) were also common. Certain foods, such as Lyme grass seed heads (Leymus arenarius), berries and marine algae, were consumed in relatively higher proportions, sometimes to the exclusion of others, both where and when they occurred most abundantly. The predominance of localized vegetation in scats suggests little movement among habitat types between feeding sessions. Unlike the case for plants, no spatial patterns were found for animal remains, likely due the animals' more vagile and ubiquitous distribution.ConclusionsOur results suggest that polar bears are foraging opportunistically in a manner consistent with maximizing intake while minimizing energy expenditure associated with movement. The frequent mixing of plant-based carbohydrate and animal-based protein could suggest use of a strategy that other Ursids employ to maximize weight gain. Further, consuming high rates of certain vegetation and land-based animals that may yield immediate energetic gains could, instead, provide other benefits such as fulfilling vitamin/mineral requirements, diluting toxins and assessing new foods for potential switching.

Dataset Information

Polar bear evolution is marked by rapid changes in gene copy number in response to dietary shift.

Publications

Polar bear evolution is marked by rapid changes in gene copy number in response to dietary shift.

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