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Bergeron LA, Besenbacher S, Zheng J, Li P, Bertelsen MF, Quintard B, Hoffman JI, Li Z, St Leger J, Shao C, Stiller J, Gilbert MTP, Schierup MH, Zhang G. Evolution of the germline mutation rate across vertebrates. Nature 2023; 615:285-291. [PMID: 36859541 PMCID: PMC9995274 DOI: 10.1038/s41586-023-05752-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 01/23/2023] [Indexed: 03/03/2023]
Abstract
The germline mutation rate determines the pace of genome evolution and is an evolving parameter itself1. However, little is known about what determines its evolution, as most studies of mutation rates have focused on single species with different methodologies2. Here we quantify germline mutation rates across vertebrates by sequencing and comparing the high-coverage genomes of 151 parent-offspring trios from 68 species of mammals, fishes, birds and reptiles. We show that the per-generation mutation rate varies among species by a factor of 40, with mutation rates being higher for males than for females in mammals and birds, but not in reptiles and fishes. The generation time, age at maturity and species-level fecundity are the key life-history traits affecting this variation among species. Furthermore, species with higher long-term effective population sizes tend to have lower mutation rates per generation, providing support for the drift barrier hypothesis3. The exceptionally high yearly mutation rates of domesticated animals, which have been continually selected on fecundity traits including shorter generation times, further support the importance of generation time in the evolution of mutation rates. Overall, our comparative analysis of pedigree-based mutation rates provides ecological insights on the mutation rate evolution in vertebrates.
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Affiliation(s)
- Lucie A Bergeron
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Søren Besenbacher
- Department of Molecular Medicine, Aarhus University, Aarhus, Denmark
| | - Jiao Zheng
- BGI-Shenzhen, Shenzhen, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | | | | | | | - Joseph I Hoffman
- Department of Animal Behaviour, Bielefeld University, Bielefeld, Germany
- British Antarctic Survey, High Cross, Cambridge, UK
| | - Zhipeng Li
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Judy St Leger
- Department of Biomedical Sciences, Cornell University, Ithaca, NY, USA
| | - Changwei Shao
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Josefin Stiller
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, NTNU, Trondheim, Norway
| | | | - Guojie Zhang
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
- Centre for Evolutionary & Organismal Biology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China.
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China.
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
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2
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Lynggaard C, Bertelsen MF, Jensen CV, Johnson MS, Frøslev TG, Olsen MT, Bohmann K. Airborne environmental DNA for terrestrial vertebrate community monitoring. Curr Biol 2022; 32:701-707.e5. [PMID: 34995490 PMCID: PMC8837273 DOI: 10.1016/j.cub.2021.12.014] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 10/11/2021] [Accepted: 12/07/2021] [Indexed: 12/15/2022]
Abstract
Biodiversity monitoring at the community scale is a critical element of assessing and studying species distributions, ecology, diversity, and movements, and it is key to understanding and tracking environmental and anthropogenic effects on natural ecosystems.1, 2, 3, 4 Vertebrates in terrestrial ecosystems are experiencing extinctions and declines in both population numbers and sizes due to increasing threats from human activities and environmental change.5, 6, 7, 8 Terrestrial vertebrate monitoring using existing methods is generally costly and laborious, and although environmental DNA (eDNA) is becoming the tool of choice to assess biodiversity, few sample types effectively capture terrestrial vertebrate diversity. We hypothesized that eDNA captured from air could allow straightforward collection and characterization of terrestrial vertebrate communities. We filtered air at three localities in the Copenhagen Zoo: a stable, outside between the outdoor enclosures, and in the Rainforest House. Through metabarcoding of airborne eDNA, we detected 49 vertebrate species spanning 26 orders and 37 families: 30 mammal, 13 bird, 4 fish, 1 amphibian, and 1 reptile species. These spanned animals kept at the zoo, species occurring in the zoo surroundings, and species used as feed in the zoo. The detected species comprise a range of taxonomic orders and families, sizes, behaviors, and abundances. We found shorter distance to the air sampling device and higher animal biomass to increase the probability of detection. We hereby show that airborne eDNA can offer a fundamentally new way of studying and monitoring terrestrial communities. 49 vertebrate species detected through metabarcoding of airborne eDNA from the zoo Detections included 30 mammal, 13 bird, 4 fish, 1 amphibian, and 1 reptile species 6 to 21 vertebrate species were detected per air filtering sample Shorter geographical distance and higher biomass increased probability of detection
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Affiliation(s)
- Christina Lynggaard
- Section for Evolutionary Genomics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark.
| | | | - Casper V Jensen
- Department of Chemistry, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Matthew S Johnson
- Department of Chemistry, University of Copenhagen, 2100 Copenhagen, Denmark; Airlabs Denmark, 2200 Copenhagen, Denmark
| | - Tobias Guldberg Frøslev
- Section for GeoGenetics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Morten Tange Olsen
- Section for Evolutionary Genomics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Kristine Bohmann
- Section for Evolutionary Genomics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark.
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3
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Natterson-Horowitz B, Baccouche BM, Mary J, Shivkumar T, Bertelsen MF, Aalkjær C, Smerup MH, Ajijola OA, Hadaya J, Wang T. Did giraffe cardiovascular evolution solve the problem of heart failure with preserved ejection fraction? Evol Med Public Health 2021; 9:248-255. [PMID: 34447575 PMCID: PMC8385250 DOI: 10.1093/emph/eoab016] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 06/04/2021] [Indexed: 11/18/2022]
Abstract
The evolved adaptations of other species can be a source of insight for novel biomedical innovation. Limitations of traditional animal models for the study of some pathologies are fueling efforts to find new approaches to biomedical investigation. One emerging approach recognizes the evolved adaptations in other species as possible solutions to human pathology. The giraffe heart, for example, appears resistant to pathology related to heart failure with preserved ejection fraction (HFpEF)—a leading form of hypertension-associated cardiovascular disease in humans. Here, we postulate that the physiological pressure-induced left ventricular thickening in giraffes does not result in the pathological cardiovascular changes observed in humans with hypertension. The mechanisms underlying this cardiovascular adaptation to high blood pressure in the giraffe may be a bioinspired roadmap for preventive and therapeutic strategies for human HFpEF.
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Affiliation(s)
- Barbara Natterson-Horowitz
- Department of Medicine, Harvard Medical School, Boston, MA, USA.,Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA.,Division of Cardiology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Basil M Baccouche
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA.,Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Jennifer Mary
- Zoobiquity Research Initiative at UCLA, Los Angeles, CA 90024, USA
| | | | | | | | - Morten H Smerup
- Department of Cardiothoracic Surgery, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Olujimi A Ajijola
- UCLA Cardiac Arrhythmia Center, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Joseph Hadaya
- UCLA Cardiac Arrhythmia Center, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.,Molecular, Cellular and Integrative Physiology Program, UCLA, Los Angeles, CA, USA
| | - Tobias Wang
- Zoophysiology, Department of Biology, Aarhus University, Aarhus, Denmark
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4
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Espinosa-Gongora C, Hansen MJ, Bertelsen MF, Bojesen AM. Polar bear-adapted Ursidibacter maritimus are remarkably conserved after generations in captivity. Mol Ecol 2021; 30:4497-4504. [PMID: 34250662 DOI: 10.1111/mec.16075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 06/15/2021] [Accepted: 07/07/2021] [Indexed: 10/20/2022]
Abstract
Most species in the bacterial family of Pasteurellaceae colonize one specific host species. Vertebrates of very different evolutionary descent including fish, turtles, marsupials, eutherians and birds are colonized by different members of Pasteurellaceae. This one-to-one microbial-host species partnership makes Pasteurellaceae species valuable candidates to study biodiversity, bacterial-host co-evolution and host adaptation, and their widespread distribution across vertebrates provide the possibility to collect a wide array of data, where wildlife species are essential. However, obtaining samples from wild animals comes with logistic, technical and ethical challenges, and previous microbiota studies have led to the presumption that captive animals are poor models for microbial studies in wildlife. Here, we show that colonization of polar bears by Ursidibacter maritimus is unaffected by factors related to captivity, reflecting a deep symbiotic bond to the host. We argue that the study of ecological and evolutionary principles in captive wildlife is possible for host-adapted taxa such as those in the Pasteurellaceae family. Moreover, studying captive, often trained animals protects wild populations from the stress associated with obtaining samples.
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Affiliation(s)
- Carmen Espinosa-Gongora
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Mie Johanne Hansen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark.,Center for Zoo and Wild Animal Health, Copenhagen Zoo, Frederiksberg, Denmark
| | - Mads Frost Bertelsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark.,Center for Zoo and Wild Animal Health, Copenhagen Zoo, Frederiksberg, Denmark
| | - Anders Miki Bojesen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
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5
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Perrin KL, Kristensen AT, Bertelsen MF, Denk D. Retrospective review of 27 European cases of fatal elephant endotheliotropic herpesvirus-haemorrhagic disease reveals evidence of disseminated intravascular coagulation. Sci Rep 2021; 11:14173. [PMID: 34238966 PMCID: PMC8266883 DOI: 10.1038/s41598-021-93478-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 06/25/2021] [Indexed: 02/06/2023] Open
Abstract
Elephant endotheliotropic herpesvirus haemorrhagic disease (EEHV-HD) is widely acknowledged as the most common cause of mortality in young Asian elephants (Elephas maximus) in captivity. The objective of the current study was to perform a blinded, retrospective pathology review of European EEHV-HD fatalities, constituting the largest systematic assessment of EEHV-HD pathology to date. Findings between viral genotypes were compared with the aim to investigate if disseminated intravascular coagulation (DIC) could be substantiated as a significant complicating factor, thereby increasing the understanding of disease pathophysiology. Immunohistochemical staining confirmed endothelial cell (EC) damage and the presence of EC intranuclear inclusion bodies, demonstrating a direct viral cytopathic effect. Microthrombi were observed in 63% of cases in several organs, including lungs, which, together with widespread haemorrhage and thrombocytopenia reported in EEHV-HD case reports, supports the presence of overt DIC as a serious haemostatic complication of active EEHV infection. Death was attributed to widespread vascular damage with multi-organ dysfunction, including severe acute myocardial haemorrhage and subsequent cardiac failure. Systemic inflammation observed in the absence of bacterial infection may be caused by cytokine release syndrome. Findings reinforce the necessity to investigate cytokine responses and haemostatic status during symptomatic and asymptomatic EEHV viraemia, to potentially support the use of anti-inflammatory treatment in conjunction with anti-viral therapy and cardiovascular support.
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Affiliation(s)
- K L Perrin
- Center for Zoo and Wild Animal Health, Copenhagen Zoo, Roskildevej 38, 2000, Frederiksberg, Denmark.
- The Department of Veterinary Clinical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Dyrlægevej 16, 1870, Frederiksberg, Denmark.
| | - A T Kristensen
- The Department of Veterinary Clinical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Dyrlægevej 16, 1870, Frederiksberg, Denmark
| | - M F Bertelsen
- Center for Zoo and Wild Animal Health, Copenhagen Zoo, Roskildevej 38, 2000, Frederiksberg, Denmark
| | - D Denk
- International Zoo Veterinary Group, Station House, Parkwood Street, Keighley, BD21 4NQ, UK
- Institute for Animal Pathology, Ludwig-Maximilians-University, Veterinärstr. 13, 80539, Munich, Germany
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6
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Greunz EM, Limón D, Bertelsen MF. Alfaxalone Sedation in Black-cheeked Lovebirds ( Agapornis nigrigenis) for Non-invasive Procedures. J Avian Med Surg 2021; 35:161-166. [PMID: 34256546 DOI: 10.1647/19-00015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Alfaxalone is an injectable neuroactive steroid anesthetic that is becoming more widely used as a sedative in a wide range of animals. The purpose of this study was to evaluate the efficacy of this drug for sedation during handling and noninvasive medical procedures in black-cheeked lovebirds (Agapornis nigrigenis). Based on a pilot study that showed that 5 mg/kg alfaxalone was inadequate, and that 20 mg/kg resulted in respiratory arrest in 1 bird, the effects of 12.6 ± 0.9 mg/kg alfaxalone administered subcutaneously was investigated in 9 birds. Despite minor movements and twitching, it was possible to handle all birds and to perform positioning for a ventrodorsal radiograph. A loss of reaction to noxious stimuli was not achieved during sedation. Times from injection to initial effect (mean ± SD) was 93 ± 48 seconds; to recumbency, 209 ± 70 seconds; to first handling for positioning the bird in lateral recumbency, 251 ± 68 seconds; to initial righting effort, 55 ± 8 minutes; and to perching for a minimum of 20 seconds, 76 ± 7 minutes. Median respiration rates between 5 to 45 minutes were 36 to 40 breaths/min; apnea was not noted in any bird. Birds received 0.5 L of oxygen/min via face mask. Oxygen saturation (SpO2) and pulse rate were measured via pulse oximetry in 8 birds continuously from 10 to 30 minutes, SpO2 values remained above 90%. During sedation, mean pulse rate decreased significantly over time (P = .007; 10 minutes = 409 ± 81 beats/min; 30 minutes = 324 ± 25 beats/min). The majority of birds had rough inductions and recoveries, which could have been minimized if birds had been placed in a more confined space. In summary, 12.6 mg/kg alfaxalone provided nearly 1 hour of stable, nonanalgesic sedation appropriate for noninvasive procedures in black-cheeked lovebirds.
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Affiliation(s)
- Eva Maria Greunz
- Center for Zoo and Wild Animal Health, Copenhagen Zoo, 2000 Frederiksberg, Denmark,
| | - Dafne Limón
- Department of Ethology and Wildlife, Veterinary College, National Autonomous University of Mexico City, 04510 Mexico City, Mexico
| | - Mads Frost Bertelsen
- Center for Zoo and Wild Animal Health, Copenhagen Zoo, 2000 Frederiksberg, Denmark
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7
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Li X, Trivedi U, Brejnrod AD, Vestergaard G, Mortensen MS, Bertelsen MF, Sørensen SJ. The microbiome of captive hamadryas baboons. Anim Microbiome 2020; 2:25. [PMID: 33499948 PMCID: PMC7807707 DOI: 10.1186/s42523-020-00040-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 06/30/2020] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND The hamadryas baboon (Papio hamadryas) is a highly social primate that lives in complex multilevel societies exhibiting a wide range of group behaviors akin to humans. In contrast to the widely studied human microbiome, there is a paucity of information on the host-associated microbiomes of nonhuman primates (NHPs). Here, our goal was to understand the microbial composition throughout different body sites of cohabiting baboons. RESULTS We analyzed 170 oral, oropharyngeal, cervical, uterine, vaginal, nasal and rectal samples from 16 hamadryas baboons via 16S rRNA gene sequencing. Additionally, raw Miseq sequencing data from 1041 comparable publicly available samples from the human oral cavity, gut and vagina were reanalyzed using the same pipeline. We compared the baboon and human microbiome of the oral cavity, gut and vagina, showing that the baboon microbiome is distinct from the human. Baboon cohabitants share similar microbial profiles in their cervix, uterus, vagina, and gut. The oral cavity, gut and vagina shared more bacterial amplicon sequence variants (ASVs) in group living baboons than in humans. The shared ASVs had significantly positive correlations between most body sites, suggesting a potential bacterial exchange throughout the body. No significant differences in gut microbiome composition were detected within the maternity line and between maternity lines, suggesting that the offspring gut microbiota is shaped primarily through bacterial exchange among cohabitants. Finally, Lactobacillus was not so predominant in baboon vagina as in the human vagina but was the most abundant genus in the baboon gut. CONCLUSIONS This study is the first to provide comprehensive analyses of the baboon microbiota across different body sites. We contrast this to human body sites and find substantially different microbiomes. This group of cohabitating baboons generally showed higher microbial diversity and remarkable similarities between body sites than were observed in humans. These data and findings from one group of baboons can form the basis of future microbiome studies in baboons and be used as a reference in research where the microbiome is expected to impact human modeling with baboons.
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Affiliation(s)
- Xuanji Li
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Urvish Trivedi
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Asker Daniel Brejnrod
- Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, University of Copenhagen, Copenhagen, Denmark
| | - Gisle Vestergaard
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Martin Steen Mortensen
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Mads Frost Bertelsen
- Center for Zoo and Wild Animal Health, Copenhagen Zoo, 2000, Frederiksberg, Denmark
| | - Søren Johannes Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100, Copenhagen, Denmark.
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8
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Da Silva MAO, Gade JT, Damsgaard C, Wang T, Heegaard S, Bertelsen MF. Morphology and evolution of the snake cornea. J Morphol 2019; 281:240-249. [PMID: 31876020 DOI: 10.1002/jmor.21094] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 12/06/2019] [Accepted: 12/15/2019] [Indexed: 11/11/2022]
Abstract
To investigate whether the thickness of the cornea in snakes correlates with overall anatomy, habitat or daily activity pattern, we measured corneal thickness using optical coherence tomography scanning in 44 species from 14 families (214 specimens) in the collection at the Natural History Museum (Denmark). Specifically, we analyzed whether the thickness of the cornea varies among species in absolute terms and relative to morphometrics, such as body length, spectacle diameter, and spectacle thickness. Furthermore, we examined whether corneal thickness reflects adaptation to different habitats and/or daily activity patterns. The snakes were defined as arboreal (n = 8), terrestrial (n = 22), fossorial (n = 7), and aquatic (n = 7); 14 species were classified as diurnal and 30 as nocturnal. We reveal that the interspecific variation in corneal thickness is largely explained by differences in body size, but find a tendency towards thicker corneas in diurnal (313 ± 227 μm) compared to nocturnal species (205 ± 169 μm). Furthermore, arboreal snakes had the thickest corneas and fossorial snakes the thinnest. Our study shows that body length, habitat, and daily activity pattern could explain the interspecific variation in corneal morphology among snakes. This study provides a quantitative analysis of the evolution of the corneal morphology in snakes, and it presents baseline values of corneal thickness of multiple snake species. We speculate that the cornea likely plays a role in snake vision, despite the fact that results from previous studies suggest that the cornea in snakes is not relevant for vision (Sivak, Vision Research, 1977, 17, 293-298).
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Affiliation(s)
| | - Jacob Thorup Gade
- Center for Zoo and Wild Animal Health, Copenhagen Zoo, Frederiksberg, Copenhagen, Denmark
| | - Christian Damsgaard
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Tobias Wang
- Zoophysiology Section, Department of Biosciences, Aarhus University, Aarhus C, Denmark
| | - Steffen Heegaard
- Eye Pathology Section, Department of Pathology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark.,Department of Ophthalmology, Rigshospitalet, University of Copenhagen, Glostrup, Denmark
| | - Mads Frost Bertelsen
- Center for Zoo and Wild Animal Health, Copenhagen Zoo, Frederiksberg, Copenhagen, Denmark
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9
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Lopes-Marques M, Machado AM, Alves LQ, Fonseca MM, Barbosa S, Sinding MHS, Rasmussen MH, Iversen MR, Frost Bertelsen M, Campos PF, da Fonseca R, Ruivo R, Castro LFC. Complete Inactivation of Sebum-Producing Genes Parallels the Loss of Sebaceous Glands in Cetacea. Mol Biol Evol 2019; 36:1270-1280. [PMID: 30895322 PMCID: PMC6526905 DOI: 10.1093/molbev/msz068] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Genomes are dynamic biological units, with processes of gene duplication and loss triggering evolutionary novelty. The mammalian skin provides a remarkable case study on the occurrence of adaptive morphological innovations. Skin sebaceous glands (SGs), for instance, emerged in the ancestor of mammals serving pivotal roles, such as lubrication, waterproofing, immunity, and thermoregulation, through the secretion of sebum, a complex mixture of various neutral lipids such as triacylglycerol, free fatty acids, wax esters, cholesterol, and squalene. Remarkably, SGs are absent in a few mammalian lineages, including the iconic Cetacea. We investigated the evolution of the key molecular components responsible for skin sebum production: Dgat2l6, Awat1, Awat2, Elovl3, Mogat3, and Fabp9. We show that all analyzed genes have been rendered nonfunctional in Cetacea species (toothed and baleen whales). Transcriptomic analysis, including a novel skin transcriptome from blue whale, supports gene inactivation. The conserved mutational pattern found in most analyzed genes, indicates that pseudogenization events took place prior to the diversification of modern Cetacea lineages. Genome and skin transcriptome analysis of the common hippopotamus highlighted the convergent loss of a subset of sebum-producing genes, notably Awat1 and Mogat3. Partial loss profiles were also detected in non-Cetacea aquatic mammals, such as the Florida manatee, and in terrestrial mammals displaying specialized skin phenotypes such as the African elephant, white rhinoceros and pig. Our findings reveal a unique landscape of “gene vestiges” in the Cetacea sebum-producing compartment, with limited gene loss observed in other mammalian lineages: suggestive of specific adaptations or specializations of skin lipids.
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Affiliation(s)
- Mónica Lopes-Marques
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, U. Porto-University of Porto, Porto, Portugal
| | - André M Machado
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, U. Porto-University of Porto, Porto, Portugal
| | - Luís Q Alves
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, U. Porto-University of Porto, Porto, Portugal.,Department of Biology, Faculty of Sciences, U. Porto-University of Porto, Porto, Portugal
| | - Miguel M Fonseca
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, U. Porto-University of Porto, Porto, Portugal
| | - Susana Barbosa
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, U. Porto-University of Porto, Porto, Portugal
| | | | | | | | | | - Paula F Campos
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, U. Porto-University of Porto, Porto, Portugal.,Department of Biology, The Bioinformatics Centre, University of Copenhagen, Copenhagen, Denmark
| | - Rute da Fonseca
- Department of Biology, The Bioinformatics Centre, University of Copenhagen, Copenhagen, Denmark.,Center for Macroecology, Evolution, and Climate, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Raquel Ruivo
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, U. Porto-University of Porto, Porto, Portugal
| | - L Filipe C Castro
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, U. Porto-University of Porto, Porto, Portugal.,Department of Biology, Faculty of Sciences, U. Porto-University of Porto, Porto, Portugal
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10
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Greunz EM, Williams C, Ringgaard S, Hansen K, Wang T, Bertelsen MF. Elimination of Intracardiac Shunting Provides Stable Gas Anesthesia in Tortoises. Sci Rep 2018; 8:17124. [PMID: 30459408 PMCID: PMC6244002 DOI: 10.1038/s41598-018-35588-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 11/08/2018] [Indexed: 11/08/2022] Open
Abstract
Inhalant anesthesia is challenging in chelonians due to a great capacity for breath-holding and an incomplete separation of the cardiac ventricle. Deoxygenated blood can recirculate back into systemic circulation by bypassing the lung in a process referred to as intracardiac right to left (R-L) shunting. Via electrocardiogram gated magnetic resonance imaging, a novel modality to investigate arterial flows in reptiles, intracardiac shunting and its elimination via atropine during gas anesthesia in tortoises (Chelonoidis carbonaria) was demonstrated. The great vessels of the heart were visualized confirming that after shunt-elimination, the flow (mean ± sd) in the pulmonary arteries increased significantly (54.6 ± 9.5 mL min−1 kg−1 vs 10.8 ± 3.4 mL min−1 kg−1; P < 0.008). Consequently, animals required significantly lower concentrations of inhaled anesthetics to maintain a stable anesthesia. To that end, the minimum anesthetic concentration (MAC) of isoflurane needed to maintain surgical anesthesia was measured. A significantly lower MAC was found after administration of atropine (mean MAC ± sd 2.2 ± 0.3% vs 3.2 ± 0.4%; P < 0.002). Previously, MAC has been indeterminable in chelonians likely due to intracardiac shunting, so this report constitutes the first MAC study performed in a tortoise.
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Affiliation(s)
- Eva Maria Greunz
- Center for Zoo and Wild Animal Health, Copenhagen Zoo, Roskildevej 38, 2000, Frederiksberg, Denmark.
| | - Catherine Williams
- Center for Zoo and Wild Animal Health, Copenhagen Zoo, Roskildevej 38, 2000, Frederiksberg, Denmark.,Section of Zoophysiology, Department of Bioscience, Aarhus University, 8000, Aarhus C, Denmark
| | - Steffen Ringgaard
- MR Research Center, Department of Clinical Medicine, Aarhus University Hospital, 8200, Aarhus N, Denmark
| | - Kasper Hansen
- Section of Zoophysiology, Department of Bioscience, Aarhus University, 8000, Aarhus C, Denmark
| | - Tobias Wang
- Section of Zoophysiology, Department of Bioscience, Aarhus University, 8000, Aarhus C, Denmark.,Aarhus Institute of Advanced Sciences, Aarhus University, 8000, Aarhus C, Denmark
| | - Mads Frost Bertelsen
- Center for Zoo and Wild Animal Health, Copenhagen Zoo, Roskildevej 38, 2000, Frederiksberg, Denmark
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11
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Schnell IB, Bohmann K, Schultze SE, Richter SR, Murray DC, Sinding MHS, Bass D, Cadle JE, Campbell MJ, Dolch R, Edwards DP, Gray TNE, Hansen T, Hoa ANQ, Noer CL, Heise-Pavlov S, Sander Pedersen AF, Ramamonjisoa JC, Siddall ME, Tilker A, Traeholt C, Wilkinson N, Woodcock P, Yu DW, Bertelsen MF, Bunce M, Gilbert MTP. Debugging diversity - a pan-continental exploration of the potential of terrestrial blood-feeding leeches as a vertebrate monitoring tool. Mol Ecol Resour 2018; 18:1282-1298. [PMID: 29877042 DOI: 10.1111/1755-0998.12912] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 04/09/2018] [Accepted: 04/18/2018] [Indexed: 01/31/2023]
Abstract
The use of environmental DNA (eDNA) has become an applicable noninvasive tool with which to obtain information about biodiversity. A subdiscipline of eDNA is iDNA (invertebrate-derived DNA), where genetic material ingested by invertebrates is used to characterize the biodiversity of the species that served as hosts. While promising, these techniques are still in their infancy, as they have only been explored on limited numbers of samples from only a single or a few different locations. In this study, we investigate the suitability of iDNA extracted from more than 3,000 haematophagous terrestrial leeches as a tool for detecting a wide range of terrestrial vertebrates across five different geographical regions on three different continents. These regions cover almost the full geographical range of haematophagous terrestrial leeches, thus representing all parts of the world where this method might apply. We identify host taxa through metabarcoding coupled with high-throughput sequencing on Illumina and IonTorrent sequencing platforms to decrease economic costs and workload and thereby make the approach attractive for practitioners in conservation management. We identified hosts in four different taxonomic vertebrate classes: mammals, birds, reptiles and amphibians, belonging to at least 42 different taxonomic families. We find that vertebrate blood ingested by haematophagous terrestrial leeches throughout their distribution is a viable source of DNA with which to examine a wide range of vertebrates. Thus, this study provides encouraging support for the potential of haematophagous terrestrial leeches as a tool for detecting and monitoring terrestrial vertebrate biodiversity.
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Affiliation(s)
- Ida Baerholm Schnell
- Section for EvoGenomics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,Center for Zoo and Wild Animal Health, Copenhagen Zoo, Frederiksberg, Denmark
| | - Kristine Bohmann
- Section for EvoGenomics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Sebastian E Schultze
- Section for EvoGenomics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Stine R Richter
- Section for EvoGenomics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Dáithí C Murray
- Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, Perth, Western Australia, Australia
| | - Mikkel-Holger S Sinding
- Section for EvoGenomics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,Greenland Institute of Natural Resources, Nuuk, Greenland
| | - David Bass
- Department of Life Sciences, The Natural History Museum, London, UK.,Cefas, Weymouth, Dorset, UK
| | - John E Cadle
- Centre ValBio, Ranomafana, Ifanadiana, Fianarantsoa, Madagascar
| | - Mason J Campbell
- Centre for Tropical Environmental and Sustainability Science (TESS) and College of Science and Engineering, James Cook University, Cairns, Queensland, Australia
| | | | - David P Edwards
- Centre for Tropical Environmental and Sustainability Science (TESS) and College of Science and Engineering, James Cook University, Cairns, Queensland, Australia.,Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | | | - Teis Hansen
- Section for EvoGenomics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | | | - Christina Lehmkuhl Noer
- Section for EvoGenomics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,Center for Zoo and Wild Animal Health, Copenhagen Zoo, Frederiksberg, Denmark
| | - Sigrid Heise-Pavlov
- Centre for Rainforest Studies at the School for Field Studies, Yungaburra, Queensland, Australia
| | - Adam F Sander Pedersen
- Department of Immunology and Microbiology, Centre for Medical Parasitology, University of Copenhagen, Copenhagen, Denmark
| | | | - Mark E Siddall
- Division of Invertebrate Zoology, Sackler Institute of Comparative Genomics, American Museum of Natural History, New York, New York
| | - Andrew Tilker
- Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany.,Global Wildlife Conservation, Austin, Texas
| | - Carl Traeholt
- Center for Zoo and Wild Animal Health, Copenhagen Zoo, Frederiksberg, Denmark
| | | | | | - Douglas W Yu
- School of Biological Sciences, University of East Anglia, Norwich, UK.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | | | - Michael Bunce
- Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, Perth, Western Australia, Australia
| | - M Thomas P Gilbert
- Section for EvoGenomics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, Perth, Western Australia, Australia.,NTNU University Museum, Trondheim, Norway
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12
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Renaud G, Petersen B, Seguin-Orlando A, Bertelsen MF, Waller A, Newton R, Paillot R, Bryant N, Vaudin M, Librado P, Orlando L. Improved de novo genomic assembly for the domestic donkey. Sci Adv 2018; 4:eaaq0392. [PMID: 29740610 PMCID: PMC5938232 DOI: 10.1126/sciadv.aaq0392] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 02/14/2018] [Indexed: 06/01/2023]
Abstract
Donkeys and horses share a common ancestor dating back to about 4 million years ago. Although a high-quality genome assembly at the chromosomal level is available for the horse, current assemblies available for the donkey are limited to moderately sized scaffolds. The absence of a better-quality assembly for the donkey has hampered studies involving the characterization of patterns of genetic variation at the genome-wide scale. These range from the application of genomic tools to selective breeding and conservation to the more fundamental characterization of the genomic loci underlying speciation and domestication. We present a new high-quality donkey genome assembly obtained using the Chicago HiRise assembly technology, providing scaffolds of subchromosomal size. We make use of this new assembly to obtain more accurate measures of heterozygosity for equine species other than the horse, both genome-wide and locally, and to detect runs of homozygosity potentially pertaining to positive selection in domestic donkeys. Finally, this new assembly allowed us to identify fine-scale chromosomal rearrangements between the horse and the donkey that likely played an active role in their divergence and, ultimately, speciation.
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Affiliation(s)
- Gabriel Renaud
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
| | - Bent Petersen
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Kongens Lyngby, Denmark
- Centre of Excellence for Omics-Driven Computational Biodiscovery, Faculty of Applied Sciences, Asian Institute of Medicine, Science and Technology, Kedah, Malaysia
| | - Andaine Seguin-Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
- National High-Throughput DNA Sequencing Center, Copenhagen, Denmark
- Laboratoire d’Anthropobiologie Moléculaire et d’Imagerie de Synthése UMR 5288, Université de Toulouse, CNRS, Université Paul Sabatier, 31000 Toulouse, France
| | - Mads Frost Bertelsen
- Center for Zoo and Wild Animal Health, Copenhagen Zoo, 2000 Frederiksberg, Denmark
| | - Andrew Waller
- Animal Health Trust, Lanwades Park, Kentford, Newmarket, Suffolk CB8 7UU, UK
| | - Richard Newton
- Animal Health Trust, Lanwades Park, Kentford, Newmarket, Suffolk CB8 7UU, UK
| | - Romain Paillot
- Animal Health Trust, Lanwades Park, Kentford, Newmarket, Suffolk CB8 7UU, UK
| | - Neil Bryant
- Animal Health Trust, Lanwades Park, Kentford, Newmarket, Suffolk CB8 7UU, UK
| | - Mark Vaudin
- Animal Health Trust, Lanwades Park, Kentford, Newmarket, Suffolk CB8 7UU, UK
| | - Pablo Librado
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
- Laboratoire d’Anthropobiologie Moléculaire et d’Imagerie de Synthése UMR 5288, Université de Toulouse, CNRS, Université Paul Sabatier, 31000 Toulouse, France
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
- Laboratoire d’Anthropobiologie Moléculaire et d’Imagerie de Synthése UMR 5288, Université de Toulouse, CNRS, Université Paul Sabatier, 31000 Toulouse, France
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13
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Malte CL, Bundgaard J, Jensen MS, Bertelsen MF, Wang T. The effects of morphine on gas exchange, ventilation pattern and ventilatory responses to hypercapnia and hypoxia in dwarf caiman (Paleosuchus palpebrosus). Comp Biochem Physiol A Mol Integr Physiol 2018; 222:60-65. [PMID: 29555580 DOI: 10.1016/j.cbpa.2018.03.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 01/25/2017] [Accepted: 03/13/2018] [Indexed: 11/28/2022]
Abstract
Morphine and other opioids cause respiratory depression in high doses and lower the ventilatory responses to hypoxia and hypercapnia in mammals. Recent studies indicate that turtles respond similarly, but although they are used routinely for post-surgical analgesia, little is known about the physiological effects of opioids in reptiles. We therefore investigated the effects of morphine (10 and 20 mg kg-1) on gas exchange and ventilation in six dwarf caiman (Paleosuchus palpebrosus) using pneumotachography in a crossover design. Intraperitoneal injections of morphine changed the ventilation pattern from a typical intermittent/periodic pattern with a few or several breaths in ventilatory bouts to single breaths and prolonged the apnoea, such that respiratory frequency was depressed, while tidal volume was elevated. Furthermore, the duration of inspiration and especially expiration was prolonged. The resulting decrease in minute ventilation was attended by a lowering of the respiratory exchange ratio (RER) (especially for 20 mg kg-1 dose) indicating CO2 retention with a long time constant for approaching the new steady state. The changes in ventilation pattern and gas exchange reached a new stable level approximately 3 h after the morphine injection and did not significantly affect steady state O2 uptake, i.e. O2 consumption. As expected, the ventilatory response to 5% O2 was lower in morphine-treated caimans, but minute ventilation upon exposure to 2% CO2 did not differ significantly different from control animals.
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Affiliation(s)
| | - Jonas Bundgaard
- Zoophysiology, Department of Bioscience, Aarhus University, Denmark
| | | | - Mads Frost Bertelsen
- Centre for Zoo and Wildlife Health, Copenhagen Zoo, Roskildevej 32, 2000 Frederiksberg, Denmark
| | - Tobias Wang
- Zoophysiology, Department of Bioscience, Aarhus University, Denmark
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14
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Da Silva MAO, Heegaard S, Wang T, Gade JT, Damsgaard C, Bertelsen MF. Morphology of the snake spectacle reflects its evolutionary adaptation and development. BMC Vet Res 2017; 13:258. [PMID: 28821248 PMCID: PMC5562989 DOI: 10.1186/s12917-017-1193-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Accepted: 08/11/2017] [Indexed: 11/10/2022] Open
Abstract
Background Covering the eye of all snakes is a transparent integumental structure known as the spectacle. In order to determine variations in spectacle thickness among species, the spectacles of 217 alcohol-preserved museum specimens of 44 species belonging to 14 different families underwent optical coherence tomography (OCT) to measure spectacular thickness. Multivariable analyses were made to determine whether family, activity period (diurnal/nocturnal) and habitat (arboreal/terrestrial/fossorial/aquatic) influenced spectacle thickness. Results The thinnest spectacles in absolute terms were found in the Usambara bush viper (Viperidae) with a thickness of 74 ± 9 μm and the absolute thickest spectacle was found in the red-tailed pipe snake (Cylindrophiidae) which had a spectacle thickness of 244 ± 57 μm. Fossorial and aquatic snakes had significantly thicker spectacles than arboreal and terrestrial snakes. When spectacle thickness was correlated to eye size (horizontal spectacle diameter), Gray’s earth snake (Uropeltidae) had the lowest ratio (1:7) and the cottonmouth (Viperidae) had the highest ratio (1:65). Multivariable and phylogenetic analyses showed that spectacular thickness could be predicted by taxonomic family and habitat, but not activity period. Conclusion This phylogenetically broad systematic study of the thickness of the snake spectacle showed that spectacular thickness varies greatly across snake species and may reflect evolutionary adaptation and development.
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Affiliation(s)
- Mari-Ann Otkjaer Da Silva
- Centre for Zoo and Wild Animal Health, Copenhagen Zoo, Roskildevej 38, DK-1870, Frederiksberg, Denmark.,Eye Pathology Section, Department of Pathology, Rigshospitalet, University of Copenhagen, Frederik V's Vej 11, DK-2100, Copenhagen, Denmark
| | - Steffen Heegaard
- Eye Pathology Section, Department of Pathology, Rigshospitalet, University of Copenhagen, Frederik V's Vej 11, DK-2100, Copenhagen, Denmark.,Department of Ophthalmology, Rigshospitalet, University of Copenhagen, Nordre Ringvej 57, DK-2600, Glostrup, Denmark
| | - Tobias Wang
- Zoophysiology, Department of Biosciences, Aarhus University, DK-8000, Aarhus C, Denmark
| | - Jacob Thorup Gade
- Centre for Zoo and Wild Animal Health, Copenhagen Zoo, Roskildevej 38, DK-1870, Frederiksberg, Denmark
| | - Christian Damsgaard
- Zoophysiology, Department of Biosciences, Aarhus University, DK-8000, Aarhus C, Denmark
| | - Mads Frost Bertelsen
- Centre for Zoo and Wild Animal Health, Copenhagen Zoo, Roskildevej 38, DK-1870, Frederiksberg, Denmark.
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15
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Bisgaard M, Xin D, Bertelsen MF, Bojesen AM, Christensen H. Prevalence of Taxa of Pasteurellaceae Among Populations of Healthy Captive Psittacine Birds. Avian Dis 2017; 61:102-106. [PMID: 28301245 DOI: 10.1637/11522-103016-reg] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Sixty-two strains of Pasteurellaceae-like bacteria were isolated from the tracheas of 87 clinically healthy psittacine birds in two Danish zoos. The isolates were identified by a combination of rpoB and 16S rRNA gene sequencing and by matrix-assisted laser desorption-ionization time of flight. Twenty-eight strains belonged to the genus Volucribacter or were related to this genus and to the unnamed taxon 34 of Bisgaard, and 28 strains were related to the unnamed taxon 44 of Bisgaard. Four strains were identified as Pasteurella multocida , two isolates were classified with the related taxon 45 of Bisgaard, and a single isolate was classified as Pasteurella sp. The investigation documented an unrecognized reservoir of rarely reported and unclassified or unnamed species of Pasteurellaceae-like bacteria in psittacine birds. The results were in accordance with a recent report on isolation of Pasteurellaceae from diseased psittacine birds, and the investigation documented that the same taxa of Pasteurellaceae-like bacteria can be isolated from apparently healthy birds as well as from diseased birds.
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Affiliation(s)
| | - Di Xin
- B School of Life Science, Beijing Institute of Technology, Beijing 100081, People's Republic of China.,C Department of Veterinary Disease Biology, University of Copenhagen, Stigbøjlen 4, DK-1870 Frederiksberg C, Denmark
| | - M F Bertelsen
- C Department of Veterinary Disease Biology, University of Copenhagen, Stigbøjlen 4, DK-1870 Frederiksberg C, Denmark.,D Center for Zoo and Wild Animal Health, Copenhagen Zoo, Roskildevej 38, DK-2000 Frederiksberg, Denmark
| | - A M Bojesen
- C Department of Veterinary Disease Biology, University of Copenhagen, Stigbøjlen 4, DK-1870 Frederiksberg C, Denmark
| | - H Christensen
- C Department of Veterinary Disease Biology, University of Copenhagen, Stigbøjlen 4, DK-1870 Frederiksberg C, Denmark
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16
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Vanmechelen B, Bertelsen MF, Rector A, Van den Oord JJ, Laenen L, Vergote V, Maes P. Identification of a novel species of papillomavirus in giraffe lesions using nanopore sequencing. Vet Microbiol 2016; 201:26-31. [PMID: 28284619 DOI: 10.1016/j.vetmic.2016.12.035] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 12/23/2016] [Accepted: 12/27/2016] [Indexed: 11/26/2022]
Abstract
Papillomaviridae form a large family of viruses that are known to infect a variety of vertebrates, including mammals, reptiles, birds and fish. Infections usually give rise to minor skin lesions but can in some cases lead to the development of malignant neoplasia. In this study, we identified a novel species of papillomavirus (PV), isolated from warts of four giraffes (Giraffa camelopardalis). The sequence of the L1 gene was determined and found to be identical for all isolates. Using nanopore sequencing, the full sequence of the PV genome could be determined. The coding region of the genome was found to contain seven open reading frames (ORF), encoding the early proteins E1, E2 and E5-E7 as well as the late proteins L1 and L2. In addition to these ORFs, a region located within the E2 gene is thought, based on sequence similarities to other papillomaviruses, to encode an E4 protein, although no start codon could be identified. Based on the sequence of the L1 gene, this novel PV was found to be most similar to Capreolus capreolus papillomavirus 1 (CcaPV1), with 67.96% nucleotide identity. We therefore suggest that the virus identified here is given the name Giraffa camelopardalis papillomavirus 1 (GcPV1) and is classified as a novel species within the genus Deltapapillomavirus, in line with the current guidelines for the nomenclature and classification of PVs.
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Affiliation(s)
- Bert Vanmechelen
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Laboratory of Clinical Virology, Rega Institute for Medical Research, Herestraat 49/Box 1040, BE3000 Leuven, Belgium.
| | - Mads Frost Bertelsen
- Center for Zoo and Wildlife Health, Copenhagen Zoo, Roskildevej 38, DK-2000 Frederiksberg, Denmark
| | - Annabel Rector
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Laboratory of Clinical Virology, Rega Institute for Medical Research, Herestraat 49/Box 1040, BE3000 Leuven, Belgium
| | - Joost J Van den Oord
- KU Leuven - University Hospitals Leuven, Department of Pathology, Laboratory Translational Cell and Tissue Research, Herestraat 49, BE3000 Leuven, Belgium
| | - Lies Laenen
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Laboratory of Clinical Virology, Rega Institute for Medical Research, Herestraat 49/Box 1040, BE3000 Leuven, Belgium
| | - Valentijn Vergote
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Laboratory of Clinical Virology, Rega Institute for Medical Research, Herestraat 49/Box 1040, BE3000 Leuven, Belgium
| | - Piet Maes
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Laboratory of Clinical Virology, Rega Institute for Medical Research, Herestraat 49/Box 1040, BE3000 Leuven, Belgium.
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17
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Gutman N, Hansen MJ, Bertelsen MF, Bojesen AM. Pasteurellaceae bacteria from the oral cavity of Tasmanian devils (Sarcophilus Harrisii) show high minimum inhibitory concentration values towards aminoglycosides and clindamycin. Lett Appl Microbiol 2016; 62:237-42. [PMID: 26744057 DOI: 10.1111/lam.12545] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 01/04/2016] [Accepted: 01/05/2016] [Indexed: 11/28/2022]
Abstract
UNLABELLED Threatened by Devil Facial Tumor Disease, the Tasmanian devil populations are vulnerable and decreasing. Additionally, the devils' biting behaviour elevates their risk of acquiring bite wound infections caused by members of the bacterial Pasteurellaceae family that are natural inhabitants of the oral microbiota. In medical management of such bite wounds, antimicrobial susceptibility profiles are crucial. Prior to this investigation, no available data on minimal inhibitory concentration (MIC) values existed. A total of 26 isolates obtained from the oral cavity of 26 healthy Tasmanian devils were tested for their antimicrobial susceptibility by broth micro dilution. Most prominently, high MIC values for clindamycin (≥4 μg ml(-1) ), gentamicin (≥8 μg ml(-1) ) and amikacin (≥32 μg ml(-1) ), were observed for 92, 77 and 73% of the strains tested respectively. This study may be used as a guideline for antimicrobial therapy against bite wound infections caused by Pasteurellaceae originating from the oral cavity of Tasmanian devils. SIGNIFICANCE AND IMPACT OF THE STUDY Tasmanian devils' aggressive behaviour makes bite wounds in fellow devils and human caretakers a common entity. Pasteurellaceae bacteria are common inhabitants of the oral microbiota of Tasmanian devils and a likely cause of bite wound infections. Here, for the first time, we report antimicrobial sensitivity profiles from a broad collection of Pasteurellaceae isolates obtained from the oral cavity of Tasmanian devils. Low MIC values were observed for the majority of the 22 antimicrobial agents included, yet nearly all strains were tolerant to clindamycin and the aminoglycosides. The work can serve as a guide for clinicians involved in treatment of bite wounds inflicted by devils in animals and humans.
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Affiliation(s)
- N Gutman
- Department of Veterinary Disease Biology, Faculty of Health and Medicine, University of Copenhagen, Frederiksberg C, Denmark
| | - M J Hansen
- Department of Veterinary Disease Biology, Faculty of Health and Medicine, University of Copenhagen, Frederiksberg C, Denmark.,Centre for Zoo and Wild Animal Health, Copenhagen Zoo, Frederiksberg, Denmark.,Institute for Marine and Antarctic Studies, University of Tasmania, Launceston, TAS, Australia
| | - M F Bertelsen
- Centre for Zoo and Wild Animal Health, Copenhagen Zoo, Frederiksberg, Denmark
| | - A M Bojesen
- Department of Veterinary Disease Biology, Faculty of Health and Medicine, University of Copenhagen, Frederiksberg C, Denmark
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18
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Johanne Hansen M, Strøm Braaten M, Miki Bojesen A, Christensen H, Sonne C, Dietz R, Frost Bertelsen M. Ursidibacter maritimus gen. nov., sp. nov. and Ursidibacter arcticus sp. nov., two new members of the family Pasteurellaceae isolated from the oral cavity of bears. Int J Syst Evol Microbiol 2015. [DOI: 10.1099/ijsem.0.000476] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Thirty-three suspected strains of the family Pasteurellaceae isolated from the oral cavity of polar and brown bears were characterized by genotypic and phenotypic tests. Phylogenetic analysis of partial 16S rRNA gene and rpoB sequences showed that the investigated isolates formed two closely related monophyletic groups, representing two novel species of a new genus. Based on 16S rRNA gene sequence comparison Bibersteinia trehalosi was the closest related species with a validly published name, with 95.4 % similarity to the polar bear group and 94.4 % similarity to the brown bear group. Otariodibacter oris was the closest related species based on rpoB sequence comparison with a similarity of 89.8 % with the polar bear group and 90 % with the brown bear group. The new genus could be separated from existing genera of the family Pasteurellaceae by three to ten phenotypic characters, and the two novel species could be separated from each other by two phenotypic characters. It is proposed that the strains should be classified as representatives of a new genus, Ursidibacter gen. nov., with two novel species: the type species Ursidibacter maritimus sp. nov., isolated from polar bears (type strain Pb43106T = CCUG 65144T = DSM 28137T, DNA G+C content 39.3 mol%), and Ursidibacter arcticus sp. nov., isolated from brown bears (type strain Bamse61T = CCUG 65145T = DSM 28138T).
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Affiliation(s)
- Mie Johanne Hansen
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Stigboejlen 4, 1870 Frederiksberg C, Denmark
- Center for Zoo and Wild Animal Health, Copenhagen Zoo, 2000 Frederiksberg, Denmark
| | - Mira Strøm Braaten
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Stigboejlen 4, 1870 Frederiksberg C, Denmark
- Center for Zoo and Wild Animal Health, Copenhagen Zoo, 2000 Frederiksberg, Denmark
| | - Anders Miki Bojesen
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Stigboejlen 4, 1870 Frederiksberg C, Denmark
| | - Henrik Christensen
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Stigboejlen 4, 1870 Frederiksberg C, Denmark
| | - Christian Sonne
- Department of Bioscience, Faculty of Science and Technology, Arctic Research Centre, Frederiksborgvej 399, PO Box 358, Aarhus University, 4000 Roskilde, Denmark
| | - Rune Dietz
- Department of Bioscience, Faculty of Science and Technology, Arctic Research Centre, Frederiksborgvej 399, PO Box 358, Aarhus University, 4000 Roskilde, Denmark
| | - Mads Frost Bertelsen
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Stigboejlen 4, 1870 Frederiksberg C, Denmark
- Center for Zoo and Wild Animal Health, Copenhagen Zoo, 2000 Frederiksberg, Denmark
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19
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Gallus S, Kumar V, Bertelsen MF, Janke A, Nilsson MA. A genome survey sequencing of the Java mouse deer (Tragulus javanicus) adds new aspects to the evolution of lineage specific retrotransposons in Ruminantia (Cetartiodactyla). Gene 2015; 571:271-8. [PMID: 26123917 DOI: 10.1016/j.gene.2015.06.064] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 06/24/2015] [Accepted: 06/25/2015] [Indexed: 10/23/2022]
Abstract
Ruminantia, the ruminating, hoofed mammals (cow, deer, giraffe and allies) are an unranked artiodactylan clade. Around 50-60 million years ago the BovB retrotransposon entered the ancestral ruminantian genome through horizontal gene transfer. A survey genome screen using 454-pyrosequencing of the Java mouse deer (Tragulus javanicus) and the lesser kudu (Tragelaphus imberbis) was done to investigate and to compare the landscape of transposable elements within Ruminantia. The family Tragulidae (mouse deer) is the only representative of Tragulina and phylogenetically important, because it represents the earliest divergence in Ruminantia. The data analyses show that, relative to other ruminantian species, the lesser kudu genome has seen an expansion of BovB Long INterspersed Elements (LINEs) and BovB related Short INterspersed Elements (SINEs) like BOVA2. In comparison the genome of Java mouse deer has fewer BovB elements than other ruminants, especially Bovinae, and has in addition a novel CHR-3 SINE most likely propagated by LINE-1. By contrast the other ruminants have low amounts of CHR SINEs but high numbers of actively propagating BovB-derived and BovB-propagated SINEs. The survey sequencing data suggest that the transposable element landscape in mouse deer (Tragulina) is unique among Ruminantia, suggesting a lineage specific evolutionary trajectory that does not involve BovB mediated retrotransposition. This shows that the genomic landscape of mobile genetic elements can rapidly change in any lineage.
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Affiliation(s)
- S Gallus
- Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
| | - V Kumar
- Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
| | - M F Bertelsen
- Center for Zoo and Wild Animal Health, Copenhagen Zoo, Roskildevej 38, DK-2000 Frederiksberg, Denmark
| | - A Janke
- Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany; Goethe University Frankfurt Institute for Ecology, Evolution & Diversity Biologicum Max-von-Laue-Str.13, D-60439 Frankfurt am Main, Germany
| | - M A Nilsson
- Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany.
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20
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Abstract
The histologic features of abnormal spectacles in 60 snakes from the 5 families of Boidae, Colubridae, Elapidae, Pythonidae, and Viperidae are described in a retrospective study conducted on specimens submitted to a private diagnostic service during a period of 15 years. Fifty-two snakes had inflammatory reactions in the spectacle. The stroma and outer epithelium of the spectacle were the layers most often involved in inflammatory disease. Lesions of the outer epithelium included edema, hyperkeratosis, and granulocyte infiltration occasionally with bacterial colonies and fungal elements. The stroma had infectious agents and inflammatory reactions in vessels and between the collagen fibrils. The inner epithelium had varying degrees of hyperplasia and hypertrophy, but no infectious agents were seen. Infectious agents in these cases included mites, bacterial disease, fungal disease, or a combination of bacterial and fungal disease. Special stains identified the bacteria most commonly involved to be Gram-positive cocci. Thirteen snakes had dysecdysis of the spectacle. Of these, 5 displayed a concurrent inflammatory reaction of the spectacle, while the remaining 8 snakes had extra keratin layers on a spectacle with an otherwise normal appearance. These keratin layers were attached to serocellular crusts located on the inner surface of the periocular scales. The cause for dyskeratotic lesions of the spectacle was not always apparent, and concurrent acariasis, other forms of dermatitis, trauma, suboptimal husbandry, and visceral disease were considered possible contributing factors. It was notable that only 4% of the submitted cases were found to have spectaculitis and/or spectacular dysecdysis.
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Affiliation(s)
- M O Da Silva
- Center for Zoo and Wild Animal Health, Copenhagen Zoo, Frederiksberg, Denmark Eye Pathology Institute, Department of Neuroscience and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - M F Bertelsen
- Center for Zoo and Wild Animal Health, Copenhagen Zoo, Frederiksberg, Denmark
| | - S Heegaard
- Eye Pathology Institute, Department of Neuroscience and Pharmacology, University of Copenhagen, Copenhagen, Denmark Department of Ophthalmology, Glostrup Hospital, University of Copenhagen, Glostrup, Denmark
| | - M M Garner
- Northwest ZooPath, Monroe, Washington, USA
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Hansen MJ, Bertelsen MF, Christensen H, Bojesen AM. Bisgaardia miroungae sp. nov., a new member of the family Pasteurellaceae isolated from the oral cavity of northern elephant seals (Mirounga angustirostris), and emended description of the genus Bisgaardia. Int J Syst Evol Microbiol 2015; 65:388-392. [DOI: 10.1099/ijs.0.065060-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A total of 17 bacterial isolates from northern elephant seals, tentatively classified within the family
Pasteurellaceae,
were further characterized by genotypic and phenotypic tests. Phylogenetic analysis of partial 16S rRNA and rpoB gene sequences showed that the isolates investigated formed a monophyletic group, closely related to the genus
Bisgaardia
within the family
Pasteurellaceae
. The rpoB gene sequence similarity was 97.2–100 % within the group and 16S rRNA gene sequence comparisons showed 99.2–99.8 % similarity within the group. According to 16S rRNA gene sequence analysis, the most closely related species with a validly published name was
Bisgaardia hudsonensis
with 96.9 % similarity and the most closely related species based on rpoB sequence comparison was
Bisgaardia
genomospecies 1 with an rpoB sequence similarity of 90.9 %. All the isolates investigated exhibited the phenotypic characteristics of the family
Pasteurellaceae
. However, these isolates could be separated from existing species of the genus
Bisgaardia
by the following characteristics: ability to grow at 42 °C, and acid production from lactose, melibiose, raffinose and l-rhamnose, but not from d-mannitol or trehalose. On the basis of both phylogenetic and phenotypic evidence, it is proposed that the strains should be classified as representatives of a novel species within the genus
Bisgaardia
: Bisgaardia miroungae sp. nov. The type strain, WildatricT ( = CCUG 65148T = DSM 28141T), was isolated from the oral cavity of a wild northern elephant seal at The Marine Mammal Center, California, USA in 2011. To include the novel species, the description of the genus
Bisgaardia
has been emended.
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Affiliation(s)
- Mie Johanne Hansen
- Center for Zoo and Wild Animal Health, Copenhagen Zoo, 2000 Frederiksberg, Denmark
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Stigboejlen 4, 1870 Frederiksberg C, Denmark
| | - Mads Frost Bertelsen
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Stigboejlen 4, 1870 Frederiksberg C, Denmark
| | - Henrik Christensen
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Stigboejlen 4, 1870 Frederiksberg C, Denmark
| | - Anders Miki Bojesen
- Center for Zoo and Wild Animal Health, Copenhagen Zoo, 2000 Frederiksberg, Denmark
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Stigboejlen 4, 1870 Frederiksberg C, Denmark
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22
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Smerup M, Damkjær M, Brøndum E, Baandrup UT, Kristiansen SB, Nygaard H, Aalkjær C, Sauer C, Buchanan R, Bertelsen MF, Østergaard K, Grøndahl C, Candy G, Hasenkam JM, Secher NH, Bie P, Wang T. The thick left ventricular wall of the giraffe heart normalises wall tension, but limits stroke volume and cardiac output. J Exp Biol 2015; 219:457-63. [DOI: 10.1242/jeb.132753] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 11/06/2015] [Indexed: 11/20/2022]
Abstract
Giraffes – the tallest extant animals on Earth – are renowned for their high central arterial blood pressure, which is necessary to secure brain perfusion. The pressure which may exceed 300 mmHg has historically been attributed to an exceptionally large heart. Recently, this has been refuted by several studies demonstrating that the mass of giraffe heart is similar to that of other mammals when expressed relative to body mass. It remains enigmatic, however, how the normal-sized giraffe heart generates such massive arterial pressures.
We hypothesized that giraffe hearts have a small intraventricular cavity and a relatively thick ventricular wall, allowing for generation of high arterial pressures at normal left ventricular wall tension. In nine anaesthetized giraffes (495±38 kg), we determined in vivo ventricular dimensions using echocardiography along with intraventricular and aortic pressures to calculate left ventricular wall stress. Cardiac output was also determined by inert gas rebreathing to provide an additional and independent estimate of stroke volume. Echocardiography and inert gas-rebreathing yielded similar cardiac outputs of 16.1±2.5 and 16.4±1.4 l min−1, respectively. End-diastolic and end-systolic volumes were 521±61 ml and 228±42 ml, yielding an ejection fraction of 56±4%, and a stroke volume of 0.59 ml kg−1. Left ventricular circumferential wall stress was 7.83±1.76 kPa. We conclude that, relative to body mass, a small left ventricular cavity and a low stroke volume characterizes the giraffe heart. The adaptations result in typical mammalian left ventricular wall tensions, but results in lowered cardiac output.
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Affiliation(s)
- Morten Smerup
- Department of Cardiothoracic Surgery, Rigshospitalet, Copenhagen, Denmark and Clinical Institute, Aarhus University, Aarhus, Denmark
| | - Mads Damkjær
- Hans Christian Andersen Children's Hospital, Odense, Denmark
- Department of Cardiovascular and Renal Research, University of Southern Denmark, Odense, Denmark
| | - Emil Brøndum
- Department of Biomedicine, Aarhus University, Aarhus, and Department of Biomedicine, Copenhagen University, Copenhagen, Denmark
| | - Ulrik T. Baandrup
- Department of Pathology, Center for Clinical Research, Vendsyssel Hospital, Aalborg University, Aalborg, Denmark
| | | | - Hans Nygaard
- Department of Thoracic and Cardiovascular Surgery and Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Christian Aalkjær
- Department of Biomedicine, Aarhus University, Aarhus, and Department of Biomedicine, Copenhagen University, Copenhagen, Denmark
| | - Cathrine Sauer
- Centre for Zoo and Wild Animal Health, Copenhagen Zoo, Frederiksberg C, Denmark
| | - Rasmus Buchanan
- Zoophysiology, Department of Biological Sciences, Aarhus University, Aarhus C, Denmark
| | | | - Kristine Østergaard
- Department of Pathology, Center for Clinical Research, Vendsyssel Hospital, Aalborg University, Aalborg, Denmark
| | - Carsten Grøndahl
- Centre for Zoo and Wild Animal Health, Copenhagen Zoo, Frederiksberg C, Denmark
| | - Geoffrey Candy
- Department of Physiology and Medicine, University of the Witwatersrand, Johannesburg, South Africa
| | - J. Michael Hasenkam
- Department of Thoracic and Cardiovascular Surgery and Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Niels H. Secher
- Department of Anesthesiology, Rigshospitalet, Copenhagen, Denmark
| | - Peter Bie
- Department of Cardiovascular and Renal Research, University of Southern Denmark, Odense, Denmark
| | - Tobias Wang
- Zoophysiology, Department of Biological Sciences, Aarhus University, Aarhus C, Denmark
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23
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Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, Ho SYW, Faircloth BC, Nabholz B, Howard JT, Suh A, Weber CC, da Fonseca RR, Li J, Zhang F, Li H, Zhou L, Narula N, Liu L, Ganapathy G, Boussau B, Bayzid MS, Zavidovych V, Subramanian S, Gabaldón T, Capella-Gutiérrez S, Huerta-Cepas J, Rekepalli B, Munch K, Schierup M, Lindow B, Warren WC, Ray D, Green RE, Bruford MW, Zhan X, Dixon A, Li S, Li N, Huang Y, Derryberry EP, Bertelsen MF, Sheldon FH, Brumfield RT, Mello CV, Lovell PV, Wirthlin M, Schneider MPC, Prosdocimi F, Samaniego JA, Vargas Velazquez AM, Alfaro-Núñez A, Campos PF, Petersen B, Sicheritz-Ponten T, Pas A, Bailey T, Scofield P, Bunce M, Lambert DM, Zhou Q, Perelman P, Driskell AC, Shapiro B, Xiong Z, Zeng Y, Liu S, Li Z, Liu B, Wu K, Xiao J, Yinqi X, Zheng Q, Zhang Y, Yang H, Wang J, Smeds L, Rheindt FE, Braun M, Fjeldsa J, Orlando L, Barker FK, Jønsson KA, Johnson W, Koepfli KP, O'Brien S, Haussler D, Ryder OA, Rahbek C, Willerslev E, Graves GR, Glenn TC, McCormack J, Burt D, Ellegren H, Alström P, Edwards SV, Stamatakis A, Mindell DP, Cracraft J, Braun EL, Warnow T, Jun W, Gilbert MTP, Zhang G. Whole-genome analyses resolve early branches in the tree of life of modern birds. Science 2014; 346:1320-31. [PMID: 25504713 PMCID: PMC4405904 DOI: 10.1126/science.1253451] [Citation(s) in RCA: 1095] [Impact Index Per Article: 109.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.
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Affiliation(s)
- Erich D Jarvis
- Department of Neurobiology, Howard Hughes Medical Institute (HHMI), and Duke University Medical Center, Durham, NC 27710, USA.
| | - Siavash Mirarab
- Department of Computer Science, The University of Texas at Austin, Austin, TX 78712, USA
| | - Andre J Aberer
- Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Bo Li
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China. College of Medicine and Forensics, Xi'an Jiaotong University Xi'an 710061, China. Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Peter Houde
- Department of Biology, New Mexico State University, Las Cruces, NM 88003, USA
| | - Cai Li
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China. Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Simon Y W Ho
- School of Biological Sciences, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Brant C Faircloth
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA. Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Benoit Nabholz
- CNRS UMR 5554, Institut des Sciences de l'Evolution de Montpellier, Université Montpellier II Montpellier, France
| | - Jason T Howard
- Department of Neurobiology, Howard Hughes Medical Institute (HHMI), and Duke University Medical Center, Durham, NC 27710, USA
| | - Alexander Suh
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala Sweden
| | - Claudia C Weber
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala Sweden
| | - Rute R da Fonseca
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Jianwen Li
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Fang Zhang
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Hui Li
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Long Zhou
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Nitish Narula
- Department of Biology, New Mexico State University, Las Cruces, NM 88003, USA. Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Onna-son, Okinawa 904-0495, Japan
| | - Liang Liu
- Department of Statistics and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Ganesh Ganapathy
- Department of Neurobiology, Howard Hughes Medical Institute (HHMI), and Duke University Medical Center, Durham, NC 27710, USA
| | - Bastien Boussau
- Laboratoire de Biométrie et Biologie Evolutive, Centre National de la Recherche Scientifique, Université de Lyon, F-69622 Villeurbanne, France
| | - Md Shamsuzzoha Bayzid
- Department of Computer Science, The University of Texas at Austin, Austin, TX 78712, USA
| | - Volodymyr Zavidovych
- Department of Neurobiology, Howard Hughes Medical Institute (HHMI), and Duke University Medical Center, Durham, NC 27710, USA
| | - Sankar Subramanian
- Environmental Futures Research Institute, Griffith University, Nathan, Queensland 4111, Australia
| | - Toni Gabaldón
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation, Dr. Aiguader 88, 08003 Barcelona, Spain. Universitat Pompeu Fabra, Barcelona, Spain. Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Salvador Capella-Gutiérrez
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation, Dr. Aiguader 88, 08003 Barcelona, Spain. Universitat Pompeu Fabra, Barcelona, Spain
| | - Jaime Huerta-Cepas
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation, Dr. Aiguader 88, 08003 Barcelona, Spain. Universitat Pompeu Fabra, Barcelona, Spain
| | - Bhanu Rekepalli
- Joint Institute for Computational Sciences, The University of Tennessee, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Kasper Munch
- Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Mikkel Schierup
- Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Bent Lindow
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Wesley C Warren
- The Genome Institute, Washington University School of Medicine, St Louis, MI 63108, USA
| | - David Ray
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA. Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA. Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA
| | - Richard E Green
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA
| | - Michael W Bruford
- Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University Cardiff CF10 3AX, Wales, UK
| | - Xiangjiang Zhan
- Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University Cardiff CF10 3AX, Wales, UK. Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Andrew Dixon
- International Wildlife Consultants, Carmarthen SA33 5YL, Wales, UK
| | - Shengbin Li
- College of Medicine and Forensics, Xi'an Jiaotong University Xi'an, 710061, China
| | - Ning Li
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100094, China
| | - Yinhua Huang
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100094, China
| | - Elizabeth P Derryberry
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA 70118, USA. Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Mads Frost Bertelsen
- Center for Zoo and Wild Animal Health, Copenhagen Zoo Roskildevej 38, DK-2000 Frederiksberg, Denmark
| | - Frederick H Sheldon
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Robb T Brumfield
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Claudio V Mello
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR 97239, USA. Brazilian Avian Genome Consortium (CNPq/FAPESPA-SISBIO Aves), Federal University of Para, Belem, Para, Brazil
| | - Peter V Lovell
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR 97239, USA
| | - Morgan Wirthlin
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR 97239, USA
| | - Maria Paula Cruz Schneider
- Brazilian Avian Genome Consortium (CNPq/FAPESPA-SISBIO Aves), Federal University of Para, Belem, Para, Brazil. Institute of Biological Sciences, Federal University of Para, Belem, Para, Brazil
| | - Francisco Prosdocimi
- Brazilian Avian Genome Consortium (CNPq/FAPESPA-SISBIO Aves), Federal University of Para, Belem, Para, Brazil. Institute of Medical Biochemistry Leopoldo de Meis, Federal University of Rio de Janeiro, Rio de Janeiro RJ 21941-902, Brazil
| | - José Alfredo Samaniego
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Amhed Missael Vargas Velazquez
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Alonzo Alfaro-Núñez
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Paula F Campos
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Bent Petersen
- Centre for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark Kemitorvet 208, 2800 Kgs Lyngby, Denmark
| | - Thomas Sicheritz-Ponten
- Centre for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark Kemitorvet 208, 2800 Kgs Lyngby, Denmark
| | - An Pas
- Breeding Centre for Endangered Arabian Wildlife, Sharjah, United Arab Emirates
| | - Tom Bailey
- Dubai Falcon Hospital, Dubai, United Arab Emirates
| | - Paul Scofield
- Canterbury Museum Rolleston Avenue, Christchurch 8050, New Zealand
| | - Michael Bunce
- Trace and Environmental DNA Laboratory Department of Environment and Agriculture, Curtin University, Perth, Western Australia 6102, Australia
| | - David M Lambert
- Environmental Futures Research Institute, Griffith University, Nathan, Queensland 4111, Australia
| | - Qi Zhou
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Polina Perelman
- Laboratory of Genomic Diversity, National Cancer Institute Frederick, MD 21702, USA. Institute of Molecular and Cellular Biology, SB RAS and Novosibirsk State University, Novosibirsk, Russia
| | - Amy C Driskell
- Smithsonian Institution National Museum of Natural History, Washington, DC 20013, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA
| | - Zijun Xiong
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Yongli Zeng
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Shiping Liu
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Zhenyu Li
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Binghang Liu
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Kui Wu
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Jin Xiao
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Xiong Yinqi
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Qiuemei Zheng
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Yong Zhang
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | | | - Jian Wang
- BGI-Shenzhen, Shenzhen 518083, China
| | - Linnea Smeds
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala Sweden
| | - Frank E Rheindt
- Department of Biological Sciences, National University of Singapore, Republic of Singapore
| | - Michael Braun
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Suitland, MD 20746, USA
| | - Jon Fjeldsa
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - F Keith Barker
- Bell Museum of Natural History, University of Minnesota, Saint Paul, MN 55108, USA
| | - Knud Andreas Jønsson
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark. Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK. Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK
| | - Warren Johnson
- Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA 22630, USA
| | - Klaus-Peter Koepfli
- Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC 20008, USA
| | - Stephen O'Brien
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia 199004. Oceanographic Center, Nova Southeastern University, Ft Lauderdale, FL 33004, USA
| | - David Haussler
- Center for Biomolecular Science and Engineering, UCSC, Santa Cruz, CA 95064, USA
| | - Oliver A Ryder
- San Diego Zoo Institute for Conservation Research, Escondido, CA 92027, USA
| | - Carsten Rahbek
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark. Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Gary R Graves
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark. Department of Vertebrate Zoology, MRC-116, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA
| | - Travis C Glenn
- Department of Environmental Health Science, University of Georgia, Athens, GA 30602, USA
| | - John McCormack
- Moore Laboratory of Zoology and Department of Biology, Occidental College, Los Angeles, CA 90041, USA
| | - Dave Burt
- Department of Genomics and Genetics, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK
| | - Hans Ellegren
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala Sweden
| | - Per Alström
- Swedish Species Information Centre, Swedish University of Agricultural Sciences Box 7007, SE-750 07 Uppsala, Sweden. Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
| | - Alexandros Stamatakis
- Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany. Institute of Theoretical Informatics, Department of Informatics, Karlsruhe Institute of Technology, D- 76131 Karlsruhe, Germany
| | - David P Mindell
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
| | - Joel Cracraft
- Department of Ornithology, American Museum of Natural History, New York, NY 10024, USA
| | - Edward L Braun
- Department of Biology and Genetics Institute, University of Florida, Gainesville, FL 32611, USA
| | - Tandy Warnow
- Department of Computer Science, The University of Texas at Austin, Austin, TX 78712, USA. Departments of Bioengineering and Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Wang Jun
- BGI-Shenzhen, Shenzhen 518083, China. Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark. Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia. Macau University of Science and Technology, Avenida Wai long, Taipa, Macau 999078, China. Department of Medicine, University of Hong Kong, Hong Kong.
| | - M Thomas P Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark. Trace and Environmental DNA Laboratory Department of Environment and Agriculture, Curtin University, Perth, Western Australia 6102, Australia.
| | - Guojie Zhang
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China. Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, DK-2100 Copenhagen, Denmark.
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24
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Alfaro-Núñez A, Frost Bertelsen M, Bojesen AM, Rasmussen I, Zepeda-Mendoza L, Tange Olsen M, Gilbert MTP. Global distribution of Chelonid fibropapilloma-associated herpesvirus among clinically healthy sea turtles. BMC Evol Biol 2014; 14:206. [PMID: 25342462 PMCID: PMC4219010 DOI: 10.1186/s12862-014-0206-z] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 09/21/2014] [Indexed: 01/09/2023] Open
Abstract
Background Fibropapillomatosis (FP) is a neoplastic disease characterized by cutaneous tumours that has been documented to infect all sea turtle species. Chelonid fibropapilloma-associated herpesvirus (CFPHV) is believed to be the aetiological agent of FP, based principally on consistent PCR-based detection of herpesvirus DNA sequences from FP tumours. We used a recently described PCR-based assay that targets 3 conserved CFPHV genes, to survey 208 green turtles (Chelonia mydas). This included both FP tumour exhibiting and clinically healthy individuals. An additional 129 globally distributed clinically healthy individual sea turtles; representing four other species were also screened. Results CFPHV DNA sequences were obtained from 37/37 (100%) FP exhibiting green turtles, and 45/300 (15%) clinically healthy animals spanning all five species. Although the frequency of infected individuals per turtle population varied considerably, most global populations contained at least one CFPHV positive individual, with the exception of various turtle species from the Arabian Gulf, Northern Indian Ocean and Puerto Rico. Haplotype analysis of the different gene markers clustered the CFPHV DNA sequences for two of the markers (UL18 and UL22) in turtles from Turks and Caicos separate to all others, regardless of host species or geographic origin. Conclusion Presence of CFPHV DNA within globally distributed samples for all five species of sea turtle was confirmed. While 100% of the FP exhibiting green turtles yielded CFPHV sequences, surprisingly, so did 15% of the clinically healthy turtles. We hypothesize that turtle populations with zero (0%) CFPHV frequency may be attributed to possible environmental differences, diet and/or genetic resistance in these individuals. Our results provide first data on the prevalence of CFPHV among seemingly healthy turtles; a factor that may not be directly correlated to the disease incidence, but may suggest of a long-term co-evolutionary latent infection interaction between CFPHV and its turtle-host across species. Finally, computational analysis of amino acid variants within the Turks and Caicos samples suggest potential functional importance in a substitution for marker UL18 that encodes the major capsid protein gene, which potentially could explain differences in pathogenicity. Nevertheless, such a theory remains to be validated by further research. Electronic supplementary material The online version of this article (doi:10.1186/s12862-014-0206-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alonzo Alfaro-Núñez
- Centre for GeoGenetics, Section for Evolutionary Genomics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350, Copenhagen K, Denmark.
| | | | - Anders Miki Bojesen
- Department of Veterinary Disease Biology, Veterinary Clinical Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Isabel Rasmussen
- Centre for GeoGenetics, Section for Evolutionary Genomics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350, Copenhagen K, Denmark.
| | - Lisandra Zepeda-Mendoza
- Centre for GeoGenetics, Section for Evolutionary Genomics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350, Copenhagen K, Denmark.
| | - Morten Tange Olsen
- Centre for GeoGenetics, Section for Evolutionary Genomics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350, Copenhagen K, Denmark.
| | - Marcus Thomas Pius Gilbert
- Centre for GeoGenetics, Section for Evolutionary Genomics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350, Copenhagen K, Denmark. .,Trace and Environmental DNA Laboratory, School of Environment and Agriculture, Curtin University, Perth, Western Australia, 6845, Australia.
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Græsli AR, Fahlman A, Evans AL, Bertelsen MF, Arnemo JM, Nielsen SS. Haematological and biochemical reference intervals for free-ranging brown bears (Ursus arctos) in Sweden. BMC Vet Res 2014; 10:183. [PMID: 25139149 PMCID: PMC4236794 DOI: 10.1186/s12917-014-0183-x] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 08/07/2014] [Indexed: 12/04/2022] Open
Abstract
Background Establishment of haematological and biochemical reference intervals is important to assess health of animals on individual and population level. Reference intervals for 13 haematological and 34 biochemical variables were established based on 88 apparently healthy free-ranging brown bears (39 males and 49 females) in Sweden. The animals were chemically immobilised by darting from a helicopter with a combination of medetomidine, tiletamine and zolazepam in April and May 2006–2012 in the county of Dalarna, Sweden. Venous blood samples were collected during anaesthesia for radio collaring and marking for ecological studies. For each of the variables, the reference interval was described based on the 95% confidence interval, and differences due to host characteristics sex and age were included if detected. To our knowledge, this is the first report of reference intervals for free-ranging brown bears in Sweden. Results The following variables were not affected by host characteristics: red blood cell, white blood cell, monocyte and platelet count, alanine transaminase, amylase, bilirubin, free fatty acids, glucose, calcium, chloride, potassium, and cortisol. Age differences were seen for the majority of the haematological variables, whereas sex influenced only mean corpuscular haemoglobin concentration, aspartate aminotransferase, lipase, lactate dehydrogenase, β-globulin, bile acids, triglycerides and sodium. Conclusions The biochemical and haematological reference intervals provided and the differences due to host factors age and gender can be useful for evaluation of health status in free-ranging European brown bears.
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Affiliation(s)
| | | | | | | | | | - Søren Saxmose Nielsen
- Department of Large Animal Sciences, University of Copenhagen, Grønnegårdsvej 8, Frederiksberg C, DK-1870, Denmark.
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Roy K, Bertelsen MF, Pors SE, Johansen KW, Kristensen AT, Kjelgaard-Hansen M, Andreasen EB, Christensen JP, Biswas PK, Bojesen AM. Inflammation-induced haemostatic response in layer chickens infected with Streptococcus equi subsp. zooepidemicus as evaluated by fibrinogen, prothrombin time and thromboelastography. Avian Pathol 2014; 43:364-70. [PMID: 25017320 DOI: 10.1080/03079457.2014.938608] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Streptococcus zooepidemicus has recently been shown to be a severe pathogen in layer chickens, where it is able to cause serious lesions in the vascular system. To evaluate the haemostatic response, 10 layer chickens were inoculated intravenously with S. zooepidemicus. Four hypotheses were tested: that the infection-induced inflammation would increase the plasma fibrinogen (Fbg) concentration, would prolong the prothrombin time (PT) and would prompt hypercoagulability or hypocoagulability as assessed by whole-blood thromboelastography (TEG), and that a possible correlation would exist between one of the TEG values and Fbg/PT. Each parameter was measured at days 1, 3 and 6 post inoculation (p.i.), and compared with the values at day 0 from each individual bird and with values obtained from non-infected control chickens (n = 10). In the infected chickens, the mean (± standard error) of Fbg was higher at day 3 p.i. (9.4 ± 1.4 g/l) and day 6 p.i. (8.0 ± 0.7 g/l) and the PT was prolonged at day 6 p.i. (168.1 ± 21.0 sec) compared with the day 0 standards (2.6 ± 0.2 g/l and 104.6 ± 2.0 sec, respectively) (P < 0.05). The majority of infected chickens demonstrated a hypercoagulable TEG result with increased mean values of the clot formation rate (α-angle) and maximal amplitude (MA) of TEG tracing at day 3 p.i. (83.1 ± 0.7°, 83.8 ± 1.4 mm) and day 6 p.i. (84.0 ± 0.4°, 89.8 ± 1.0 mm) compared with the day 0 values (75.8 ± 2.2° and 66.9 ± 1.4 mm, respectively) (P < 0.05). In control birds, the means of Fbg (1.5 ± 0.1 g/l), PT (79.4 ± 6.4 sec), TEG-α (76.7 ± 1.5°) and TEG-MA (64.0 ± 2.3 mm) were lower at day 6 compared with values observed for the infected chickens (P < 0.05). A negative correlation coefficient (-0.71) was found between the clot formation time (TEG-K) and Fbg at day 1 in the control group (P = 0.02). In conclusion, infection with S. zooepidemicus following intravenous injection in layer chickens induced haemostatic alterations including hyperfibrinogenaemia, prolonged PT, and hypercoagulability as measured by increased TEG-α and TEG-MA.
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Affiliation(s)
- Krisna Roy
- a Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences , University of Copenhagen , Frederiksberg C, Copenhagen , Denmark
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Stevens H, Bertelsen MF, Sijmons S, Van Ranst M, Maes P. Characterization of a novel polyomavirus isolated from a fibroma on the trunk of an African elephant (Loxodonta africana). PLoS One 2013; 8:e77884. [PMID: 24205012 PMCID: PMC3799753 DOI: 10.1371/journal.pone.0077884] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Accepted: 09/06/2013] [Indexed: 11/19/2022] Open
Abstract
Viruses of the family Polyomaviridae infect a wide variety of avian and mammalian hosts with a broad spectrum of outcomes including asymptomatic infection, acute systemic disease, and tumor induction. In this study a novel polyomavirus, the African elephant polyomavirus 1 (AelPyV-1) found in a protruding hyperplastic fibrous lesion on the trunk of an African elephant (Loxodonta africana) was characterized. The AelPyV-1 genome is 5722 bp in size and is one of the largest polyomaviruses characterized to date. Analysis of the AelPyV-1 genome reveals five putative open-reading frames coding for the classic small and large T antigens in the early region, and the VP1, VP2 and VP3 capsid proteins in the late region. In the area preceding the VP2 start codon three putative open-reading frames, possibly coding for an agnoprotein, could be localized. A regulatory, non-coding region separates the 2 coding regions. Unique for polyomaviruses is the presence of a second 854 bp long non-coding region between the end of the early region and the end of the late region. Based on maximum likelihood phylogenetic analyses of the large T antigen of the AelPyV-1 and 61 other polyomavirus sequences, AelPyV-1 clusters within a heterogeneous group of polyomaviruses that have been isolated from bats, new world primates and rodents.
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Affiliation(s)
- Hans Stevens
- Laboratory of Clinical Virology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | | | - Steven Sijmons
- Laboratory of Clinical Virology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Marc Van Ranst
- Laboratory of Clinical Virology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Piet Maes
- Laboratory of Clinical Virology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- * E-mail:
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Wiedemann C, Hribal R, Ringleb J, Bertelsen MF, Rasmusen K, Andersen CY, Kristensen SG, Jewgenow K. Preservation of Primordial Follicles from Lions by Slow Freezing and Xenotransplantation of Ovarian Cortex into an Immunodeficient Mouse. Reprod Domest Anim 2012; 47 Suppl 6:300-4. [DOI: 10.1111/rda.12081] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Accepted: 07/09/2012] [Indexed: 11/29/2022]
Affiliation(s)
- C Wiedemann
- Leibniz Institute for Zoo and Wildlife Research; Berlin; Germany
| | - R Hribal
- Leibniz Institute for Zoo and Wildlife Research; Berlin; Germany
| | - J Ringleb
- Leibniz Institute for Zoo and Wildlife Research; Berlin; Germany
| | - MF Bertelsen
- Centre for Zoo and Wild Animal Health; Copenhagen Zoo; Copenhagen; Denmark
| | | | - CY Andersen
- Laboratory of Reproductive Biology; University Hospital of Copenhagen; Rigshospitalet; Copenhagen; Denmark
| | - SG Kristensen
- Laboratory of Reproductive Biology; University Hospital of Copenhagen; Rigshospitalet; Copenhagen; Denmark
| | - K Jewgenow
- Leibniz Institute for Zoo and Wildlife Research; Berlin; Germany
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Nielsen SCA, Mourier T, Baandrup U, Søland TM, Bertelsen MF, Gilbert MTP, Nielsen LP. Probable transmission of coxsackie B3 virus from human to chimpanzee, Denmark. Emerg Infect Dis 2012; 18:1163-5. [PMID: 22709557 PMCID: PMC3376799 DOI: 10.3201/eid1807.111689] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
In 2010, a chimpanzee died at Copenhagen Zoo following an outbreak of respiratory disease among chimpanzees in the zoo. Identification of coxsackie B3 virus, a common human pathogen, as the causative agent, and its severe manifestation, raise questions about pathogenicity and transmissibility among humans and other primates.
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Hydeskov HB, Guardabassi L, Aalbaek B, Olsen KEP, Nielsen SS, Bertelsen MF. Salmonella prevalence among reptiles in a zoo education setting. Zoonoses Public Health 2012; 60:291-5. [PMID: 22835051 DOI: 10.1111/j.1863-2378.2012.01521.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Clinically healthy reptiles may shed Salmonella and therefore act as a potential zoonotic threat. Most people in Northern European countries are rarely exposed to reptiles, but many zoos have education departments where children have direct contact with this group of animals. The objectives of this study were to determine the prevalence and serotype distribution of Salmonella among reptiles in the Education Department (n = 55) at Copenhagen Zoo and compare it to the Zoo's main reptile collection (n = 145) to evaluate the zoonotic risk. Salmonella was isolated from cloacal swabs by selective enrichment, and a single isolate from each positive sample was further identified by biochemical tests and serotyped. The overall prevalence was 35% (69/200) with significant difference between the Education Department (64%, 35/55) and the main reptile collection (23%, 34/145). A total of 28 serotypes were detected. Ten serotypes were isolated from more than one specimen and four from more than one species. Salmonella enterica subsp. enterica serovar Eastbourne was the predominant serotype (32%, 22/69) and was also the serotype isolated from most reptile species (n = 7). Transmission of serotypes from one department to another was very limited indicated by the serotype distribution. Despite the relative high prevalence observed among the reptiles in the Zoo's Education Department compared to the reptiles in the Zoo's main reptile collection, no Salmonella cases have been linked to the Zoo, and Salmonella ser. Eastbourne is very rarely isolated from humans in Denmark. Simple hygienic procedures such as hand washing which is consistently carried out following handling of reptiles at the Education Department may reduce the risk and therefore contribute to this low prevalence.
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Affiliation(s)
- H B Hydeskov
- Centre for Zoo and Wild Animal Health, Copenhagen Zoo, Frederiksberg, Denmark.
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Bie P, Grøndahl C, Bertelsen MF, Hørlyck A, Hasenkam JM, Wang T, Brøndum ET, Candy G, Kristensen BA. Renal hemodynamics in the anesthetized giraffe. FASEB J 2012. [DOI: 10.1096/fasebj.26.1_supplement.1069.5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Peter Bie
- Inst. Molecular MedicineUniv Southern DenmarkOdenseDenmark
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Hummelshøj T, Nissen J, Munthe-Fog L, Koch C, Frost Bertelsen M, Garred P. Allelic lineages of the ficolin genes (FCNs) are passed from ancestral to descendant primates. PLoS One 2011; 6:e28187. [PMID: 22194813 PMCID: PMC3240626 DOI: 10.1371/journal.pone.0028187] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2011] [Accepted: 11/02/2011] [Indexed: 12/02/2022] Open
Abstract
The ficolins recognize carbohydrates and acetylated compounds on microorganisms and dying host cells and are able to activate the lectin pathway of the complement system. In humans, three ficolin genes have been identified: FCN1, FCN2 and FCN3, which encode ficolin-1, ficolin-2 and ficolin-3, respectively. Rodents have only two ficolins designated ficolin-A and ficolin-B that are closely related to human ficolin-1, while the rodent FCN3 orthologue is a pseudogene. Ficolin-2 and ficolin-3 have so far only been observed in humans. Thus, we performed a systematic investigation of the FCN genes in non-human primates. The exons and intron-exon boundaries of the FCN1-3 genes were sequenced in the following primate species: chimpanzee, gorilla, orangutan, rhesus macaque, cynomolgus macaque, baboon and common marmoset. We found that the exon organisation of the FCN genes was very similar between all the non-human primates and the human FCN genes. Several variations in the FCN genes were found in more than one primate specie suggesting that they were carried from one species to another including humans. The amino acid diversity of the ficolins among human and non-human primate species was estimated by calculating the Shannon entropy revealing that all three proteins are generally highly conserved. Ficolin-1 and ficolin-2 showed the highest diversity, whereas ficolin-3 was more conserved. Ficolin-2 and ficolin-3 were present in non-human primate sera with the same characteristic oligomeric structures as seen in human serum. Taken together all the FCN genes show the same characteristics in lower and higher primates. The existence of trans-species polymorphisms suggests that different FCN allelic lineages may be passed from ancestral to descendant species.
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Affiliation(s)
- Tina Hummelshøj
- Laboratory of Molecular Medicine, Department of Clinical Immunology, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Janna Nissen
- Laboratory of Molecular Medicine, Department of Clinical Immunology, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lea Munthe-Fog
- Laboratory of Molecular Medicine, Department of Clinical Immunology, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Claus Koch
- Department of Cancer and Inflammation, Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | | | - Peter Garred
- Laboratory of Molecular Medicine, Department of Clinical Immunology, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
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Thomsen PD, Schauser K, Bertelsen MF, Vejlsted M, Grøndahl C, Christensen K. Meiotic studies in infertile domestic pig-babirusa hybrids. Cytogenet Genome Res 2010; 132:124-8. [PMID: 20924163 DOI: 10.1159/000320421] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/10/2010] [Indexed: 11/19/2022] Open
Abstract
Mating of a babirusa (Babyrousa babyrussa) boar and a domestic sow (Sus scrofa) resulted in the birth of 5 live domestic pig-babirusa hybrid piglets. Chromosome analysis of one of the surviving males confirmed that they were domestic pig-babirusa hybrids by revealing the presence of a complete haploid set of 19 porcine chromosomes as well as a complete haploid set of 19 babirusa chromosomes in the karyotype. None of the surviving piglets, two males and one female, had shown signs of sexual maturity at age 27 months. Histological examination of gonadal biopsies from the 2 males revealed that both were azoospermatic. Immunostaining revealed SCP3-positive axial elements in the nuclei of primary spermatocytes, indicating that they were progressing through leptotene and zygotene of meiotic prophase. However, the presence of multiple short stretches of axial elements in pachytene nuclei indicated that this phase was blocked, probably due to aberrant chromosome pairing. Histological examination of the ovaries revealed follicular structures, but oocytes within them were generally degenerated. We conclude that both male and female pig-babirusa hybrids were infertile, most likely due to germ cell death resulting from abnormalities of chromosome pairing during meiotic prophase.
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Affiliation(s)
- P D Thomsen
- Departments of Basic Animal and Veterinary Sciences, Faculty of Life Sciences, University of Copenhagen, Groennegaardsvej 7, Frederiksberg, Denmark.
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Nejsum P, Bertelsen MF, Betson M, Stothard JR, Murrell KD. Molecular evidence for sustained transmission of zoonotic Ascaris suum among zoo chimpanzees (Pan troglodytes). Vet Parasitol 2010; 171:273-6. [PMID: 20400228 DOI: 10.1016/j.vetpar.2010.03.030] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2010] [Accepted: 03/23/2010] [Indexed: 10/19/2022]
Abstract
Chimpanzees in the Copenhagen Zoo frequently excrete ascarid worms onto the cage floor in spite of a regular anthelmintic treatment program. Previously it had been shown that the source of the infections was of pig origin. However, it was unknown whether the recurrence of the infection was due to reintroduction of eggs from an external source or to a sustained transmission cycle within the zoo. We found that isolated eggs were able to embryonate to the infective J3 stage and PCR-RFLP analysis on the ITS region amplified from single embryonated eggs suggest these to be Ascaris suum. In addition, sequence analysis of the cox1 gene ('barcoding') on expelled worms followed by cluster analysis revealed that the chimpanzees are infected with pig A. suum which now, in spite of control efforts, has stabilized into a permanent transmission cycle in the zoo's chimpanzee troop.
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Affiliation(s)
- Peter Nejsum
- Danish Centre for Experimental Parasitology, Department of Veterinary Disease Biology, Faculty of Life Sciences, University of Copenhagen, Dyrlaegevej 100, DK-1870, Frederiksberg C, Copenhagen, Denmark
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