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Houzelstein D, Eozenou C, Lagos CF, Elzaiat M, Bignon-Topalovic J, Gonzalez I, Laville V, Schlick L, Wankanit S, Madon P, Kirtane J, Athalye A, Buonocore F, Bigou S, Conway GS, Bohl D, Achermann JC, Bashamboo A, McElreavey K. A conserved NR5A1-responsive enhancer regulates SRY in testis-determination. Nat Commun 2024; 15:2796. [PMID: 38555298 PMCID: PMC10981742 DOI: 10.1038/s41467-024-47162-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 03/21/2024] [Indexed: 04/02/2024] Open
Abstract
The Y-linked SRY gene initiates mammalian testis-determination. However, how the expression of SRY is regulated remains elusive. Here, we demonstrate that a conserved steroidogenic factor-1 (SF-1)/NR5A1 binding enhancer is required for appropriate SRY expression to initiate testis-determination in humans. Comparative sequence analysis of SRY 5' regions in mammals identified an evolutionary conserved SF-1/NR5A1-binding motif within a 250 bp region of open chromatin located 5 kilobases upstream of the SRY transcription start site. Genomic analysis of 46,XY individuals with disrupted testis-determination, including a large multigenerational family, identified unique single-base substitutions of highly conserved residues within the SF-1/NR5A1-binding element. In silico modelling and in vitro assays demonstrate the enhancer properties of the NR5A1 motif. Deletion of this hemizygous element by genome-editing, in a novel in vitro cellular model recapitulating human Sertoli cell formation, resulted in a significant reduction in expression of SRY. Therefore, human NR5A1 acts as a regulatory switch between testis and ovary development by upregulating SRY expression, a role that may predate the eutherian radiation. We show that disruption of an enhancer can phenocopy variants in the coding regions of SRY that cause human testis dysgenesis. Since disease causing variants in enhancers are currently rare, the regulation of gene expression in testis-determination offers a paradigm to define enhancer activity in a key developmental process.
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Affiliation(s)
- Denis Houzelstein
- Institut Pasteur, Université Paris Cité, Human Developmental Genetics Unit, F-75015, Paris, France.
- Centre National de la Recherche Scientifique, CNRS, UMR 3738, Paris, France.
| | - Caroline Eozenou
- Institut Pasteur, Université Paris Cité, Human Developmental Genetics Unit, F-75015, Paris, France
- Centre National de la Recherche Scientifique, CNRS, UMR 3738, Paris, France
- Institut Cochin, Université Paris Cité, INSERM, CNRS, Paris, France
| | - Carlos F Lagos
- Chemical Biology & Drug Discovery Lab, Escuela de Química y Farmacia, Facultad de Medicina y Ciencia, Universidad San Sebastián, Campus Los Leones, Lota 2465 Providencia, 7510157, Santiago, Chile
- Centro Ciencia & Vida, Fundación Ciencia & Vida, Av. del Valle Norte 725, Huechuraba, 8580702, Santiago, Chile
| | - Maëva Elzaiat
- Institut Pasteur, Université Paris Cité, Human Developmental Genetics Unit, F-75015, Paris, France
- Centre National de la Recherche Scientifique, CNRS, UMR 3738, Paris, France
| | - Joelle Bignon-Topalovic
- Institut Pasteur, Université Paris Cité, Human Developmental Genetics Unit, F-75015, Paris, France
- Centre National de la Recherche Scientifique, CNRS, UMR 3738, Paris, France
| | - Inma Gonzalez
- Centre National de la Recherche Scientifique, CNRS, UMR 3738, Paris, France
- Institut Pasteur, Université Paris Cité, Epigenomics, Proliferation, and the Identity of Cells Unit, F-75015, Paris, France
| | - Vincent Laville
- Centre National de la Recherche Scientifique, CNRS, UMR 3738, Paris, France
- Institut Pasteur, Université Paris Cité, Stem Cells and Development Unit, F-75015, Paris, France
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, F-75015, Paris, France
| | - Laurène Schlick
- Institut Pasteur, Université Paris Cité, Human Developmental Genetics Unit, F-75015, Paris, France
- Centre National de la Recherche Scientifique, CNRS, UMR 3738, Paris, France
| | - Somboon Wankanit
- Institut Pasteur, Université Paris Cité, Human Developmental Genetics Unit, F-75015, Paris, France
- Centre National de la Recherche Scientifique, CNRS, UMR 3738, Paris, France
- Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Prochi Madon
- Department of Assisted Reproduction and Genetics, Jaslok Hospital and Research Centre, Mumbai, India
| | - Jyotsna Kirtane
- Department of Pediatric Surgery, Jaslok Hospital and Research Centre, Mumbai, India
| | - Arundhati Athalye
- Department of Assisted Reproduction and Genetics, Jaslok Hospital and Research Centre, Mumbai, India
| | - Federica Buonocore
- Genetics and Genomic Medicine Research & Teaching Department, UCL GOS Institute of Child Health, University College London, London, United Kingdom
| | - Stéphanie Bigou
- ICV-iPS core facility, Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Paris, France
| | - Gerard S Conway
- Institute for Women's Health, University College London, London, United Kingdom
| | - Delphine Bohl
- ICV-iPS core facility, Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Paris, France
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Paris, France
| | - John C Achermann
- Genetics and Genomic Medicine Research & Teaching Department, UCL GOS Institute of Child Health, University College London, London, United Kingdom
| | - Anu Bashamboo
- Institut Pasteur, Université Paris Cité, Human Developmental Genetics Unit, F-75015, Paris, France
- Centre National de la Recherche Scientifique, CNRS, UMR 3738, Paris, France
| | - Ken McElreavey
- Institut Pasteur, Université Paris Cité, Human Developmental Genetics Unit, F-75015, Paris, France.
- Centre National de la Recherche Scientifique, CNRS, UMR 3738, Paris, France.
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2
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Rogers Flattery CN, Abdulla M, Barton SA, Michlich JM, Trut LN, Kukekova AV, Hecht EE. The brain of the silver fox (Vulpes vulpes): a neuroanatomical reference of cell-stained histological and MRI images. Brain Struct Funct 2023; 228:1177-1189. [PMID: 37160458 PMCID: PMC11192273 DOI: 10.1007/s00429-023-02648-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 04/21/2023] [Indexed: 05/11/2023]
Abstract
Although the silver fox (Vulpes vulpes) has been largely overlooked by neuroscientists, it has the potential to serve as a powerful model for the investigation of brain-behavior relationships. The silver fox is a melanistic variant of the red fox. Within this species, the long-running Russian farm-fox experiment has resulted in different strains bred to show divergent behavior. Strains bred for tameness, aggression, or without selection on behavior present an excellent opportunity to investigate neuroanatomical changes underlying behavioral characteristics. Here, we present a histological and MRI neuroanatomical reference of a fox from the conventional strain, which is bred without behavioral selection. This can provide an anatomical basis for future studies of the brains of foxes from this particular experiment, as well as contribute to an understanding of fox brains in general. In addition, this can serve as a resource for comparative neuroscience and investigations into neuroanatomical variation among the family Canidae, the order Carnivora, and mammals more broadly.
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Affiliation(s)
| | - Munawwar Abdulla
- Department of Human Evolutionary Biology, Harvard University, 11 Divinity Ave, Cambridge, MA, 02138, USA
| | - Sophie A Barton
- Department of Human Evolutionary Biology, Harvard University, 11 Divinity Ave, Cambridge, MA, 02138, USA
| | - Jenny M Michlich
- Department of Human Evolutionary Biology, Harvard University, 11 Divinity Ave, Cambridge, MA, 02138, USA
| | - Lyudmila N Trut
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Anna V Kukekova
- Department of Animal Sciences, College of ACES, University of Illinois at Urbana-Champaign, Urbana, USA
| | - Erin E Hecht
- Department of Human Evolutionary Biology, Harvard University, 11 Divinity Ave, Cambridge, MA, 02138, USA.
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3
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Deng YP, Wang W, Fu YT, Nie Y, Xie Y, Liu GH. Morphological and molecular evidence reveals a new species of chewing louse Pancola ailurus n. sp. (Phthiraptera: Trichodectidae) from the endangered Chinese red panda Ailurus styani. Int J Parasitol Parasites Wildl 2022; 20:31-38. [PMID: 36619891 PMCID: PMC9811220 DOI: 10.1016/j.ijppaw.2022.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 12/21/2022] [Accepted: 12/21/2022] [Indexed: 12/28/2022]
Abstract
Lice are six-legged, wingless, insect parasites of mammals and birds, and include two main functional groups: blood-sucking lice and chewing lice. However, it is still not clear whether the Chinese red panda Ailurus styani is infested with the parasitic louse. In the present study, we describe a new genus and a species of chewing louse, Pancola ailurus (Phthiraptera: Trichodectidae) based on morphological and molecular datasets. The morphological features showed that Pancola is closer to Paratrichodectes. The genetic divergence of cox1 and 12S rRNA among the Pancola ailurus n. sp. and other Trichodectidae lice was 29.7 - 34.6% and 38.9 - 43.6%, respectively. Phylogenetic analyses based on the available mitochondrial gene sequences showed that P. ailurus n. sp. is more closely related to Trichodectes canis and Geomydoecus aurei than to Felicola subrostratus and together nested within the family Trichodectidae. This study is the first record of parasitic lice from the endangered Chinese red panda A. styani and highlights the importance of integrating morphological and molecular datasets for the identification and discrimination of new louse species.
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Affiliation(s)
- Yuan-Ping Deng
- Research Center for Parasites & Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan Province, 410128, China
| | - Wei Wang
- The Centre for Bioinnovation, School of Science and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, 4556, Australia
| | - Yi-Tian Fu
- Research Center for Parasites & Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan Province, 410128, China
| | - Yu Nie
- Research Center for Parasites & Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan Province, 410128, China
| | - Yue Xie
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan Province, 611130, China,Corresponding author.
| | - Guo-Hua Liu
- Research Center for Parasites & Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan Province, 410128, China,Corresponding author.
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4
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Drabeck DH, Holt J, McGaugh SE. Widespread convergent evolution of alpha-neurotoxin resistance in African mammals. Biol Lett 2022; 18:20220361. [PMID: 36448295 PMCID: PMC9709510 DOI: 10.1098/rsbl.2022.0361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 11/07/2022] [Indexed: 12/05/2022] Open
Abstract
Convergent evolution is central to the study of adaptation and has been used to understand both the limits of evolution and the diverse patterns and processes which result in adaptive change. Resistance to snake venom alpha-neurotoxins (αNTXs) is a case of widespread convergence having evolved several times in snakes, lizards and mammals. Despite extreme toxicity of αNTXs, substitutions in its target, the nicotinic acetylcholine receptor (nAChR), prevent αNTX binding and render species resistant. Recently, the published meerkat (Herpestidae) genome revealed that meerkats have the same substitutions in nAChR as the venom-resistant Egyptian mongoose (Herpestidae), suggesting that venom-resistant nAChRs may be ancestral to Herpestids. Like the mongoose, many other species of feliform carnivores prey on venomous snakes, though their venom resistance has never been explored. To evaluate the prevalence and ancestry of αNTX resistance in mammals, we generate a dataset of mammalian nAChR using museum specimens and public datasets. We find five instances of convergent evolution within feliform carnivores, and an additional eight instances across all mammals sampled. Tests of selection show that these substitutions are evolving under positive selection. Repeated convergence suggests that this adaptation played an important role in the evolution of mammalian physiology and potentially venom evolution.
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Affiliation(s)
- Danielle H. Drabeck
- Department of Ecology, Evolution, and Behavior, University of Minnesota, 1987 Upper Buford Circle, St Paul, MN 55108, USA
| | - Jennifer Holt
- Department of Ecology, Evolution, and Behavior, University of Minnesota, 1987 Upper Buford Circle, St Paul, MN 55108, USA
| | - Suzanne E. McGaugh
- Department of Ecology, Evolution, and Behavior, University of Minnesota, 1987 Upper Buford Circle, St Paul, MN 55108, USA
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5
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Dickinson E, Elminowski EE, Flores D, Eldridge EI, Granatosky MC, Hartstone‐Rose A. A morphological analysis of carnivoran ossicles from Rancho La Brea. J Morphol 2022; 283:1337-1349. [PMID: 36041006 PMCID: PMC9826070 DOI: 10.1002/jmor.21506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 08/02/2022] [Accepted: 08/16/2022] [Indexed: 01/11/2023]
Abstract
The morphology of the mammalian middle ear-including the size, shape, and stiffness of individual ossicles-controls their vibrational response to sound and, is closely related to an animal's auditory capabilities. While the relationship between middle ear morphology and hearing frequency has been explored in living carnivorans, the size and shape of ossicles in fossil carnivorans have been sparsely documented. In this study, we present the first morphological data on four iconic carnivoran taxa from the Rancho La Brea Tar Pits: Smilodon fatalis, Panthera atrox, Canis dirus, and Arctodus simus. These data are contextualized with samples of extant felids, canids, and ursids to determine the extent to which the ossicles of these iconic fossil taxa resemble their living relatives. Six, five, and seven linear measurements were taken from the malleus, incus, and stapes, respectively. Comparisons of geometric means reveal that the ossicles of fossil canids and felids are similar in size to living analogs, but those of A. simus are significantly larger than those of any living ursid. Further, principal components analyses demonstrate close morphological affinities between fossil and extant taxa within canids and felids, and again, a greater disparity between fossil and extant ursids. Canids and ursids occupy distinct regions of the morphospace, yet both overlap the morphological range spanned by felids. While some elements-for example, the stapes-require further specimens to facilitate more nuanced interpretations of variation, our findings underscore the need for concerted efforts towards identifying and preserving these bones within fossil assemblages.
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Affiliation(s)
- Edwin Dickinson
- Department of Biological SciencesNorth Carolina State UniversityRaleighNorth CarolinaUSA,Department of AnatomyNew York Institute of Technology College of Osteopathic MedicineOld WestburyNew YorkUSA
| | - Erin E. Elminowski
- Department of Biological SciencesNorth Carolina State UniversityRaleighNorth CarolinaUSA,College of Veterinary MedicineUniversity of TennesseeKnoxvilleTennesseeUnited States
| | - Deanna Flores
- Department of Biological SciencesNorth Carolina State UniversityRaleighNorth CarolinaUSA,Department of Biological SciencesSam Houston State UniversityHuntsvilleTexasUSA,Department of Earth ScienceUniversity of OregonEugeneOregonUSA
| | - Emma I. Eldridge
- Department of Biological SciencesNorth Carolina State UniversityRaleighNorth CarolinaUSA,College of Veterinary MedicineNorth Carolina State UniversityRaleighNorth CarolinaUnited States
| | - Michael C. Granatosky
- Department of AnatomyNew York Institute of Technology College of Osteopathic MedicineOld WestburyNew YorkUSA
| | - Adam Hartstone‐Rose
- Department of Biological SciencesNorth Carolina State UniversityRaleighNorth CarolinaUSA
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6
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Morelli S, Diakou A, Di Cesare A, Colombo M, Traversa D. Canine and Feline Parasitology: Analogies, Differences, and Relevance for Human Health. Clin Microbiol Rev 2021; 34:e0026620. [PMID: 34378954 PMCID: PMC8404700 DOI: 10.1128/cmr.00266-20] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Cats and dogs are treated as family members by most pet owners. Therefore, a high quality of veterinary care and preventive medicine is imperative for animal health and welfare and for the protection of humans from zoonotic pathogens. There is a general perception of cats being treated as "small dogs," especially in the field of clinical parasitology. As a result, several important differences between the two animal species are not taken into proper consideration and are often overlooked. Dogs and cats are profoundly different under evolutionary, biological, ethological, behavioral, and immunological standpoints. These differences impact clinical features, diagnosis, and control of canine and feline parasites and transmission risk for humans. This review outlines the most common parasitoses and vector-borne diseases of dogs and cats, with a focus on major convergences and divergences, and discusses parasites that have (i) evolved based on different preys for dogs and cats, (ii) adapted due to different immunological or behavioral animal profiles, and (iii) developed more similarities than differences in canine and feline infections and associated diseases. Differences, similarities, and peculiarities of canine and feline parasitology are herein reviewed in three macrosections: (i) carnivorism, vegetarianism, anatomy, genetics, and parasites, (ii) evolutionary adaptation of nematodes, including veterinary reconsideration and zoonotic importance, and (iii) behavior and immune system driving ectoparasites and transmitted diseases. Emphasis is given to provide further steps toward a more accurate evaluation of canine and feline parasitology in a changing world in terms of public health relevance and One Health approach.
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Affiliation(s)
- Simone Morelli
- Faculty of Veterinary Medicine, University of Teramo, Teramo, Italy
| | - Anastasia Diakou
- Faculty of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Angela Di Cesare
- Faculty of Veterinary Medicine, University of Teramo, Teramo, Italy
| | | | - Donato Traversa
- Faculty of Veterinary Medicine, University of Teramo, Teramo, Italy
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7
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Phenotyping in the era of genomics: MaTrics—a digital character matrix to document mammalian phenotypic traits. Mamm Biol 2021. [DOI: 10.1007/s42991-021-00192-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
AbstractA new and uniquely structured matrix of mammalian phenotypes, MaTrics (Mammalian Traits for Comparative Genomics) in a digital form is presented. By focussing on mammalian species for which genome assemblies are available, MaTrics provides an interface between mammalogy and comparative genomics.MaTrics was developed within a project aimed to find genetic causes of phenotypic traits of mammals using Forward Genomics. This approach requires genomes and comprehensive and recorded information on homologous phenotypes that are coded as discrete categories in a matrix. MaTrics is an evolving online resource providing information on phenotypic traits in numeric code; traits are coded either as absent/present or with several states as multistate. The state record for each species is linked to at least one reference (e.g., literature, photographs, histological sections, CT scans, or museum specimens) and so MaTrics contributes to digitalization of museum collections. Currently, MaTrics covers 147 mammalian species and includes 231 characters related to structure, morphology, physiology, ecology, and ethology and available in a machine actionable NEXUS-format*. Filling MaTrics revealed substantial knowledge gaps, highlighting the need for phenotyping efforts. Studies based on selected data from MaTrics and using Forward Genomics identified associations between genes and certain phenotypes ranging from lifestyles (e.g., aquatic) to dietary specializations (e.g., herbivory, carnivory). These findings motivate the expansion of phenotyping in MaTrics by filling research gaps and by adding taxa and traits. Only databases like MaTrics will provide machine actionable information on phenotypic traits, an important limitation to genomics. MaTrics is available within the data repository Morph·D·Base (www.morphdbase.de).
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8
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Noonan MJ, Fagan WF, Fleming CH. A semi‐variance approach to visualising phylogenetic autocorrelation. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Michael J. Noonan
- Department of Biology The University of British Columbia Okanagan Kelowna BC Canada
| | - William F. Fagan
- Department of Biology University of Maryland College Park College Park MD USA
| | - Christen H. Fleming
- Department of Biology University of Maryland College Park College Park MD USA
- Conservation Ecology Center Smithsonian Conservation Biology Institute Front Royal VI USA
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9
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Cserhati M. A tail of two pandas- whole genome k-mer signature analysis of the red panda (Ailurus fulgens) and the Giant panda (Ailuropoda melanoleuca). BMC Genomics 2021; 22:228. [PMID: 33794768 PMCID: PMC8015091 DOI: 10.1186/s12864-021-07531-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 03/14/2021] [Indexed: 11/29/2022] Open
Abstract
Background The red panda (Ailurus fulgens) is a riddle of morphology, making it hard to tell whether it is an ursid, a procyonid, a mustelid, or a member of its own family. Previous genetic studies have given quite contradictory results as to its phylogenetic placement. Results A recently developed whole genome-based algorithm, the Whole Genome K-mer Signature algorithm was used to analyze the genomes of 28 species of Carnivora, including A. fulgens and several felid, ursid, mustelid, one mephitid species. This algorithm has the advantage of holistically using all the information in the genomes of these species. Being a genomics-based algorithm, it also reduces stochastic error to a minimum. Besides the whole genome, the mitochondrial DNA from 52 mustelids, mephitids, ursids, procyonids and A. fulgens were aligned to draw further phylogenetic inferences. The results from the whole genome study suggested that A. fulgens is a member of the mustelid clade (p = 9·10− 97). A. fulgens also separates from the mephitid Spilogala gracilis. The giant panda, Ailuropoda melanoleuca also clusters away from A. fulgens, together with other ursids (p = 1.2·10− 62). This could be due to the geographic isolation of A. fulgens from other mustelid species. However, results from the mitochondrial study as well as neighbor-joining methods based on the sequence identity matrix suggests that A. fulgens forms a monophyletic group. A Maximum Likelihood tree suggests that A. fulgens and Ursidae form a monophyletic group, although the bootstrap value is weak. Conclusions The main conclusion that we can draw from this study is that on a whole genome level A. fulgens possibly belongs to the mustelid clade, and not an ursid or a mephitid. This despite the fact that previously some researchers classified A. fulgens and A. melanoleuca as relatives. Since the genotype determines the phenotype, molecular-based classification takes precedence over morphological classifications. This affirms the results of some previous studies, which studied smaller portions of the genome. However, mitochondrial analyses based on neighbor-joining and maximum likelihood methods suggest otherwise. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07531-3.
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Affiliation(s)
- Matyas Cserhati
- Independent Scholar, 2615C Muscatel Avenue, Rosemead, CA, 91770, USA.
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10
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Allio R, Tilak MK, Scornavacca C, Avenant NL, Kitchener AC, Corre E, Nabholz B, Delsuc F. High-quality carnivoran genomes from roadkill samples enable comparative species delineation in aardwolf and bat-eared fox. eLife 2021; 10:e63167. [PMID: 33599612 PMCID: PMC7963486 DOI: 10.7554/elife.63167] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 02/16/2021] [Indexed: 12/26/2022] Open
Abstract
In a context of ongoing biodiversity erosion, obtaining genomic resources from wildlife is essential for conservation. The thousands of yearly mammalian roadkill provide a useful source material for genomic surveys. To illustrate the potential of this underexploited resource, we used roadkill samples to study the genomic diversity of the bat-eared fox (Otocyon megalotis) and the aardwolf (Proteles cristatus), both having subspecies with similar disjunct distributions in Eastern and Southern Africa. First, we obtained reference genomes with high contiguity and gene completeness by combining Nanopore long reads and Illumina short reads. Then, we showed that the two subspecies of aardwolf might warrant species status (P. cristatus and P. septentrionalis) by comparing their genome-wide genetic differentiation to pairs of well-defined species across Carnivora with a new Genetic Differentiation index (GDI) based on only a few resequenced individuals. Finally, we obtained a genome-scale Carnivora phylogeny including the new aardwolf species.
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Affiliation(s)
- Rémi Allio
- Institut des Sciences de l’Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de MontpellierMontpellierFrance
| | - Marie-Ka Tilak
- Institut des Sciences de l’Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de MontpellierMontpellierFrance
| | - Celine Scornavacca
- Institut des Sciences de l’Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de MontpellierMontpellierFrance
| | - Nico L Avenant
- National Museum and Centre for Environmental Management, University of the Free StateBloemfonteinSouth Africa
| | - Andrew C Kitchener
- Department of Natural Sciences, National Museums ScotlandEdinburghUnited Kingdom
| | - Erwan Corre
- CNRS, Sorbonne Université, CNRS, ABiMS, Station Biologique de RoscoffRoscoffFrance
| | - Benoit Nabholz
- Institut des Sciences de l’Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de MontpellierMontpellierFrance
- Institut Universitaire de France (IUF)ParisFrance
| | - Frédéric Delsuc
- Institut des Sciences de l’Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de MontpellierMontpellierFrance
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11
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Patterns and tempo of PCSK9 pseudogenizations suggest an ancient divergence in mammalian cholesterol homeostasis mechanisms. Genetica 2021; 149:1-19. [PMID: 33515402 PMCID: PMC7929951 DOI: 10.1007/s10709-021-00113-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 01/04/2021] [Indexed: 01/06/2023]
Abstract
Proprotein convertase subtilisin/kexin type 9 (PCSK9) plays a central role in cholesterol homeostasis in humans as a major regulator of LDLR levels. PCSK9 is an intriguing protease in that it does not act by proteolysis but by preventing LDLR recirculation from endosomes to the plasma membrane. This, and the inexistence of any other proteolytic substrate but itself could suggest that PCSK9 is an exquisite example of evolutionary fine-tuning. However, the gene has been lost in several mammalian species, and null alleles are present (albeit at low frequencies) in some human populations without apparently deleterious health effects, raising the possibility that the PCSK9 may have become dispensable in the mammalian lineage. To address this issue, we systematically recovered, assembled, corrected, annotated and analysed publicly available PCSK9 sequences for 420 eutherian species to determine the distribution, frequencies, mechanisms and timing of PCSK9 pseudogenization events, as well as the evolutionary pressures underlying the preservation or loss of the gene. We found a dramatic difference in the patterns of PCSK9 retention and loss between Euarchontoglires—where there is strong pressure for gene preservation—and Laurasiatheria, where multiple independent events have led to PCSK9 loss in most species. These results suggest that there is a fundamental difference in the regulation of cholesterol metabolism between Euarchontoglires and Laurasiatheria, which in turn has important implications for the use of Laurasiatheria species (e.g. pigs) as animal models of human cholesterol-related diseases.
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Caraballo DA, Montani ME, Martínez LM, Antoniazzi LR, Sambrana TC, Fernández C, Cisterna DM, Beltrán FJ, Colombo VC. Heterogeneous taxonomic resolution of cytochrome b gene identification of bats from Argentina: Implications for field studies. PLoS One 2021; 15:e0244750. [PMID: 33382800 PMCID: PMC7775095 DOI: 10.1371/journal.pone.0244750] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 12/15/2020] [Indexed: 11/19/2022] Open
Abstract
Bats are among the most diverse, widespread, and abundant mammals. In Argentina, 67 species of bats have been recorded, belonging to 5 families and 29 genera. These high levels of biodiversity are likely to complicate identification at fieldwork, especially between closely related species, where external morphology-based approaches are the only immediate means for a priori species assignment. The use of molecular markers can enhance species identification, and acquires particular relevance in capture-release studies. In this study, we discuss the extent of the use of the mitochondrial cytochrome b gene for species identification, comparing external morphology identification with a molecular phylogenetic classification based on this marker, under the light of current bat systematics. We analyzed 33 samples collected in an eco-epidemiological survey in the province of Santa Fe (Argentina). We further sequenced 27 museum vouchers to test the accuracy of cytochrome b -based phylogenies in taxonomic identification of bats occurring in the Pampean/Chacoan regions of Argentina. The cytochrome b gene was successfully amplified in all Molossid and Vespertilionid species except for Eptesicus, for which we designed a new reverse primer. The resulting Bayesian phylogeny was congruent with current systematics. Cytochrome b proved useful for species-level delimitation in non-conflicting genera (Eumops, Dasypterus, Molossops) and has infrageneric resolution in more complex lineages (Eptesicus, Myotis, Molossus). We discuss four sources of incongruence that may act separately or in combination: 1) molecular processes, 2) biology, 3) limitations in identification, and 4) errors in the current taxonomy. The present study confirms the general applicability of cytochrome b -based phylogenies in eco-epidemiological studies, but its resolution and reliability depend mainly, but not solely, on the level of genetic differentiation within each bat genus.
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Affiliation(s)
- Diego A. Caraballo
- Instituto de Zoonosis Luis Pasteur, Ciudad Autónoma de Buenos Aires, Argentina
- * E-mail:
| | - María E. Montani
- Museo Provincial de Ciencias Naturales “Dr. Ángel Gallardo”, Rosario, Santa Fe, Argentina
- Programa de Investigaciones de Biodiversidad Argentina (PIDBA), Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán, San Miguel de Tucumán, Tucumán, Argentina
- Programa de Conservación de los Murciélagos de Argentina (PCMA), San Miguel de Tucumán, Tucumán, Argentina
| | - Leila M. Martínez
- Servicio de Neurovirosis, Instituto Nacional de Enfermedades Infecciosas, Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) “Dr. Carlos G. Malbrán”, Ciudad Autónoma de Buenos Aires, Argentina
| | - Leandro R. Antoniazzi
- Laboratorio de Ecología de Enfermedades (LEcEn), Instituto de Ciencias Veterinarias del Litoral (ICiVet-Litoral), Universidad Nacional del Litoral (UNL) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Esperanza, Santa Fe, Argentina
| | - Tomás C. Sambrana
- Departamento de Zoonosis, Laboratorio Central de Referencia, Dirección de Promoción y Prevención, Ministerio de Salud de la provincia de Santa Fe, Ciudad de Santa Fe, Santa Fe, Argentina
| | - Camilo Fernández
- Laboratorio de Ecología de Enfermedades (LEcEn), Instituto de Ciencias Veterinarias del Litoral (ICiVet-Litoral), Universidad Nacional del Litoral (UNL) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Esperanza, Santa Fe, Argentina
| | - Daniel M. Cisterna
- Servicio de Neurovirosis, Instituto Nacional de Enfermedades Infecciosas, Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) “Dr. Carlos G. Malbrán”, Ciudad Autónoma de Buenos Aires, Argentina
| | - Fernando J. Beltrán
- Instituto de Zoonosis Luis Pasteur, Ciudad Autónoma de Buenos Aires, Argentina
| | - Valeria C. Colombo
- Servicio de Neurovirosis, Instituto Nacional de Enfermedades Infecciosas, Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) “Dr. Carlos G. Malbrán”, Ciudad Autónoma de Buenos Aires, Argentina
- Laboratorio de Ecología de Enfermedades (LEcEn), Instituto de Ciencias Veterinarias del Litoral (ICiVet-Litoral), Universidad Nacional del Litoral (UNL) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Esperanza, Santa Fe, Argentina
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Benevento M, Trotta S, Iarussi F, Caterino C, Jarussi V, Solarino B. Multidisciplinary analysis of bite marks in a fatal human dog attack: A case report. Leg Med (Tokyo) 2020; 48:101816. [PMID: 33242824 DOI: 10.1016/j.legalmed.2020.101816] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/24/2020] [Accepted: 11/12/2020] [Indexed: 10/23/2022]
Abstract
INTRODUCTION Lethal injuries by animal attacks are a matter of concern for the forensic pathologist; the presented case illustrates a two dogs attack on a 61-year-old man. The authors have focused on a multidisciplinary approach involving forensic pathologists and veterinarians. MATERIALS AND METHODS The victim was cycling in the countryside when he was attacked by two dogs that came out of a large house. He was found lying in the street by the homeowners who called for help. The victim was transported to the hospital where he died five days later. According to recovery data and medico-legal autopsy findings the cause of death was septic shock. RESULTS Forensic pathologists and veterinarians multidisciplinary evaluation revealed lacerations, abrasions, and multiple small punctures constituting bite marks over the entire body. Six skin dowels with bite marks were taken and compared with the dental cast of the dogs. CONCLUSION A comparison of the dog dental casts and the bite marks on the victim's body allowed the identification of the animals involved in the attack.
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Affiliation(s)
| | - Silvia Trotta
- Institute of Legal Medicine, University of Bari, Italy.
| | - Fabrizio Iarussi
- Department of Emergency and Organ Transplants, Veterinary Section, University of Bari, Italy
| | | | - Valerio Jarussi
- Specialista in Malattie dei piccoli animali, Dipartimento di Prevenzione, SIAV "C", ASL/FG Sud, Foggia, Italy
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Noren SR. Postnatal development of diving physiology: implications of anthropogenic disturbance for immature marine mammals. ACTA ACUST UNITED AC 2020; 223:223/17/jeb227736. [PMID: 32917778 DOI: 10.1242/jeb.227736] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Marine mammals endure extended breath-holds while performing active behaviors, which has fascinated scientists for over a century. It is now known that these animals have large onboard oxygen stores and utilize oxygen-conserving mechanisms to prolong aerobically supported dives to great depths, while typically avoiding (or tolerating) hypoxia, hypercarbia, acidosis and decompression sickness (DCS). Over the last few decades, research has revealed that diving physiology is underdeveloped at birth. Here, I review the postnatal development of the body's oxygen stores, cardiorespiratory system and other attributes of diving physiology for pinnipeds and cetaceans to assess how physiological immaturity makes young marine mammals vulnerable to disturbance. Generally, the duration required for body oxygen stores to mature varies across species in accordance with the maternal dependency period, which can be over 2 years long in some species. However, some Arctic and deep-diving species achieve mature oxygen stores comparatively early in life (prior to weaning). Accelerated development in these species supports survival during prolonged hypoxic periods when calves accompany their mothers under sea ice and to the bathypelagic zone, respectively. Studies on oxygen utilization patterns and heart rates while diving are limited, but the data indicate that immature marine mammals have a limited capacity to regulate heart rate (and hence oxygen utilization) during breath-hold. Underdeveloped diving physiology, in combination with small body size, limits diving and swimming performance. This makes immature marine mammals particularly vulnerable to mortality during periods of food limitation, habitat alterations associated with global climate change, fishery interactions and other anthropogenic disturbances, such as exposure to sonar.
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Affiliation(s)
- Shawn R Noren
- Institute of Marine Science, University of California, Santa Cruz, CA 95060, USA
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15
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Mae Y, Nagara K, Miyazaki M, Katsura Y, Enomoto Y, Koga A. Complex intragene deletion leads to oculocutaneous albinism in tanuki (Japanese raccoon dog). Genome 2020; 63:517-523. [PMID: 32783776 DOI: 10.1139/gen-2020-0049] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Tanuki (Nyctereutes procyonoides viverrinus), or Japanese raccoon dog, is a canine native to Japan. Tanuki with complete oculocutaneous albinism are relatively frequent in mountainous areas of mainland Japan. Tyrosinase, which is encoded by the TYR gene, is an enzyme essential for the biosynthesis of melanin pigment. We examined the structure and nucleotide sequence of TYR in an albino tanuki and found that the third exon was removed due to a deletion of approximately 11 kb. In addition, two nonsynonymous nucleotide substitutions were found in the fifth exon. These mutations are possible causes of the albino phenotype; however, the order of occurrence is unclear. Even if the 11-kb deletion was not the first of these mutations, it is considered to cause a total loss of the tyrosinase function because the third exon carries codons for one of the two copper-binding sites of tyrosinase and these sites are essential for the enzyme function. Intriguingly, the deletion was not a simple removal of an 11-kb segment: an internal portion was retained as a segment in the reverse orientation. We propose possible formation processes for this mutation that involve multiple DNA scission events, or an inversion followed by a deletion.
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Affiliation(s)
- Yuji Mae
- Iida City Zoo, Iida, Nagano 395-0046, Japan
| | | | - Manabu Miyazaki
- Manabu Miyazaki Photography Office, Iijima, Nagano 399-3705, Japan
| | - Yukako Katsura
- Primate Research Institute, Kyoto University, Inuyama, Aichi 484-8506, Japan
| | - Yuki Enomoto
- Primate Research Institute, Kyoto University, Inuyama, Aichi 484-8506, Japan
| | - Akihiko Koga
- Primate Research Institute, Kyoto University, Inuyama, Aichi 484-8506, Japan
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16
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Noonan MJ, Fleming CH, Tucker MA, Kays R, Harrison A, Crofoot MC, Abrahms B, Alberts SC, Ali AH, Altmann J, Antunes PC, Attias N, Belant JL, Beyer DE, Bidner LR, Blaum N, Boone RB, Caillaud D, de Paula RC, de la Torre JA, Dekker J, DePerno CS, Farhadinia M, Fennessy J, Fichtel C, Fischer C, Ford A, Goheen JR, Havmøller RW, Hirsch BT, Hurtado C, Isbell LA, Janssen R, Jeltsch F, Kaczensky P, Kaneko Y, Kappeler P, Katna A, Kauffman M, Koch F, Kulkarni A, LaPoint S, Leimgruber P, Macdonald DW, Markham AC, McMahon L, Mertes K, Moorman CE, Morato RG, Moßbrucker AM, Mourão G, O'Connor D, Oliveira‐Santos LGR, Pastorini J, Patterson BD, Rachlow J, Ranglack DH, Reid N, Scantlebury DM, Scott DM, Selva N, Sergiel A, Songer M, Songsasen N, Stabach JA, Stacy‐Dawes J, Swingen MB, Thompson JJ, Ullmann W, Vanak AT, Thaker M, Wilson JW, Yamazaki K, Yarnell RW, Zieba F, Zwijacz‐Kozica T, Fagan WF, Mueller T, Calabrese JM. Effects of body size on estimation of mammalian area requirements. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2020; 34:1017-1028. [PMID: 32362060 PMCID: PMC7496598 DOI: 10.1111/cobi.13495] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 11/27/2019] [Accepted: 12/24/2019] [Indexed: 06/08/2023]
Abstract
Accurately quantifying species' area requirements is a prerequisite for effective area-based conservation. This typically involves collecting tracking data on species of interest and then conducting home-range analyses. Problematically, autocorrelation in tracking data can result in space needs being severely underestimated. Based on the previous work, we hypothesized the magnitude of underestimation varies with body mass, a relationship that could have serious conservation implications. To evaluate this hypothesis for terrestrial mammals, we estimated home-range areas with global positioning system (GPS) locations from 757 individuals across 61 globally distributed mammalian species with body masses ranging from 0.4 to 4000 kg. We then applied block cross-validation to quantify bias in empirical home-range estimates. Area requirements of mammals <10 kg were underestimated by a mean approximately15%, and species weighing approximately100 kg were underestimated by approximately50% on average. Thus, we found area estimation was subject to autocorrelation-induced bias that was worse for large species. Combined with the fact that extinction risk increases as body mass increases, the allometric scaling of bias we observed suggests the most threatened species are also likely to be those with the least accurate home-range estimates. As a correction, we tested whether data thinning or autocorrelation-informed home-range estimation minimized the scaling effect of autocorrelation on area estimates. Data thinning required an approximately93% data loss to achieve statistical independence with 95% confidence and was, therefore, not a viable solution. In contrast, autocorrelation-informed home-range estimation resulted in consistently accurate estimates irrespective of mass. When relating body mass to home range size, we detected that correcting for autocorrelation resulted in a scaling exponent significantly >1, meaning the scaling of the relationship changed substantially at the upper end of the mass spectrum.
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Affiliation(s)
- Michael J. Noonan
- Smithsonian Conservation Biology InstituteNational Zoological Park1500 Remount RoadFront RoyalVA22630U.S.A.
- Department of BiologyUniversity of MarylandCollege ParkMD20742U.S.A.
| | - Christen H. Fleming
- Smithsonian Conservation Biology InstituteNational Zoological Park1500 Remount RoadFront RoyalVA22630U.S.A.
- Department of BiologyUniversity of MarylandCollege ParkMD20742U.S.A.
| | - Marlee A. Tucker
- Senckenberg Biodiversity and Climate Research CentreSenckenberg Gesellschaft für NaturforschungSenckenberganlage 25Frankfurt (Main)60325Germany
- Department of Biological SciencesGoethe UniversityMax‐von‐Laue‐Straße 9Frankfurt (Main)60438Germany
- Department of Environmental ScienceInstitute for Wetland and Water ResearchRadboud UniversityP.O. Box 9010NijmegenGLNL‐6500The Netherlands
| | - Roland Kays
- North Carolina Museum of Natural SciencesBiodiversity LabRaleighNC27601U.S.A.
- Fisheries, Wildlife, and Conservation Biology Program, College of Natural Resources Campus Box 8001North Carolina State UniversityRaleighNC27695U.S.A.
| | - Autumn‐Lynn Harrison
- Migratory Bird CenterSmithsonian Conservation Biology InstituteWashingtonD.C.20013U.S.A.
| | - Margaret C. Crofoot
- Department of AnthropologyUniversity of California, DavisDavisCA95616U.S.A.
- Smithsonian Tropical Research InstituteBalboa Ancon0843‐03092Republic of Panama
| | - Briana Abrahms
- Environmental Research DivisionNOAA Southwest Fisheries Science CenterMontereyCA93940U.S.A.
| | - Susan C. Alberts
- Departments of Biology and Evolutionary AnthropologyDuke UniversityDurhamNC27708U.S.A.
| | | | - Jeanne Altmann
- Department of Ecology and EvolutionPrinceton University106A Guyot HallPrincetonNJ08544U.S.A.
| | - Pamela Castro Antunes
- Department of EcologyFederal University of Mato Grosso do SulCampo GrandeMS79070–900Brazil
| | - Nina Attias
- Programa de Pós‐Graduaçao em Biologia Animal, Universidade Federal do Mato Grosso do SulCidade UniversitáriaAv. Costa e SilvaCampo GrandeMato Grosso do Sul79070‐900Brazil
| | - Jerrold L. Belant
- Camp Fire Program in Wildlife Conservation, State University of New YorkCollege of Environmental Science and ForestrySyracuseNY13210U.S.A.
| | - Dean E. Beyer
- Michigan Department of Natural Resources1990 U.S. 41 SouthMarquetteMI49855U.S.A.
| | - Laura R. Bidner
- Department of AnthropologyUniversity of California, DavisDavisCA95616U.S.A.
- Mpala Research CentreNanyuki555–104000Kenya
| | - Niels Blaum
- University of Potsdam, Plant Ecology and Nature ConservationAm Mühlenberg 3Potsdam14476Germany
| | - Randall B. Boone
- Natural Resource Ecology LaboratoryColorado State UniversityFort CollinsCO80523U.S.A.
- Department of Ecosystem Science and SustainabilityColorado State UniversityFort CollinsCO80523U.S.A.
| | - Damien Caillaud
- Department of AnthropologyUniversity of California, DavisDavisCA95616U.S.A.
| | - Rogerio Cunha de Paula
- National Research Center for Carnivores ConservationChico Mendes Institute for the Conservation of BiodiversityEstrada Municipal Hisaichi Takebayashi 8600AtibaiaSP12952‐011Brazil
| | - J. Antonio de la Torre
- Instituto de Ecología, Universidad Nacional Autónoma de Mexico and CONACyTCiudad UniversitariaMexicoD.F.04318Mexico
| | - Jasja Dekker
- Jasja Dekker DierecologieEnkhuizenstraat 26ArnhemWZ6843The Netherlands
| | - Christopher S. DePerno
- Fisheries, Wildlife, and Conservation Biology Program, College of Natural Resources Campus Box 8001North Carolina State UniversityRaleighNC27695U.S.A.
| | - Mohammad Farhadinia
- Wildlife Conservation Research Unit, Department of ZoologyUniversity of OxfordTubney House, OxfordshireOxfordOX13 5QLU.K.
- Future4Leopards FoundationTehranIran
| | | | - Claudia Fichtel
- German Primate CenterBehavioral Ecology & Sociobiology UnitKellnerweg 4Göttingen37077Germany
| | - Christina Fischer
- Restoration Ecology, Department of Ecology and Ecosystem ManagementTechnische Universität MünchenEmil‐Ramann‐Straße 6Freising85354Germany
| | - Adam Ford
- The Irving K. Barber School of Arts and Sciences, Unit 2: BiologyThe University of British ColumbiaOkanagan Campus, SCI 109, 1177 Research RoadKelownaBCV1V 1V7Canada
| | - Jacob R. Goheen
- Department of Zoology and PhysiologyUniversity of WyomingLaramieWY82071U.S.A.
| | | | - Ben T. Hirsch
- Zoology and Ecology, College of Science and EngineeringJames Cook UniversityTownsvilleQLD4811Australia
| | - Cindy Hurtado
- Museo de Historia NaturalUniversidad Nacional Mayor de San MarcosLima15072Peru
- Department of Forest Resources ManagementThe University of British ColumbiaVancouverBCV6T 1Z4Canada
| | - Lynne A. Isbell
- Department of AnthropologyUniversity of California, DavisDavisCA95616U.S.A.
- Mpala Research CentreNanyuki555–104000Kenya
| | - René Janssen
- Bionet NatuuronderzoekValderstraat 39Stein6171ELThe Netherlands
| | - Florian Jeltsch
- University of Potsdam, Plant Ecology and Nature ConservationAm Mühlenberg 3Potsdam14476Germany
| | - Petra Kaczensky
- Norwegian Institute for Nature Research — NINASluppenTrondheimNO‐7485Norway
- Research Institute of Wildlife Ecology, University of Veterinary MedicineSavoyenstraße 1ViennaA‐1160Austria
| | - Yayoi Kaneko
- Tokyo University of Agriculture and TechnologyTokyo183–8509Japan
| | - Peter Kappeler
- German Primate CenterBehavioral Ecology & Sociobiology UnitKellnerweg 4Göttingen37077Germany
| | - Anjan Katna
- Ashoka Trust for Research in Ecology and the Environment (ATREE)BangaloreKarnataka560064India
- Manipal Academy of Higher EducationManipalKarnataka576104India
| | - Matthew Kauffman
- U.S. Geological Survey, Wyoming Cooperative Fish and Wildlife Research Unit, Department of Zoology and PhysiologyUniversity of WyomingLaramieWY82071U.S.A.
| | - Flavia Koch
- German Primate CenterBehavioral Ecology & Sociobiology UnitKellnerweg 4Göttingen37077Germany
| | - Abhijeet Kulkarni
- Ashoka Trust for Research in Ecology and the Environment (ATREE)BangaloreKarnataka560064India
| | - Scott LaPoint
- Max Planck Institute for OrnithologyVogelwarte RadolfzellAm Obstberg 1RadolfzellD‐78315Germany
- Black Rock Forest65 Reservoir RoadCornwallNY12518U.S.A.
| | - Peter Leimgruber
- Smithsonian Conservation Biology InstituteNational Zoological Park1500 Remount RoadFront RoyalVA22630U.S.A.
| | - David W. Macdonald
- Wildlife Conservation Research Unit, Department of ZoologyUniversity of OxfordTubney House, OxfordshireOxfordOX13 5QLU.K.
| | | | - Laura McMahon
- Office of Applied ScienceDepartment of Natural ResourcesRhinelanderWI54501U.S.A.
| | - Katherine Mertes
- Smithsonian Conservation Biology InstituteNational Zoological Park1500 Remount RoadFront RoyalVA22630U.S.A.
| | - Christopher E. Moorman
- Fisheries, Wildlife, and Conservation Biology Program, College of Natural Resources Campus Box 8001North Carolina State UniversityRaleighNC27695U.S.A.
| | - Ronaldo G. Morato
- National Research Center for Carnivores ConservationChico Mendes Institute for the Conservation of BiodiversityEstrada Municipal Hisaichi Takebayashi 8600AtibaiaSP12952‐011Brazil
- Institute for the Conservation of Neotropical Carnivores – Pró‐CarnívorosAtibaiaSao Paulo12945‐010Brazil
| | | | - Guilherme Mourão
- Embrapa PantanalRua 21 de setembro 1880Corumb´aMS79320–900Brazil
| | - David O'Connor
- Department of Biological SciencesGoethe UniversityMax‐von‐Laue‐Straße 9Frankfurt (Main)60438Germany
- San Diego Zoo Institute of Conservation Research15600 San Pasqual Valley RoadEscondidoCA92027U.S.A.
- National Geographic Partners1145 17th Street NWWashingtonD.C.20036U.S.A.
| | | | - Jennifer Pastorini
- Centre for Conservation and Research26/7 C2 Road, KodigahawewaJulpallamaTissamaharama82600Sri Lanka
- Anthropologisches InstitutUniversität ZürichWinterthurerstrasse 190Zurich8057Switzerland
| | - Bruce D. Patterson
- Integrative Research CenterField Museum of Natural HistoryChicagoIL60605U.S.A.
| | - Janet Rachlow
- Department of Fish and Wildlife SciencesUniversity of Idaho875 Perimeter Drive MS 1136MoscowID83844‐1136U.S.A.
| | - Dustin H. Ranglack
- Department of BiologyUniversity of Nebraska at KearneyKearneyNE68849U.S.A.
| | - Neil Reid
- Institute for Global Food Security (IGFS), School of Biological SciencesQueen's University BelfastBelfastBT9 5DLU.K.
| | - David M. Scantlebury
- School of Biological SciencesQueen's University Belfast19 Chlorine GardensBelfastNorthern IrelandBT9 5DLU.K.
| | - Dawn M. Scott
- School of Life SciencesKeele UniversityKeeleStaffordshireST5 5BGU.K.
| | - Nuria Selva
- Institute of Nature ConservationPolish Academy of SciencesMickiewicza 33Krakow31–120Poland
| | - Agnieszka Sergiel
- Institute of Nature ConservationPolish Academy of SciencesMickiewicza 33Krakow31–120Poland
| | - Melissa Songer
- Smithsonian Conservation Biology InstituteNational Zoological Park1500 Remount RoadFront RoyalVA22630U.S.A.
| | - Nucharin Songsasen
- Smithsonian Conservation Biology InstituteNational Zoological Park1500 Remount RoadFront RoyalVA22630U.S.A.
| | - Jared A. Stabach
- Smithsonian Conservation Biology InstituteNational Zoological Park1500 Remount RoadFront RoyalVA22630U.S.A.
| | - Jenna Stacy‐Dawes
- San Diego Zoo Institute of Conservation Research15600 San Pasqual Valley RoadEscondidoCA92027U.S.A.
| | - Morgan B. Swingen
- Fisheries, Wildlife, and Conservation Biology Program, College of Natural Resources Campus Box 8001North Carolina State UniversityRaleighNC27695U.S.A.
- 1854 Treaty Authority4428 Haines RoadDuluthMN55811U.S.A.
| | - Jeffrey J. Thompson
- Asociación Guyra Paraguay – CONACYTParque Ecológico Asunción VerdeAsuncion1101Paraguay
- Instituto SaiteCoronel Felix Cabrera 166Asuncion1101Paraguay
| | - Wiebke Ullmann
- University of Potsdam, Plant Ecology and Nature ConservationAm Mühlenberg 3Potsdam14476Germany
| | - Abi Tamim Vanak
- Ashoka Trust for Research in Ecology and the Environment (ATREE)BangaloreKarnataka560064India
- Wellcome Trust/DBT India AllianceHyderabad500034India
- School of Life SciencesUniversity of KwaZulu‐NatalWestvilleDurban4041South Africa
| | - Maria Thaker
- Centre for Ecological SciencesIndian Institute of ScienceBangalore560012India
| | - John W. Wilson
- Department of Zoology & EntomologyUniversity of PretoriaPretoria0002South Africa
| | - Koji Yamazaki
- Ibaraki Nature MuseumZoological Laboratory700 OsakiBando‐cityIbaraki306–0622Japan
- Forest Ecology LaboratoryDepartment of Forest ScienceTokyo University of Agriculture1‐1‐1 SakuragaokaSetagaya‐KuTokyo156–8502Japan
| | - Richard W. Yarnell
- School of Animal, Rural and Environmental SciencesNottingham Trent UniversityBrackenhurst CampusSouthwellNG25 0QFU.K.
| | - Filip Zieba
- Tatra National ParkKúznice 1Zakopane34–500Poland
| | | | - William F. Fagan
- Department of BiologyUniversity of MarylandCollege ParkMD20742U.S.A.
| | - Thomas Mueller
- Senckenberg Biodiversity and Climate Research CentreSenckenberg Gesellschaft für NaturforschungSenckenberganlage 25Frankfurt (Main)60325Germany
- Department of Biological SciencesGoethe UniversityMax‐von‐Laue‐Straße 9Frankfurt (Main)60438Germany
| | - Justin M. Calabrese
- Smithsonian Conservation Biology InstituteNational Zoological Park1500 Remount RoadFront RoyalVA22630U.S.A.
- Department of BiologyUniversity of MarylandCollege ParkMD20742U.S.A.
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17
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Lamarca AP, Schrago CG. Fast speciations and slow genes: uncovering the root of living canids. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz181] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Despite ongoing efforts relying on computationally intensive tree-building methods and large datasets, the deeper phylogenetic relationships between living canid genera remain controversial. We demonstrate that this issue arises fundamentally from the uncertainty of root placement as a consequence of the short length of the branch connecting the major canid clades, which probably resulted from a fast radiation during the early diversification of extant Canidae. Using both nuclear and mitochondrial genes, we investigate the position of the canid root and its consistency by using three rooting methods. We find that mitochondrial genomes consistently retrieve a root node separating the tribe Canini from the remaining canids, whereas nuclear data mostly recover a root that places the Urocyon foxes as the sister lineage of living canids. We demonstrate that, to resolve the canid root, the nuclear segments sequenced so far are significantly less informative than mitochondrial genomes. We also propose that short intervals between speciations obscure the place of the true root, because methods are susceptible to stochastic error in the presence of short internal branches near the root.
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Affiliation(s)
- Alessandra P Lamarca
- Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Carlos G Schrago
- Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
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18
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Inthong N, Sutacha K, Kaewmongkol S, Sinsiri R, Sribuarod K, Sirinarumitr K, Sirinarumitr T. Feline panleukopenia virus as the cause of diarrhea in a banded linsang (Prionodon linsang) in Thailand. J Vet Med Sci 2019; 81:1763-1768. [PMID: 31548471 PMCID: PMC6943334 DOI: 10.1292/jvms.19-0238] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
A banded linsang (Prionodon linsang) presented at our hospital with clinical signs of acute diarrhea. Fecal samples were positive for canine parvovirus (CPV) as determined by polymerase chain reaction with primers specific for both CPV and feline panleukopenia virus (FPV). The full-length VP2 was cloned, sequenced, and compared with sequences of FPV and CPV strains reported in GenBank. The amino acids that determined the host range were similar to those of FPV. Moreover, amino acid analysis of VP2 revealed over 98% homology to FPV. The FPV isolate was closely related with FPV isolates from Japan, South Korea, and China. To the best of our knowledge, this is the first study to report that banded linsang can be infected with FPV.
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Affiliation(s)
- Natnaree Inthong
- Department of Veterinary Technology, Faculty of Veterinary Technology, Kasetsart University, Bangkok 10900, Thailand.,Center for Agricultural Biotechnology, Kasetsart University, Kamphaeng Sean Campus, Nakhon Pathom 73140, Thailand.,Center of Excellence on Agricultural Biotechnology (AG-BIO/PERDO-CHE), Bangkok 10900, Thailand
| | - Kaset Sutacha
- The Veterinary Teaching Hospital, Bang Khaen campus, Faculty of Veterinary Medicine, Kasetsart University, Bangkok 10900, Thailand
| | - Sarawan Kaewmongkol
- Department of Veterinary Technology, Faculty of Veterinary Technology, Kasetsart University, Bangkok 10900, Thailand
| | - Rungthiwa Sinsiri
- Molecular Diagnostic Laboratory, Faculty of Veterinary Medicine, Kasetsart University, Bangkok 10900, Thailand
| | - Kriangsak Sribuarod
- Khlong Saeng Wildlife Research Station, Wildlife Research Division, Wildlife Conservation Bureau, Department of National Park, Wildlife and Plant Conservation, Ministry of Natural Resources and Environment, Bangkok 10900, Thailand
| | - Kaitkanoke Sirinarumitr
- Center of Excellence on Agricultural Biotechnology (AG-BIO/PERDO-CHE), Bangkok 10900, Thailand.,Department of Small Animal Clinical Sciences, Faculty of Veterinary Medicine, Kasetsart University, Bangkok 10900, Thailand
| | - Theerapol Sirinarumitr
- Center of Excellence on Agricultural Biotechnology (AG-BIO/PERDO-CHE), Bangkok 10900, Thailand.,Department of Pathology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok 10900, Thailand
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19
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Macdonald DW, Campbell LAD, Kamler JF, Marino J, Werhahn G, Sillero-Zubiri C. Monogamy: Cause, Consequence, or Corollary of Success in Wild Canids? Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00341] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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20
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Dell L, Innocenti GM, Hilgetag CC, Manger PR. Cortical and thalamic connectivity of occipital visual cortical areas 17, 18, 19, and 21 of the domestic ferret (
Mustela putorius furo
). J Comp Neurol 2019; 527:1293-1314. [DOI: 10.1002/cne.24631] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 12/19/2018] [Accepted: 01/02/2019] [Indexed: 12/21/2022]
Affiliation(s)
- Leigh‐Anne Dell
- Institute of Computational Neuroscience, University Medical Center Hamburg‐Eppendorf Hamburg Germany
| | - Giorgio M. Innocenti
- Department of NeuroscienceKarolinska Institute Stockholm Sweden
- Brain and Mind InstituteÉcole Polytechnique Fédérale de Lausanne Lausanne Switzerland
| | - Claus C. Hilgetag
- Institute of Computational Neuroscience, University Medical Center Hamburg‐Eppendorf Hamburg Germany
- Department of Health SciencesBoston University Boston Massachusetts
| | - Paul R. Manger
- School of Anatomical Sciences, Faculty of Health Sciences, University of the Witwatersrand Johannesburg South Africa
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21
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Cai YL, Mai CL, Yu X, Liao WB. Effect of population density on relationship between pre- and postcopulatory sexual traits. ANIM BIOL 2019. [DOI: 10.1163/15707563-20181057] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Abstract
Sexual selection theory states that the premating (ornaments and armaments) sexual traits should trade off with the postmating (testes and ejaculates) sexual traits, assuming that growing and maintaining these traits is expensive and that total reproductive investments are limited. Male-male competition and sperm competition are predicted to affect how males allocate their finite resources to these traits. Here, we studied relative expenditure on pre- and postmating sexual traits among 82 species for three mammalian orders with varying population density using comparative phylogenetic analysis. The results showed that population density affected sexual size dimorphism (SSD) in both Artiodactyla and Carnivora, but not in Primates. However, relative testis mass and sperm size were not affected by population density. Moreover, we did not find associations between the SSD and testis mass or sperm size in three taxonomic groups. The interspecific relationships between pre- and postcopulatory sexual traits did not change with increased population density. Our findings suggest that population density did not affect variation in the relationship between pre- and postcopulatory sexual traits for these three mammalian orders.
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Affiliation(s)
- Yun Lin Cai
- 1Department of Urology, the Second Clinical Medical College of North Sichuan Medical College, Nanchong, 637000, China
| | - Chun Lan Mai
- 2Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, 637009, China
| | - Xin Yu
- 2Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, 637009, China
| | - Wen Bo Liao
- 2Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, 637009, China
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22
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Moros-Nicolás C, Leza A, Chevret P, Guillén-Martínez A, González-Brusi L, Boué F, Lopez-Bejar M, Ballesta J, Avilés M, Izquierdo-Rico MJ. Analysis of ZP1 gene reveals differences in zona pellucida composition in carnivores. Reprod Fertil Dev 2018; 30:272-285. [PMID: 28679462 DOI: 10.1071/rd17022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 06/03/2017] [Indexed: 12/30/2022] Open
Abstract
The zona pellucida (ZP) is an extracellular envelope that surrounds mammalian oocytes. This coat participates in the interaction between gametes, induction of the acrosome reaction, block of polyspermy and protection of the oviductal embryo. Previous studies suggested that carnivore ZP was formed by three glycoproteins (ZP2, ZP3 and ZP4), with ZP1 being a pseudogene. However, a recent study in the cat found that all four proteins were expressed. In the present study, in silico and molecular analyses were performed in several carnivores to clarify the ZP composition in this order of mammals. The in silico analysis demonstrated the presence of the ZP1 gene in five carnivores: cheetah, panda, polar bear, tiger and walrus, whereas in the Antarctic fur seal and the Weddell seal there was evidence of pseudogenisation. Molecular analysis showed the presence of four ZP transcripts in ferret ovaries (ZP1, ZP2, ZP3 and ZP4) and three in fox ovaries (ZP2, ZP3 and ZP4). Analysis of the fox ZP1 gene showed the presence of a stop codon. The results strongly suggest that all four ZP genes are expressed in most carnivores, whereas ZP1 pseudogenisation seems to have independently affected three families (Canidae, Otariidae and Phocidae) of the carnivore tree.
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Affiliation(s)
- C Moros-Nicolás
- Department of Cell Biology and Histology, Faculty of Medicine, Biomedical Research Institute of Murcia (IMIB-Arrixaca-UMU), University of Murcia, 30100, Murcia, Spain
| | - A Leza
- Department of Cell Biology and Histology, Faculty of Medicine, Biomedical Research Institute of Murcia (IMIB-Arrixaca-UMU), University of Murcia, 30100, Murcia, Spain
| | - P Chevret
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, CNRS, Université de Lyon, Université Claude Bernard Lyon 1, 69622, Villeurbanne, France
| | - A Guillén-Martínez
- Department of Cell Biology and Histology, Faculty of Medicine, Biomedical Research Institute of Murcia (IMIB-Arrixaca-UMU), University of Murcia, 30100, Murcia, Spain
| | - L González-Brusi
- Department of Cell Biology and Histology, Faculty of Medicine, Biomedical Research Institute of Murcia (IMIB-Arrixaca-UMU), University of Murcia, 30100, Murcia, Spain
| | - F Boué
- ANSES, Nancy Laboratory for Rabies and Wildlife, CS 40009, 54220 Malzéville, France
| | - M Lopez-Bejar
- Department of Animal Health and Anatomy, Universitat Autònoma de Barcelona, 08193, Barcelona, Spain
| | - J Ballesta
- Department of Cell Biology and Histology, Faculty of Medicine, Biomedical Research Institute of Murcia (IMIB-Arrixaca-UMU), University of Murcia, 30100, Murcia, Spain
| | - M Avilés
- Department of Cell Biology and Histology, Faculty of Medicine, Biomedical Research Institute of Murcia (IMIB-Arrixaca-UMU), University of Murcia, 30100, Murcia, Spain
| | - M J Izquierdo-Rico
- Department of Cell Biology and Histology, Faculty of Medicine, Biomedical Research Institute of Murcia (IMIB-Arrixaca-UMU), University of Murcia, 30100, Murcia, Spain
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23
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Adega F, Matoso Silva R, Kjöllerström HJ, Vercammen P, Raudsepp T, Collares-Pereira MJ, Fernandes C, do Mar Oom M, Chaves R. Comparative Chromosome Painting in Genets (Carnivora, Viverridae, Genetta), the Only Known Feliforms with a Highly Rearranged Karyotype. Cytogenet Genome Res 2018; 156:35-44. [PMID: 30086546 DOI: 10.1159/000491868] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/26/2018] [Indexed: 11/19/2022] Open
Abstract
Mammalian carnivores have been extensively studied by cross-species chromosome painting, which indicated a high degree of karyotypic conservatism in the cat-like suborder Feliformia relative to the ancestral carnivore karyotype (ACK). The first exception to this high degree of karyotypic conservation in feliforms was recently confirmed in genets, mesocarnivores belonging to the basal family Viverridae. Here, we present a comparative analysis of the chromosome rearrangements among 2 subspecies of the small-spotted genet Genetta genetta (the Iberian nominate and the Arabian grantii) and the panther genet G. maculata, the 2 most common and widespread genets, using whole-chromosome paints from the domestic cat (Felis catus). The chromosome homology maps and the presence of numerous interstitial telomeric sites in both genet species strengthen the hypothesis that a highly rearranged karyotype compared to the ACK may occur throughout Genetta. The karyotype of G. maculata appears to have undergone more rearrangements than that of G. genetta, which is an older lineage. Notably, we identified a tandem fusion distinguishing G. g. genetta and G. g.grantii. As G. g. grantii is morphologically and genetically distinctive, and tandem fusions have been associated with substantial postzygotic isolation in mammals, this cytogenetic finding flags the subspecies for future taxonomic investigations.
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24
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Zrzavý J, Duda P, Robovský J, Okřinová I, Pavelková Řičánková V. Phylogeny of the Caninae (Carnivora): Combining morphology, behaviour, genes and fossils. ZOOL SCR 2018. [DOI: 10.1111/zsc.12293] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Jan Zrzavý
- Department of Zoology; Faculty of Science; University of South Bohemia; České Budějovice Czech Republic
| | - Pavel Duda
- Department of Zoology; Faculty of Science; University of South Bohemia; České Budějovice Czech Republic
- Center for Theoretical Study; Charles University and Czech Academy of Sciences; Prague Czech Republic
| | - Jan Robovský
- Department of Zoology; Faculty of Science; University of South Bohemia; České Budějovice Czech Republic
| | - Isabela Okřinová
- Department of Zoology; Faculty of Science; University of South Bohemia; České Budějovice Czech Republic
| | - Věra Pavelková Řičánková
- Department of Zoology; Faculty of Science; University of South Bohemia; České Budějovice Czech Republic
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25
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Comprehensive skin microbiome analysis reveals the uniqueness of human skin and evidence for phylosymbiosis within the class Mammalia. Proc Natl Acad Sci U S A 2018; 115:E5786-E5795. [PMID: 29871947 PMCID: PMC6016819 DOI: 10.1073/pnas.1801302115] [Citation(s) in RCA: 132] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Skin forms a critical protective barrier between a mammal and its external environment. Baseline data on the mammalian skin microbiome elucidates which microorganisms are found on healthy skin and provides insight into mammalian evolutionary history. To our knowledge, this study represents the largest existing mammalian skin microbiome survey. Our findings demonstrate that human skin is distinct, not only from other Primates, but from all 10 mammalian orders sampled. Identifying significant similarities between branching of mammalian phylogenetic trees and relatedness trees for their corresponding microbial communities raises the possibility that mammals have experienced coevolution between skin microbiota and their corresponding host species. Skin is the largest organ of the body and represents the primary physical barrier between mammals and their external environment, yet the factors that govern skin microbial community composition among mammals are poorly understood. The objective of this research was to generate a skin microbiota baseline for members of the class Mammalia, testing the effects of host species, geographic location, body region, and biological sex. Skin from the back, torso, and inner thighs of 177 nonhuman mammals was sampled, representing individuals from 38 species and 10 mammalian orders. Animals were sampled from farms, zoos, households, and the wild. The DNA extracts from all skin swabs were amplified by PCR and sequenced, targeting the V3-V4 regions of bacterial and archaeal 16S rRNA genes. Previously published skin microbiome data from 20 human participants, sampled and sequenced using an identical protocol to the nonhuman mammals, were included to make this a comprehensive analysis. Human skin microbial communities were distinct and significantly less diverse than all other sampled mammalian orders. The factor most strongly associated with microbial community data for all samples was whether the host was a human. Within nonhuman samples, host taxonomic order was the most significant factor influencing skin microbiota, followed by the geographic location of the habitat. By comparing the congruence between host phylogeny and microbial community dendrograms, we observed that Artiodactyla (even-toed ungulates) and Perissodactyla (odd-toed ungulates) had significant congruence, providing evidence of phylosymbiosis between skin microbial communities and their hosts.
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26
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Machado FA, Zahn TMG, Marroig G. Evolution of morphological integration in the skull of Carnivora (Mammalia): Changes in Canidae lead to increased evolutionary potential of facial traits. Evolution 2018; 72:1399-1419. [PMID: 29803199 DOI: 10.1111/evo.13495] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 04/20/2018] [Indexed: 12/14/2022]
Abstract
Morphological integration refers to the fact that different phenotypic traits of organisms are not fully independent from each other, and tend to covary to different degrees. The covariation among traits is thought to reflect properties of the species' genetic architecture and thus can have an impact on evolutionary responses. Furthermore, if morphological integration changes along the history of a group, inferences of past selection regimes might be problematic. Here, we evaluated the stability and evolution of the morphological integration of skull traits in Carnivora by using evolutionary simulations and phylogenetic comparative methods. Our results show that carnivoran species are able to respond to natural selection in a very similar way. Our comparative analyses show that the phylogenetic signal for pattern of integration is lower than that observed for morphology (trait averages), and that integration was stable throughout the evolution of the group. That notwithstanding, Canidae differed from other families by having higher integration, evolvability, flexibility, and allometric coefficients on the facial region. These changes might have allowed canids to rapidly adapt to different food sources, helping to explain not only the phenotypic diversification of the family, but also why humans were able to generate such a great diversity of dog breeds through artificial selection.
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Affiliation(s)
- Fabio Andrade Machado
- División Mastozoologa, Museo Argentino de Ciencias Naturales, "Bernardino Rivadavia". Av. Ángel Gallardo 470 (C1405DJR), Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Thiago Macek Gonçalves Zahn
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, SP 05508-090, Brazil
| | - Gabriel Marroig
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, SP 05508-090, Brazil
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27
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Boessenecker RW, Churchill M. The last of the desmatophocid seals: a new species of Allodesmus from the upper Miocene of Washington, USA, and a revision of the taxonomy of Desmatophocidae. Zool J Linn Soc 2018. [DOI: 10.1093/zoolinnean/zlx098] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Robert W Boessenecker
- Department of Geology and Environmental Geosciences, College of Charleston, Charleston, SC, USA
- University of California Museum of Paleontology, University of California, Berkeley, CA, USA
| | - Morgan Churchill
- Department of Biology, University of Wisconsin Oshkosh, Oshkosh, WI, USA
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28
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Lowe AD, Bawazeer S, Watson DG, McGill S, Burchmore RJS, Pomeroy PPP, Kennedy MW. Rapid changes in Atlantic grey seal milk from birth to weaning - immune factors and indicators of metabolic strain. Sci Rep 2017; 7:16093. [PMID: 29170469 PMCID: PMC5700954 DOI: 10.1038/s41598-017-16187-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 11/08/2017] [Indexed: 11/21/2022] Open
Abstract
True seals have the shortest lactation periods of any group of placental mammal. Most are capital breeders that undergo short, intense lactations, during which they fast while transferring substantial proportions of their body reserves to their pups, which they then abruptly wean. Milk was collected from Atlantic grey seals (Halichoerus grypus) periodically from birth until near weaning. Milk protein profiles matured within 24 hours or less, indicating the most rapid transition from colostrum to mature phase lactation yet observed. There was an unexpected persistence of immunoglobulin G almost until weaning, potentially indicating prolonged trans-intestinal transfer of IgG. Among components of innate immune protection were found fucosyllactose and siallylactose that are thought to impede colonisation by pathogens and encourage an appropriate milk-digestive and protective gut microbiome. These oligosaccharides decreased from early lactation to almost undetectable levels by weaning. Taurine levels were initially high, then fell, possibly indicative of taurine dependency in seals, and progressive depletion of maternal reserves. Metabolites that signal changes in the mother’s metabolism of fats, such as nicotinamide and derivatives, rose from virtual absence, and acetylcarnitines fell. It is therefore possible that indicators of maternal metabolic strain exist that signal the imminence of weaning.
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Affiliation(s)
- Amanda D Lowe
- Institute of Biodiversity, Animal Health & Comparative Medicine, and School of Life Sciences, Graham Kerr Building, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, Scotland, UK
| | - Sami Bawazeer
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow, G4 0RE, Scotland, UK
| | - David G Watson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow, G4 0RE, Scotland, UK
| | - Suzanne McGill
- Institute of Infection, Immunity and Inflammation, and Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow, Garscube Campus, Glasgow, G12 1QH, Scotland, UK
| | - Richard J S Burchmore
- Institute of Infection, Immunity and Inflammation, and Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow, Garscube Campus, Glasgow, G12 1QH, Scotland, UK
| | - P P Paddy Pomeroy
- Sea Mammal Research Unit, Scottish Oceans Institute, University of St Andrews, St Andrews, Fife, United Kingdom
| | - Malcolm W Kennedy
- Institute of Biodiversity, Animal Health & Comparative Medicine, and School of Life Sciences, Graham Kerr Building, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, Scotland, UK.
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29
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Ito Y, Enju C, Li J, Tanaka N. Evolutionary distinctiveness and conservation priority of the endangered Najas ancistrocarpa (Hydrocharitaceae). SYST BIODIVERS 2017. [DOI: 10.1080/14772000.2017.1358219] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Yu Ito
- Plant Phylogenetics and Conservation Group, Centre for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, P. R. China
| | - Chigaya Enju
- College of Agro-biological Resource Sciences, University of Tsukuba, Tsukuba 305-8577, Japan
| | - Jie Li
- Plant Phylogenetics and Conservation Group, Centre for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, P. R. China
| | - Norio Tanaka
- Tsukuba Botanical Garden, National Museum of Nature and Science, Tsukuba 305-0005, Japan
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30
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Anyone with a Long-Face? Craniofacial Evolutionary Allometry (CREA) in a Family of Short-Faced Mammals, the Felidae. Evol Biol 2017. [DOI: 10.1007/s11692-017-9421-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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31
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Regional distribution of cholinergic, catecholaminergic, serotonergic and orexinergic neurons in the brain of two carnivore species: The feliform banded mongoose ( Mungos mungo ) and the caniform domestic ferret ( Mustela putorius furo ). J Chem Neuroanat 2017; 82:12-28. [DOI: 10.1016/j.jchemneu.2017.04.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 04/11/2017] [Accepted: 04/11/2017] [Indexed: 11/24/2022]
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32
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Panciroli E, Janis C, Stockdale M, Martín-Serra A. Correlates between calcaneal morphology and locomotion in extant and extinct carnivorous mammals. J Morphol 2017; 278:1333-1353. [DOI: 10.1002/jmor.20716] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 04/10/2017] [Accepted: 05/20/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Elsa Panciroli
- School of Geosciences; University of Edinburgh; Edinburgh United Kingdom
- Department of Natural Sciences; National Museum of Scotland, Chambers Street; Edinburgh United Kingdom
- Department of Earth Sciences; University of Bristol; Bristol United Kingdom
| | - Christine Janis
- Department of Earth Sciences; University of Bristol; Bristol United Kingdom
- Department of Ecology and Evolutionary Biology; Brown University; Providence Rhode Island United States of America
| | | | - Alberto Martín-Serra
- Department of Earth Sciences; University of Oxford, South Parks Road; Oxford OX1 3AN, United Kingdom
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33
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Johnson PJ, Noonan MJ, Kitchener AC, Harrington LA, Newman C, Macdonald DW. Rensching cats and dogs: feeding ecology and fecundity trends explain variation in the allometry of sexual size dimorphism. ROYAL SOCIETY OPEN SCIENCE 2017; 4:170453. [PMID: 28680689 PMCID: PMC5493931 DOI: 10.1098/rsos.170453] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 06/01/2017] [Indexed: 06/07/2023]
Abstract
The tendency for sexual size dimorphism (SSD) to increase with body mass in taxa where males are larger, and to decrease when females are larger, is known as Rensch's rule. In mammals, where the trend occurs, it is believed to be the result of a competitive advantage for larger males, while female mass is constrained by the energetics of reproduction. Here, we examine the allometry of SSD within the Felidae and Canidae, demonstrating distinctly different patterns: in felids, there is positive allometric scaling, while there is no trend in canids. We hypothesize that feeding ecology, via its effect on female spacing patterns, is responsible for the difference; larger male mass may be advantageous only where females are dispersed such that males can defend access to them. This is supported by the observation that felids are predominately solitary, and all are obligate carnivores. Similarly, carnivorous canids are more sexually dimorphic than insectivores and omnivores, but carnivory does not contribute to a Rensch effect as dietary variation occurs across the mass spectrum. The observed inter-familial differences are also consistent with reduced constraints on female mass in the canids, where litter size increases with body mass, versus no observable allometry in the felids.
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Affiliation(s)
- P. J. Johnson
- Wildlife Conservation Research Unit, Zoology Department, The Recanati-Kaplan Centre, University of Oxford, Tubney House, Abingdon Road, Tubney, Abingdon OX13 5QL, UK
| | - M. J. Noonan
- Wildlife Conservation Research Unit, Zoology Department, The Recanati-Kaplan Centre, University of Oxford, Tubney House, Abingdon Road, Tubney, Abingdon OX13 5QL, UK
- Smithsonian Conservation Biology Institute, National Zoological Park, 1500 Remount Road, Front Royal, VA 22630, USA
| | - A. C. Kitchener
- Department of Natural Sciences, National Museums Scotland, Chambers Street, Edinburgh EH1 1JF, UK
- Institute of Geography, School of Geosciences, University of Edinburgh, Drummond Street, Edinburgh EH9 3PX, UK
| | - L. A. Harrington
- Wildlife Conservation Research Unit, Zoology Department, The Recanati-Kaplan Centre, University of Oxford, Tubney House, Abingdon Road, Tubney, Abingdon OX13 5QL, UK
| | - C. Newman
- Wildlife Conservation Research Unit, Zoology Department, The Recanati-Kaplan Centre, University of Oxford, Tubney House, Abingdon Road, Tubney, Abingdon OX13 5QL, UK
| | - D. W. Macdonald
- Wildlife Conservation Research Unit, Zoology Department, The Recanati-Kaplan Centre, University of Oxford, Tubney House, Abingdon Road, Tubney, Abingdon OX13 5QL, UK
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Jespersen A, Jensen HE, Agger JF, Heegaard PMH, Damborg P, Aalbæk B, Hammer AS. The effect of color type on early wound healing in farmed mink (Neovison vison). BMC Vet Res 2017; 13:135. [PMID: 28532438 PMCID: PMC5440898 DOI: 10.1186/s12917-017-1052-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 05/08/2017] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Individual differences of mink, including color type, are speculated to affect the course of wound healing, thereby impacting wound assessment and management on the farms, as well as the assessment of wounds in forensic cases. In this study, we examined the effect of color type on early wound healing in farmed mink. Full thickness excisional wounds (2 × 2 cm) were made on the back in 18 mink of the color types Brown, Silverblue and Blue Iris. Gross and microscopic pathology of the wounds was evaluated 2 days post-wounding together with degree of wound size reduction, presence of bacteria and blood analyses. RESULTS Pathological examination on day 2 showed the greatest mean wound size reduction in Brown mink (11.0%) followed by Blue Iris (7.9%) and Silverblue (1.6%). Bacteria were cultured from all wounds, and predominantly Staphylococcus species were recovered in mixed or pure culture. Histopathology from day 2 wounds showed a scab overlying necrotic wound edges, which were separated from underlying vital tissue by a demarcation zone rich in polymorphonuclear leukocytes. Fibroblasts and plump endothelial cells were more numerous in the deeper tissues. Complete blood count parameters were within normal ranges in most cases, however, the mink showed mildly to markedly decreased hematocrit and six mink of the color types Silverblue and Blue Iris showed moderately elevated numbers of circulating segmented neutrophils on day 2. There was a marked increase in concentration of serum amyloid A from day 0 to day 2 in all color types. CONCLUSIONS We have described differences in early wound healing between mink of the color types Brown, Silverblue and Blue Iris by use of an experimental wound model in farmed mink. The most pronounced difference pertained to the degree of wound size reduction which was greatest in Brown mink, followed by Blue Iris and Silverblue, respectively.
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Affiliation(s)
- A. Jespersen
- Kopenhagen Fur, Langagervej 60, DK-2600 Glostrup, Denmark
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Ridebanevej 3, DK-1870 Frederiksberg C, Denmark
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Ridebanevej 3, DK-1870 Frederiksberg C, Denmark
| | - H. E. Jensen
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Ridebanevej 3, DK-1870 Frederiksberg C, Denmark
| | - J. F. Agger
- Department of Large Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Grønnegårdsvej 8, DK-1870 Frederiksberg C, Denmark
| | - P. M. H. Heegaard
- National Veterinary Institute, Technical University of Denmark, Bülowsvej 27, DK-1870 Frederiksberg C, Denmark
| | - P. Damborg
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Ridebanevej 3, DK-1870 Frederiksberg C, Denmark
| | - B. Aalbæk
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Ridebanevej 3, DK-1870 Frederiksberg C, Denmark
| | - A. S. Hammer
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Ridebanevej 3, DK-1870 Frederiksberg C, Denmark
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35
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Feijoo M, Parada A. Macrosystematics of eutherian mammals combining HTS data to expand taxon coverage. Mol Phylogenet Evol 2017; 113:76-83. [PMID: 28487261 DOI: 10.1016/j.ympev.2017.05.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 05/04/2017] [Accepted: 05/04/2017] [Indexed: 02/04/2023]
Abstract
In the last few years high-throughput sequencing technologies have permitted significant advances in mammalian phylogenetic studies from a genomic perspective. However, these studies have been restricted to a sparse number of species with available reference genomes. Thus, several issues inside the eutherian mammals phylogeny remain unresolved. This may be due in part to limited taxon sampling, as taxonomic density is known to affect phylogenetic resolution. In this context, we present a protocol to increase taxon coverage using high-throughput sequencing data (RNA or DNA) generated for other biological studies and available in public databases. Following this procedure we addressed pending or controversial issues concerning the phylogenetic position of Dermoptera, Pholidota and Chiroptera, considering multiple and independent loci. Also for Chiroptera and Arctoidea we evaluated the relationships of the lineages that compose it. Although the maximum number of genes used is moderate (95), in some cases taxon coverage doubles that of previous related studies. Globally, all coalescent-based (STAR, MP-EST and ASTRAL) and concatenated (IQ-TREE and BEAST2) methods used for species tree reconstruction were consistent to each other and most of interrogated nodes received high statistical support.
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Affiliation(s)
- M Feijoo
- Departamento de Ecología y Evolución, Facultad de Ciencias, Universidad de la República, Montevideo CP 11400, Uruguay.
| | - A Parada
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia CP 5090000, Chile.
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36
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Zhou Y, Wang SR, Ma JZ. Comprehensive species set revealing the phylogeny and biogeography of Feliformia (Mammalia, Carnivora) based on mitochondrial DNA. PLoS One 2017; 12:e0174902. [PMID: 28358848 PMCID: PMC5373635 DOI: 10.1371/journal.pone.0174902] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 03/18/2017] [Indexed: 11/18/2022] Open
Abstract
Extant Feliformia species are one of the most diverse radiations of Carnivora (~123 species). Despite substantial recent interest in their conservation, diversification, and systematic study, no previous phylogeny contains a comprehensive species set, and no biogeography of this group is available. Here, we present a phylogenetic estimate for Feliformia with a comprehensive species set and establish a historical biogeography based on mitochondrial DNA. Both the Bayesian and maximum likelihood phylogeny for Feliformia are elucidated in our analyses and are strongly consistent with many groups recognized in previous studies. The mitochondrial phylogenetic relationships of Felidae were for the first time successfully reconstructed in our analyses with strong supported. When divergence times and dispersal/vicariance histories were compared with historical sea level changes, four dispersal and six vicariance events were identified. These vicariance events were closely related with global sea level changes. The transgression of sea into the lowland plains between Eurasia and Africa may have caused the vicariance in these regions. A fall in the sea level during late Miocene to Pliocene produced the Bering strait land bridge, which assisted the migration of American Feliformia ancestors from Asia to North America. In contrast with the ‘sweepstakes hypothesis’, our results suggest that the climate cooling during 30–27 Ma assisted Feliformia migration from the African mainland to Madagascar by creating a short-lived ice bridge across the Mozambique Channel. Lineages-through-time plots revealed a large increase in lineages since the Mid-Miocene. During the Mid-Miocene Climatic Optimum, the ecosystems and population of Feliformia rapidly expanded. Subsequent climate cooling catalyzed immigration, speciation, and the extinction of Feliformia.
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Affiliation(s)
- Yu Zhou
- College of Wildlife Resources, Northeast Forestry University, Harbin, China
- Feline Research Center of Chinese State Forestry Administration, Northeast Forestry University, Harbin, China
| | - Si-Rui Wang
- College of Wildlife Resources, Northeast Forestry University, Harbin, China
| | - Jian-Zhang Ma
- College of Wildlife Resources, Northeast Forestry University, Harbin, China
- Feline Research Center of Chinese State Forestry Administration, Northeast Forestry University, Harbin, China
- * E-mail:
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37
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Turner EC, Sawyer EK, Kaas JH. Optic nerve, superior colliculus, visual thalamus, and primary visual cortex of the northern elephant seal (Mirounga angustirostris) and California sea lion (Zalophus californianus). J Comp Neurol 2017; 525:2109-2132. [PMID: 28188622 DOI: 10.1002/cne.24188] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 01/31/2017] [Accepted: 02/01/2017] [Indexed: 11/07/2022]
Abstract
The northern elephant seal (Mirounga angustirostris) and California sea lion (Zalophus californianus) are members of a diverse clade of carnivorous mammals known as pinnipeds. Pinnipeds are notable for their large, ape-sized brains, yet little is known about their central nervous system. Both the northern elephant seal and California sea lion spend most of their lives at sea, but each also spends time on land to breed and give birth. These unique coastal niches may be reflected in specific evolutionary adaptations to their sensory systems. Here, we report on components of the visual pathway in these two species. We found evidence for two classes of myelinated fibers within the pinniped optic nerve, those with thick myelin sheaths (elephant seal: 9%, sea lion: 7%) and thin myelin sheaths (elephant seal: 91%, sea lion: 93%). In order to investigate the architecture of the lateral geniculate nucleus, superior colliculus, and primary visual cortex, we processed brain sections from seal and sea lion pups for Nissl substance, cytochrome oxidase, and vesicular glutamate transporters. As in other carnivores, the dorsal lateral geniculate nucleus consisted of three main layers, A, A1, and C, while each superior colliculus similarly consisted of seven distinct layers. The sea lion visual cortex is located at the posterior side of cortex between the upper and lower banks of the postlateral sulcus, while the elephant seal visual cortex extends far more anteriorly along the dorsal surface and medial wall. These results are relevant to comparative studies related to the evolution of large brains.
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Affiliation(s)
- Emily C Turner
- Department of Psychology, Vanderbilt University, Nashville, Tennessee
| | - Eva K Sawyer
- Department of Psychology, Vanderbilt University, Nashville, Tennessee.,Department of Bioengineering, University of California, Berkeley, California
| | - Jon H Kaas
- Department of Psychology, Vanderbilt University, Nashville, Tennessee
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38
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Botton-Divet L, Cornette R, Houssaye A, Fabre AC, Herrel A. Swimming and running: a study of the convergence in long bone morphology among semi-aquatic mustelids (Carnivora: Mustelidae). Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blw027] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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39
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Pyšková K, Storch D, Horáček I, Kauzál O, Pyšek P. Golden jackal ( Canis aureus) in the Czech Republic: the first record of a live animal and its long-term persistence in the colonized habitat. Zookeys 2016:151-163. [PMID: 28138295 PMCID: PMC5240352 DOI: 10.3897/zookeys.641.10946] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 12/12/2016] [Indexed: 11/12/2022] Open
Abstract
A golden jackal (Canis aureus) individual was recorded ~40 km east of Prague in the Czech Republic. It is the first record of a living golden jackal in the country; up to now several individuals have been recorded but all of them were either shot dead or killed by a vehicle. The observed animal was documented by camera traps set up for research of carnivore diversity in different habitats in the study area. It was first photographed on 19 June 2015, and in total there were 57 records made by 12 traps until 24 March 2016 when the animal was still present in the area. Forty-nine of the 57 records were made in a shrubby grassland over an area of ~100 ha, 39% of sightings were during the day and 61% in the night. There were two distinct peaks in the circadian activity of the animal, from 4 to 10 a.m., and from 6 p.m. to midnight. We also review the verified records of the golden jackal in the Czech Republic, some of which were only published in local hunting magazines. However, the observation reported in this paper represents the first evidence of a long-term occurrence in Europe of the same golden jackal individual, that persisted for at least nine months and over winter, northwest of Hungarian-Austrian border where the population has been known to reproduce.
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Affiliation(s)
- Klára Pyšková
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, CZ-12844 Prague 2, Czech Republic; Institute of Botany, Department of Invasion Ecology, The Czech Academy of Sciences, CZ-25243 Průhonice, Czech Republic
| | - David Storch
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, CZ-12844 Prague 2, Czech Republic; Center for Theoretical Study, Charles University and The Czech Academy of Sciences, Jilská 1, CZ-11000, Prague 1, Czech Republic
| | - Ivan Horáček
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, CZ-12844 Prague 2, Czech Republic; Department of Zoology, Faculty of Science, Charles University, Viničná 7, CZ-12844 Prague 2, Czech Republic
| | - Ondřej Kauzál
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, CZ-12844 Prague 2, Czech Republic; Institute of Botany, Department of Invasion Ecology, The Czech Academy of Sciences, CZ-25243 Průhonice, Czech Republic
| | - Petr Pyšek
- Institute of Botany, Department of Invasion Ecology, The Czech Academy of Sciences, CZ-25243 Průhonice, Czech Republic; Department of Ecology, Faculty of Science, Charles University, Viničná 7, CZ-12844 Prague 2, Czech Republic
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40
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Noonan MJ, Johnson PJ, Kitchener AC, Harrington LA, Newman C, Macdonald DW. Sexual size dimorphism in musteloids: An anomalous allometric pattern is explained by feeding ecology. Ecol Evol 2016; 6:8495-8501. [PMID: 28031801 PMCID: PMC5167046 DOI: 10.1002/ece3.2480] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 08/17/2016] [Accepted: 08/18/2016] [Indexed: 11/16/2022] Open
Abstract
Rensch's rule states that sexual size dimorphism (SSD) increases with body size in taxa where males are larger, and decreases when females are larger. The dominant explanation for the trend is currently that competitive advantage for males is greater in larger individuals, whereas female size is constrained by the energetics of rearing offspring. This rule holds for a variety of vertebrate taxa, and opposing trends are rare. We examine the allometry of SSD within the Musteloidea and demonstrate a hypo-allometry contrary to Rensch's rule, with lower SSD associated with larger body size. We provide evidence that feeding ecology is involved. Where diet promotes group-living, the optimal strategy for the males of larger species is often not to attempt to defend access to multiple females, obviating any competitive advantage of relatively greater size. We conclude that the effect of feeding ecology on mating systems may be a hitherto neglected factor explaining variation in SSD.
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Affiliation(s)
- Michael J. Noonan
- Wildlife Conservation Research UnitZoology DepartmentThe Recanati‐Kaplan CentreUniversity of OxfordTubneyAbingdonUK
| | - Paul J. Johnson
- Wildlife Conservation Research UnitZoology DepartmentThe Recanati‐Kaplan CentreUniversity of OxfordTubneyAbingdonUK
| | - Andrew C. Kitchener
- Department of Natural SciencesNational Museums ScotlandEdinburghUK
- Institute of GeographySchool of GeosciencesUniversity of EdinburghEdinburghUK
| | - Lauren A. Harrington
- Wildlife Conservation Research UnitZoology DepartmentThe Recanati‐Kaplan CentreUniversity of OxfordTubneyAbingdonUK
| | - Chris Newman
- Wildlife Conservation Research UnitZoology DepartmentThe Recanati‐Kaplan CentreUniversity of OxfordTubneyAbingdonUK
| | - David W. Macdonald
- Wildlife Conservation Research UnitZoology DepartmentThe Recanati‐Kaplan CentreUniversity of OxfordTubneyAbingdonUK
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41
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Veron S, Penone C, Clergeau P, Costa GC, Oliveira BF, São-Pedro VA, Pavoine S. Integrating data-deficient species in analyses of evolutionary history loss. Ecol Evol 2016; 6:8502-8514. [PMID: 28031802 PMCID: PMC5167052 DOI: 10.1002/ece3.2390] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 07/20/2016] [Accepted: 08/01/2016] [Indexed: 11/11/2022] Open
Abstract
There is an increasing interest in measuring loss of phylogenetic diversity and evolutionary distinctiveness which together depict the evolutionary history of conservation interest. Those losses are assessed through the evolutionary relationships between species and species threat status or extinction probabilities. Yet, available information is not always sufficient to quantify the threat status of species that are then classified as data deficient. Data‐deficient species are a crucial issue as they cause incomplete assessments of the loss of phylogenetic diversity and evolutionary distinctiveness. We aimed to explore the potential bias caused by data‐deficient species in estimating four widely used indices: HEDGE, EDGE, PDloss, and Expected PDloss. Second, we tested four different widely applicable and multitaxa imputation methods and their potential to minimize the bias for those four indices. Two methods are based on a best‐ vs. worst‐case extinction scenarios, one is based on the frequency distribution of threat status within a taxonomic group and one is based on correlates of extinction risks. We showed that data‐deficient species led to important bias in predictions of evolutionary history loss (especially high underestimation when they were removed). This issue was particularly important when data‐deficient species tended to be clustered in the tree of life. The imputation method based on correlates of extinction risks, especially geographic range size, had the best performance and enabled us to improve risk assessments. Solving threat status of DD species can fundamentally change our understanding of loss of phylogenetic diversity. We found that this loss could be substantially higher than previously found in amphibians, squamate reptiles, and carnivores. We also identified species that are of high priority for the conservation of evolutionary distinctiveness.
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Affiliation(s)
- Simon Veron
- Centre d'Ecologie et des Sciences de la Conservation (CESCO UMR7204) Sorbonne Universités, MNHN, CNRS, UPMC CP51, 55-61 rue Buffon 75005 Paris France
| | | | - Philippe Clergeau
- Centre d'Ecologie et des Sciences de la Conservation (CESCO UMR7204) Sorbonne Universités, MNHN, CNRS, UPMC CP51, 55-61 rue Buffon 75005 Paris France
| | - Gabriel C Costa
- Laboratório de Biogeografia e Macroecologia Departamento de Ecologia Universidade Federal do Rio Grande do Norte Natal Brazil
| | - Brunno F Oliveira
- Laboratório de Biogeografia e Macroecologia Departamento de Ecologia Universidade Federal do Rio Grande do Norte Natal Brazil
| | - Vinícius A São-Pedro
- Laboratório de Biogeografia e Macroecologia Departamento de Ecologia Universidade Federal do Rio Grande do Norte Natal Brazil; Laboratório de Ecologia Sensorial Departamento de Fisiologia Universidade Federal do Rio Grande do Norte Natal Brazil
| | - Sandrine Pavoine
- Centre d'Ecologie et des Sciences de la Conservation (CESCO UMR7204) Sorbonne Universités, MNHN, CNRS, UPMC CP51, 55-61 rue Buffon 75005 Paris France
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42
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Botton-Divet L, Cornette R, Fabre AC, Herrel A, Houssaye A. Morphological Analysis of Long Bones in Semi-aquatic Mustelids and their Terrestrial Relatives. Integr Comp Biol 2016; 56:1298-1309. [DOI: 10.1093/icb/icw124] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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43
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Gatesy J, Meredith RW, Janecka JE, Simmons MP, Murphy WJ, Springer MS. Resolution of a concatenation/coalescence kerfuffle: partitioned coalescence support and a robust family‐level tree for Mammalia. Cladistics 2016; 33:295-332. [DOI: 10.1111/cla.12170] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/30/2016] [Indexed: 12/14/2022] Open
Affiliation(s)
- John Gatesy
- Department of Biology University of California Riverside CA 92521 USA
| | - Robert W. Meredith
- Department of Biology and Molecular Biology Montclair State University Montclair NJ 07043 USA
| | - Jan E. Janecka
- Department of Biological Sciences Duquesne University Pittsburgh PA 15282 USA
| | - Mark P. Simmons
- Department of Biology Colorado State University Fort Collins CO 80523 USA
| | - William J. Murphy
- Department of Veterinary Integrative Biosciences Texas A&M University College Station TX 77843 USA
| | - Mark S. Springer
- Department of Biology University of California Riverside CA 92521 USA
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44
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Ercoli MD, Álvarez A, Busker F, Morales MM, Julik E, Smith HF, Adrian B, Barton M, Bhagavatula K, Poole M, Shahsavan M, Wechsler R, Fisher RE. Myology of the Head, Neck, and Thoracic Region of the Lesser Grison (Galictis cuja) in Comparison with the Red Panda (Ailurus fulgens) and Other Carnivorans: Phylogenetic and Functional Implications. J MAMM EVOL 2016. [DOI: 10.1007/s10914-016-9339-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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45
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Sawyer EK, Turner EC, Kaas JH. Somatosensory brainstem, thalamus, and cortex of the California sea lion (Zalophus californianus). J Comp Neurol 2016; 524:1957-75. [PMID: 26878587 PMCID: PMC4833517 DOI: 10.1002/cne.23984] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 02/08/2016] [Accepted: 02/09/2016] [Indexed: 12/18/2022]
Abstract
Pinnipeds (sea lions, seals, and walruses) are notable for many reasons, including their ape-sized brains, their adaptation to a coastal niche that combines mastery of the sea with strong ties to land, and the remarkable abilities of their trigeminal whisker system. However, little is known about the central nervous system of pinnipeds. Here we report on the somatosensory areas of the nervous system of the California sea lion (Zalophus californianus). Using stains for Nissl, cytochrome oxidase, and vesicular glutamate transporters, we investigated the primary somatosensory areas in the brainstem, thalamus, and cortex in one sea lion pup and the external anatomy of the brain in a second pup. We find that the sea lion's impressive array of whiskers is matched by a large trigeminal representation in the brainstem with well-defined parcellation that resembles the barrelettes found in rodents but scaled upward in size. The dorsal column nuclei are large and distinct. The ventral posterior nucleus of the thalamus has divisions, with a large area for the presumptive head representation. Primary somatosensory cortex is located in the neocortex just anterior to the main vertical fissure, and precisely locating it as we do here is useful for comparing the highly gyrified pinniped cortex with that of other carnivores. To our knowledge this work is the first comprehensive report on the central nervous system areas for any sensory system in a pinniped. The results may be useful both in the veterinary setting and for comparative studies related to brain evolution.
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Affiliation(s)
- Eva K Sawyer
- Neuroscience Graduate Program, Vanderbilt University, Nashville, Tennessee, 37240
| | - Emily C Turner
- Department of Psychology, Vanderbilt University, Nashville, Tennessee, 37240
| | - Jon H Kaas
- Department of Psychology, Vanderbilt University, Nashville, Tennessee, 37240
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46
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Canoville A, de Buffrénil V, Laurin M. Microanatomical diversity of amniote ribs: an exploratory quantitative study. Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12779] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Aurore Canoville
- Bonn University; Steinmann Institute for Geology; Mineralogy and Paleontology; Nußallee 8 53115 Bonn Germany
| | - Vivian de Buffrénil
- CR2P; Centre de Recherches sur la Paléobiodiversité et les Paléoenvironnements; Sorbonne Universités; CNRS/MNHN/UPMC; Muséum National d'Histoire Naturelle; Bâtiment de Géologie; Case postale 48, 43 rue Buffon, F-75231 Paris Cedex 05 Paris France
| | - Michel Laurin
- CR2P; Centre de Recherches sur la Paléobiodiversité et les Paléoenvironnements; Sorbonne Universités; CNRS/MNHN/UPMC; Muséum National d'Histoire Naturelle; Bâtiment de Géologie; Case postale 48, 43 rue Buffon, F-75231 Paris Cedex 05 Paris France
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47
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Churchill M, Clementz MT. The evolution of aquatic feeding in seals: insights from
Enaliarctos
(Carnivora: Pinnipedimorpha), the oldest known seal. J Evol Biol 2015; 29:319-34. [DOI: 10.1111/jeb.12783] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 10/06/2015] [Accepted: 10/09/2015] [Indexed: 11/28/2022]
Affiliation(s)
- M. Churchill
- Department of Anatomy New York Institute of Technology Old Westbury NY USA
- Department of Geology and Geophysics University of Wyoming Laramie WY USA
- Program in Ecology University of Wyoming Laramie WY USA
| | - M. T. Clementz
- Department of Geology and Geophysics University of Wyoming Laramie WY USA
- Program in Ecology University of Wyoming Laramie WY USA
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48
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Veron S, Davies TJ, Cadotte MW, Clergeau P, Pavoine S. Predicting loss of evolutionary history: Where are we? Biol Rev Camb Philos Soc 2015; 92:271-291. [PMID: 26467982 DOI: 10.1111/brv.12228] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 09/10/2015] [Accepted: 09/17/2015] [Indexed: 01/29/2023]
Abstract
The Earth's evolutionary history is threatened by species loss in the current sixth mass extinction event in Earth's history. Such extinction events not only eliminate species but also their unique evolutionary histories. Here we review the expected loss of Earth's evolutionary history quantified by phylogenetic diversity (PD) and evolutionary distinctiveness (ED) at risk. Due to the general paucity of data, global evolutionary history losses have been predicted for only a few groups, such as mammals, birds, amphibians, plants, corals and fishes. Among these groups, there is now empirical support that extinction threats are clustered on the phylogeny; however this is not always a sufficient condition to cause higher loss of phylogenetic diversity in comparison to a scenario of random extinctions. Extinctions of the most evolutionarily distinct species and the shape of phylogenetic trees are additional factors that can elevate losses of evolutionary history. Consequently, impacts of species extinctions differ among groups and regions, and even if global losses are low within large groups, losses can be high among subgroups or within some regions. Further, we show that PD and ED are poorly protected by current conservation practices. While evolutionary history can be indirectly protected by current conservation schemes, optimizing its preservation requires integrating phylogenetic indices with those that capture rarity and extinction risk. Measures based on PD and ED could bring solutions to conservation issues, however they are still rarely used in practice, probably because the reasons to protect evolutionary history are not clear for practitioners or due to a lack of data. However, important advances have been made in the availability of phylogenetic trees and methods for their construction, as well as assessments of extinction risk. Some challenges remain, and looking forward, research should prioritize the assessment of expected PD and ED loss for more taxonomic groups and test the assumption that preserving ED and PD also protects rare species and ecosystem services. Such research will be useful to inform and guide the conservation of Earth's biodiversity and the services it provides.
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Affiliation(s)
- Simon Veron
- Centre d'Ecologie et des Sciences de la Conservation (CESCO UMR7204), Sorbonne Universités, MNHN, CNRS, UPMC, CP51, 55-61 rue Buffon, 75005 Paris, France
| | - T Jonathan Davies
- Department of Biology, McGill University, 1205 ave Docteur Penfield, Montreal, Quebec H3A 1B1, Canada.,African Centre for DNA Barcoding, University of Johannesburg, APK Campus, PO Box 524, Auckland Park 2006, Johannesburg, South Africa
| | - Marc W Cadotte
- Department of Biology, University of Toronto Scarborough, 1265 Military Trail, Toronto, Ontario M1C 1A4, Canada
| | - Philippe Clergeau
- Centre d'Ecologie et des Sciences de la Conservation (CESCO UMR7204), Sorbonne Universités, MNHN, CNRS, UPMC, CP51, 55-61 rue Buffon, 75005 Paris, France
| | - Sandrine Pavoine
- Centre d'Ecologie et des Sciences de la Conservation (CESCO UMR7204), Sorbonne Universités, MNHN, CNRS, UPMC, CP51, 55-61 rue Buffon, 75005 Paris, France.,Mathematical Ecology Research Group, Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, U.K
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Noonan MJ, Newman C, Buesching CD, Macdonald DW. Evolution and function of fossoriality in the Carnivora: implications for group-living. Front Ecol Evol 2015. [DOI: 10.3389/fevo.2015.00116] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Doronina L, Churakov G, Shi J, Brosius J, Baertsch R, Clawson H, Schmitz J. Exploring Massive Incomplete Lineage Sorting in Arctoids (Laurasiatheria, Carnivora). Mol Biol Evol 2015; 32:3194-204. [PMID: 26337548 DOI: 10.1093/molbev/msv188] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Freed from the competition of large raptors, Paleocene carnivores could expand their newly acquired habitats in search of prey. Such changing conditions might have led to their successful distribution and rapid radiation. Today, molecular evolutionary biologists are faced, however, with the consequences of such accelerated adaptive radiations, because they led to sequential speciation more rapidly than phylogenetic markers could be fixed. The repercussions being that current genealogies based on such markers are incongruent with species trees.Our aim was to explore such conflicting phylogenetic zones of evolution during the early arctoid radiation, especially to distinguish diagnostic from misleading phylogenetic signals, and to examine other carnivore-related speciation events. We applied a combination of high-throughput computational strategies to screen carnivore and related genomes in silico for randomly inserted retroposed elements that we then used to identify inconsistent phylogenetic patterns in the Arctoidea group, which is well known for phylogenetic discordances.Our combined retrophylogenomic and in vitro wet lab approach detected hundreds of carnivore-specific insertions, many of them confirming well-established splits or identifying and solving conflicting species distributions. Our systematic genome-wide screens for Long INterspersed Elements detected homoplasy-free markers with insertion-specific truncation points that we used to distinguish phylogenetically informative markers from conflicting signals. The results were independently confirmed by phylogenetic diagnostic Short INterspersed Elements. As statistical analysis ruled out ancestral hybridization, these doubly verified but still conflicting patterns were statistically determined to be genomic remnants from a time of ancestral incomplete lineage sorting that especially accompanied large parts of Arctoidea evolution.
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Affiliation(s)
- Liliya Doronina
- Institute of Experimental Pathology, ZMBE, University of Münster, Münster, Germany
| | - Gennady Churakov
- Institute of Experimental Pathology, ZMBE, University of Münster, Münster, Germany Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Jingjing Shi
- Institute of Experimental Pathology, ZMBE, University of Münster, Münster, Germany
| | - Jürgen Brosius
- Institute of Experimental Pathology, ZMBE, University of Münster, Münster, Germany Institute of Evolutionary and Medical Genomics, Brandenburg Medical School (MHB), Neuruppin, Germany
| | - Robert Baertsch
- Department of Biomolecular Engineering, University of California, Santa Cruz
| | - Hiram Clawson
- Department of Biomolecular Engineering, University of California, Santa Cruz
| | - Jürgen Schmitz
- Institute of Experimental Pathology, ZMBE, University of Münster, Münster, Germany
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