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Herrick J. Kimura's Theory of Non-Adaptive Radiation and Peto's Paradox: A Missing Link? BIOLOGY 2023; 12:1140. [PMID: 37627024 PMCID: PMC10452704 DOI: 10.3390/biology12081140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 08/07/2023] [Accepted: 08/15/2023] [Indexed: 08/27/2023]
Abstract
Karyotype diversity reflects genome integrity and stability. A strong correlation between karyotype diversity and species richness, meaning the number of species in a phylogenetic clade, was first reported in mammals over forty years ago: in mammalian phylogenetic clades, the standard deviation of karyotype diversity (KD) closely corresponded to species richness (SR) at the order level. These initial studies, however, did not control for phylogenetic signal, raising the possibility that the correlation was due to phylogenetic relatedness among species in a clade. Accordingly, karyotype diversity trivially reflects species richness simply as a passive consequence of adaptive radiation. A more recent study in mammals controlled for phylogenetic signals and established the correlation as phylogenetically independent, suggesting that species richness cannot, in itself, explain the observed corresponding karyotype diversity. The correlation is, therefore, remarkable because the molecular mechanisms contributing to karyotype diversity are evolutionarily independent of the ecological mechanisms contributing to species richness. Recently, it was shown in salamanders that the two processes generating genome size diversity and species richness were indeed independent and operate in parallel, suggesting a potential non-adaptive, non-causal but biologically meaningful relationship. KD depends on mutational input generating genetic diversity and reflects genome stability, whereas species richness depends on ecological factors and reflects natural selection acting on phenotypic diversity. As mutation and selection operate independently and involve separate and unrelated evolutionary mechanisms-there is no reason a priori to expect such a strong, let alone any, correlation between KD and SR. That such a correlation exists is more consistent with Kimura's theory of non-adaptive radiation than with ecologically based adaptive theories of macro-evolution, which are not excluded in Kimura's non-adaptive theory. The following reviews recent evidence in support of Kimura's proposal, and other findings that contribute to a wider understanding of the molecular mechanisms underlying the process of non-adaptive radiation.
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Affiliation(s)
- John Herrick
- Independent Researcher, 3, rue des Jeûneurs, 75002 Paris, France
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Christmas MJ, Kaplow IM, Genereux DP, Dong MX, Hughes GM, Li X, Sullivan PF, Hindle AG, Andrews G, Armstrong JC, Bianchi M, Breit AM, Diekhans M, Fanter C, Foley NM, Goodman DB, Goodman L, Keough KC, Kirilenko B, Kowalczyk A, Lawless C, Lind AL, Meadows JRS, Moreira LR, Redlich RW, Ryan L, Swofford R, Valenzuela A, Wagner F, Wallerman O, Brown AR, Damas J, Fan K, Gatesy J, Grimshaw J, Johnson J, Kozyrev SV, Lawler AJ, Marinescu VD, Morrill KM, Osmanski A, Paulat NS, Phan BN, Reilly SK, Schäffer DE, Steiner C, Supple MA, Wilder AP, Wirthlin ME, Xue JR, Birren BW, Gazal S, Hubley RM, Koepfli KP, Marques-Bonet T, Meyer WK, Nweeia M, Sabeti PC, Shapiro B, Smit AFA, Springer MS, Teeling EC, Weng Z, Hiller M, Levesque DL, Lewin HA, Murphy WJ, Navarro A, Paten B, Pollard KS, Ray DA, Ruf I, Ryder OA, Pfenning AR, Lindblad-Toh K, Karlsson EK. Evolutionary constraint and innovation across hundreds of placental mammals. Science 2023; 380:eabn3943. [PMID: 37104599 PMCID: PMC10250106 DOI: 10.1126/science.abn3943] [Citation(s) in RCA: 60] [Impact Index Per Article: 60.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 12/16/2022] [Indexed: 04/29/2023]
Abstract
Zoonomia is the largest comparative genomics resource for mammals produced to date. By aligning genomes for 240 species, we identify bases that, when mutated, are likely to affect fitness and alter disease risk. At least 332 million bases (~10.7%) in the human genome are unusually conserved across species (evolutionarily constrained) relative to neutrally evolving repeats, and 4552 ultraconserved elements are nearly perfectly conserved. Of 101 million significantly constrained single bases, 80% are outside protein-coding exons and half have no functional annotations in the Encyclopedia of DNA Elements (ENCODE) resource. Changes in genes and regulatory elements are associated with exceptional mammalian traits, such as hibernation, that could inform therapeutic development. Earth's vast and imperiled biodiversity offers distinctive power for identifying genetic variants that affect genome function and organismal phenotypes.
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Affiliation(s)
- Matthew J. Christmas
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 32 Uppsala, Sweden
| | - Irene M. Kaplow
- Department of Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | | | - Michael X. Dong
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 32 Uppsala, Sweden
| | - Graham M. Hughes
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Xue Li
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
- Morningside Graduate School of Biomedical Sciences, UMass Chan Medical School, Worcester, MA 01605, USA
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Patrick F. Sullivan
- Department of Genetics, University of North Carolina Medical School, Chapel Hill, NC 27599, USA
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Allyson G. Hindle
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Gregory Andrews
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Joel C. Armstrong
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Matteo Bianchi
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 32 Uppsala, Sweden
| | - Ana M. Breit
- School of Biology and Ecology, University of Maine, Orono, ME 04469, USA
| | - Mark Diekhans
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Cornelia Fanter
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Nicole M. Foley
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA
| | - Daniel B. Goodman
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA
| | | | - Kathleen C. Keough
- Fauna Bio, Inc., Emeryville, CA 94608, USA
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94158, USA
- Gladstone Institutes, San Francisco, CA 94158, USA
| | - Bogdan Kirilenko
- Faculty of Biosciences, Goethe-University, 60438 Frankfurt, Germany
- LOEWE Centre for Translational Biodiversity Genomics, 60325 Frankfurt, Germany
- Senckenberg Research Institute, 60325 Frankfurt, Germany
| | - Amanda Kowalczyk
- Department of Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Colleen Lawless
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Abigail L. Lind
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94158, USA
- Gladstone Institutes, San Francisco, CA 94158, USA
| | - Jennifer R. S. Meadows
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 32 Uppsala, Sweden
| | - Lucas R. Moreira
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Ruby W. Redlich
- Department of Biological Sciences, Mellon College of Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Louise Ryan
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Ross Swofford
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Alejandro Valenzuela
- Department of Experimental and Health Sciences, Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Franziska Wagner
- Museum of Zoology, Senckenberg Natural History Collections Dresden, 01109 Dresden, Germany
| | - Ola Wallerman
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 32 Uppsala, Sweden
| | - Ashley R. Brown
- Department of Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Joana Damas
- The Genome Center, University of California Davis, Davis, CA 95616, USA
| | - Kaili Fan
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA 01605, USA
| | - John Gatesy
- Division of Vertebrate Zoology, American Museum of Natural History, New York, NY 10024, USA
| | - Jenna Grimshaw
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA
| | - Jeremy Johnson
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Sergey V. Kozyrev
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 32 Uppsala, Sweden
| | - Alyssa J. Lawler
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
- Department of Biological Sciences, Mellon College of Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Voichita D. Marinescu
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 32 Uppsala, Sweden
| | - Kathleen M. Morrill
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
- Morningside Graduate School of Biomedical Sciences, UMass Chan Medical School, Worcester, MA 01605, USA
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Austin Osmanski
- Medical Scientist Training Program, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Nicole S. Paulat
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA
| | - BaDoi N. Phan
- Department of Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Medical Scientist Training Program, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Steven K. Reilly
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Daniel E. Schäffer
- Department of Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Cynthia Steiner
- Conservation Genetics, San Diego Zoo Wildlife Alliance, Escondido, CA 92027, USA
| | - Megan A. Supple
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Aryn P. Wilder
- Conservation Genetics, San Diego Zoo Wildlife Alliance, Escondido, CA 92027, USA
| | - Morgan E. Wirthlin
- Department of Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - James R. Xue
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | | | - Bruce W. Birren
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Steven Gazal
- Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | | | - Klaus-Peter Koepfli
- Center for Species Survival, Smithsonian’s National Zoo and Conservation Biology Institute, Washington, DC 20008, USA
- Computer Technologies Laboratory, ITMO University, St. Petersburg 197101, Russia
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA 22630, USA
| | - Tomas Marques-Bonet
- Catalan Institution of Research and Advanced Studies (ICREA), 08010 Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), 08036 Barcelona, Spain
- Department of Medicine and Life Sciences, Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, 08003 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Barcelona, Spain
| | - Wynn K. Meyer
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA
| | - Martin Nweeia
- Department of Comprehensive Care, School of Dental Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
- Department of Vertebrate Zoology, Canadian Museum of Nature, Ottawa, Ontario K2P 2R1, Canada
- Department of Vertebrate Zoology, Smithsonian Institution, Washington, DC 20002, USA
- Narwhal Genome Initiative, Department of Restorative Dentistry and Biomaterials Sciences, Harvard School of Dental Medicine, Boston, MA 02115, USA
| | - Pardis C. Sabeti
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | | | - Mark S. Springer
- Department of Evolution, Ecology and Organismal Biology, University of California Riverside, Riverside, CA 92521, USA
| | - Emma C. Teeling
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Michael Hiller
- Faculty of Biosciences, Goethe-University, 60438 Frankfurt, Germany
- LOEWE Centre for Translational Biodiversity Genomics, 60325 Frankfurt, Germany
- Senckenberg Research Institute, 60325 Frankfurt, Germany
| | | | - Harris A. Lewin
- The Genome Center, University of California Davis, Davis, CA 95616, USA
- Department of Evolution and Ecology, University of California Davis, Davis, CA 95616, USA
- John Muir Institute for the Environment, University of California Davis, Davis, CA 95616, USA
| | - William J. Murphy
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA
| | - Arcadi Navarro
- Catalan Institution of Research and Advanced Studies (ICREA), 08010 Barcelona, Spain
- Department of Medicine and Life Sciences, Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, 08003 Barcelona, Spain
- BarcelonaBeta Brain Research Center, Pasqual Maragall Foundation, 08005 Barcelona, Spain
- CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), 08003 Barcelona, Spain
| | - Benedict Paten
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Katherine S. Pollard
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94158, USA
- Gladstone Institutes, San Francisco, CA 94158, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - David A. Ray
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA
| | - Irina Ruf
- Division of Messel Research and Mammalogy, Senckenberg Research Institute and Natural History Museum Frankfurt, 60325 Frankfurt am Main, Germany
| | - Oliver A. Ryder
- Conservation Genetics, San Diego Zoo Wildlife Alliance, Escondido, CA 92027, USA
- Department of Evolution, Behavior and Ecology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92039, USA
| | - Andreas R. Pfenning
- Department of Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Kerstin Lindblad-Toh
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 32 Uppsala, Sweden
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Elinor K. Karlsson
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA 01605, USA
- Program in Molecular Medicine, UMass Chan Medical School, Worcester, MA 01605, USA
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Gavrilov VM, Golubeva TB, Bushuev AV. Metabolic rate, sleep duration, and body temperature in evolution of mammals and birds: the influence of geological time of principal groups divergence. Zookeys 2023; 1148:1-27. [DOI: 10.3897/zookeys.1148.93458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 01/11/2023] [Indexed: 02/16/2023] Open
Abstract
This study contains an analysis of basal metabolic rate (BMR) in 1817 endothermic species. The aim was to establish how metabolic scaling varies between the main groups of endotherms during evolution. The data for all the considered groups were combined and the common exponent in the allometric relationship between the BMR and body weight was established as b = 0.7248. Reduced to the common slope, the relative metabolic rate forms the following series: Neognathae – Passeriformes – 1.00, Neognathae – Non-Passeriformes – 0.75, Palaeognathae – 0.53, Eutheria – 0.57, Marsupialia – 0.44, and Monotremata – 0.26. The main finding is that the metabolic rate in the six main groups of mammals and birds consistently increases as the geological time of the group’s divergence approaches the present. In parallel, the average body temperature in the group rises, the duration of sleep decreases and the duration of activity increases. BMR in a taxon correlates with its evolutionary age: the later a clade diverged, the higher is its metabolic rate and the longer is its activity period; group exponents decrease as group divergence nears present times while with increase metabolic rate during activity, they not only do not decrease but can increase. Sleep duration in mammals was on average 40% longer than in birds while BMR, in contrast, was 40% higher in birds. The evolution of metabolic scaling, body temperature, sleep duration, and activity during the development of endothermic life forms is demonstrated, allowing for a better understanding of the underlying principles of endothermy formation.
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Kim YR, Kim HR, Kim JY, Myeong HH, Kang JH, Kim BJ, Lee HJ. Spatio-temporal genetic structure of the striped field mouse (Apodemus agrarius) populations inhabiting national parks in South Korea: Implications for conservation and management of protected areas. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2023.1038058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Population or habitat connectivity is a key component in maintaining species and community-level regional biodiversity as well as intraspecific genetic diversity. Ongoing human activities cause habitat destruction and fragmentation, which exacerbate the connectivity due to restricted animal movements across local habitats, eventually resulting in the loss of biodiversity. The Baekdudaegan Mountain Range (BMR) on the Korean Peninsula represents “biodiversity hotspots” and eight of the 22 Korean national parks are located within the BMR. Given the striped field mouse (Apodemus agrarius) is the most common and ecologically important small mammals in these protected areas, the population genetic assessment of this species will allow for identifying “genetic diversity hotspots” and also “genetic barriers” that may hinder gene flow, and will therefore inform on effective conservation and management efforts for the national park habitats. We collected samples from hair, tail, or buccal swabs for 252 A. agrarius individuals in 2015 and 2019. By using mitochondrial DNA cytochrome b (cyt b) sequences and nine microsatellite loci, we determined levels of genetic diversity, genetic differentiation, and gene flow among eight national park populations of A. agrarius along the BMR. We found high levels of genetic diversity but the occurrences of inbreeding for all the nine samples analyzed. Our results also indicated that there was detectable temporal genetic variation between the 2015 and 2019 populations in the Jirisan National Park, which is probably due to a short-term decline in genetic diversity caused by reduced population sizes. We also found a well-admixed shared gene pool among the national park populations. However, a significant positive correlation between geographic and genetic distances was detected only in mtDNA but not microsatellites, which might be attributed to different dispersal patterns between sexes. There was a genetic barrier to animal movements around the Woraksan National Park areas. The poor habitat connectivity surrounding these areas can be improved by establishing an ecological corridor. Our findings of the presence of genetic barriers in some protected areas provide insights into the conservation and management efforts to improve the population or habitat connectivity among the national parks.
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Seeber PA, Epp LS. Environmental
DNA
and metagenomics of terrestrial mammals as keystone taxa of recent and past ecosystems. Mamm Rev 2022. [DOI: 10.1111/mam.12302] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Peter A. Seeber
- Limnological Institute University of Konstanz Konstanz Germany
| | - Laura S. Epp
- Limnological Institute University of Konstanz Konstanz Germany
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A Bocage Landscape Restricts the Gene Flow of Pest Vole Populations. Life (Basel) 2022; 12:life12060800. [PMID: 35743831 PMCID: PMC9225191 DOI: 10.3390/life12060800] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 05/17/2022] [Accepted: 05/24/2022] [Indexed: 11/17/2022] Open
Abstract
The population dynamics of most animal species inhabiting agro-ecosystems may be determined by landscape characteristics, with agricultural intensification and the reduction of natural habitats influencing dispersal and hence limiting gene flow. Increasing landscape complexity would thus benefit many endangered species by providing different ecological niches, but it could also lead to undesired effects in species that can act as crop pests and disease reservoirs. We tested the hypothesis that a highly variegated landscape influences patterns of genetic structure in agricultural pest voles. Ten populations of fossorial water vole, Arvicola scherman, located in a bocage landscape in Atlantic NW Spain were studied using DNA microsatellite markers and a graph-based model. The results showed a strong isolation-by-distance pattern with a significant genetic correlation at smaller geographic scales, while genetic differentiation at larger geographic scales indicated a hierarchical pattern of up to eight genetic clusters. A metapopulation-type structure was observed, immersed in a landscape with a low proportion of suitable habitats. Matrix scale rather than matrix heterogeneity per se may have an important effect upon gene flow, acting as a demographic sink. The identification of sub-populations, considered to be independent management units, allows the establishment of feasible population control efforts in this area. These insights support the use of agro-ecological tools aimed at recreating enclosed field systems when planning integrated managements for controlling patch-dependent species such as grassland voles.
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Frank HER, Amato K, Trautwein M, Maia P, Liman ER, Nichols LM, Schwenk K, Breslin PAS, Dunn RR. The evolution of sour taste. Proc Biol Sci 2022; 289:20211918. [PMID: 35135352 PMCID: PMC8826303 DOI: 10.1098/rspb.2021.1918] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The evolutionary history of sour taste has been little studied. Through a combination of literature review and trait mapping on the vertebrate phylogenetic tree, we consider the origin of sour taste, potential cases of the loss of sour taste, and those factors that might have favoured changes in the valence of sour taste-from aversive to appealing. We reconstruct sour taste as having evolved in ancient fish. By contrast to other tastes, sour taste does not appear to have been lost in any major vertebrate taxa. For most species, sour taste is aversive. Animals, including humans, that enjoy the sour taste triggered by acidic foods are exceptional. We conclude by considering why sour taste evolved, why it might have persisted as vertebrates made the transition to land and what factors might have favoured the preference for sour-tasting, acidic foods, particularly in hominins, such as humans.
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Affiliation(s)
- Hannah E. R. Frank
- Department of Crop and Soil Sciences North Carolina State University, Raleigh, USA
| | - Katie Amato
- Department of Anthropology, Northwestern University, Evanston, IL, USA
| | - Michelle Trautwein
- Entomology Department, Institute for Biodiversity Science and Sustainability, California Academy of Sciences, San Francisco, USA
| | - Paula Maia
- Department of Anthropology, Northwestern University, Evanston, IL, USA
| | - Emily R. Liman
- Department of Biological Sciences, Section of Neurobiology, University of Southern California, Los Angeles, CA, USA
| | - Lauren M. Nichols
- Department of Applied Ecology, North Carolina State University, Raleigh, USA
| | - Kurt Schwenk
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Paul A. S. Breslin
- Department of Nutritional Sciences, Rutgers The State University of New Jersey, New Brunswick, NJ, USA,Monell Chemical Senses Center, Philadelphia, PA, USA
| | - Robert R. Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, USA,Center for Evolutionary Hologenomics, University of Copenhagen, Copenhagen, Denmark
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Delu V, Dharambir Singh, Sumit Dookia, Priya, Kiran. Seasonal food preferences and group activity pattern of Blackbuck Antilope cervicapra (L., 1758) (Mammalia: Cetartiodactyla: Bovidae) in a semi-arid region of western Haryana, India. JOURNAL OF THREATENED TAXA 2021. [DOI: 10.11609/jott.7086.13.13.19937-19947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
To evaluate food preferences and group activity patterns, a fragmented population of Blackbuck Antilope cervicapra was selected for observation in a semi-arid ecosystem of western Haryana. A field survey was conducted fortnightly, from dawn to dusk, between September 2019 and August 2020, covering every season. Scan sampling and quadrat methods were used to record data on group size and vegetation. Group sizes ranged from 3 to 72 individuals. Based on visual observation, blackbuck seasonally consumed 26 species belonging to 25 families with varied preferences, out of a total of 53 plant species documented from the study site. Some plant species with high medicinal and therapeutic values were preferred, including Artemisia scoparia, Cucumis callous, Ziziphus jujuba, and Ziziphus nummularia. Unlike most herbivores, Blackbuck also consumed the toxic and medicinally rich Calotropis procera. We suggest that zoos which house blackbuck include these preferred wild plant species in their diet. Observations on group activity were analyzed on hourly, monthly and seasonal bases, and converted into time percentages. Group foraging activity was at a maximum in the monsoon (62%) and minimum in winter (50%), followed by resting: maximum in winter (21%) and minimum (12%) in monsoon, largely influenced by food availability. Foraging/walking ratio was at a maximum (5.2) in monsoon and minimum (3.1) in winter, and was correlated with the number of group sightings (maximum in winter and minimum in monsoon) in nearby farmland, when the animals faced food scarcity in their natural habitat and fed on crops.
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Santos F, Lima MGM, Espinosa S, Ahumada JA, Jansen PA, Spironello WR, Hurtado J, Juen L, Peres CA. Site and species contribution to β-diversity in terrestrial mammal communities: Evidence from multiple Neotropical forest sites. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 789:147946. [PMID: 34058582 DOI: 10.1016/j.scitotenv.2021.147946] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 05/16/2021] [Accepted: 05/17/2021] [Indexed: 06/12/2023]
Abstract
In a scenario where escalating human activities lead to several environmental changes and, consequently, affect mammal abundance and distribution, β-diversity may increase due to differences among sites. Using the ecological uniqueness approach, we analyzed β-diversity patterns of ground-dwelling mammal communities recorded through comprehensive camera trap monitoring within eight tropical forests protected areas in Mesoamerica and South America under variable landscape contexts. We aimed to investigate whether the contribution of single sites (LCBD) and single species (SCBD) to overall β-diversity could be explained by community metrics and environmental variables, and by species metrics and biological traits, respectively. Total β-diversity was also partitioned into species replacement and richness difference. We related LCBD to species richness, total relative abundance, functional indices, and environmental variables (tree basal area, protected area size, NDVI, and precipitation seasonality), and SCBD to species naïve occupancy, relative abundance, and morphoecological traits via beta regression. Our findings showed that LCBD was primarily explained by variation in species richness, rather than relative abundance and functional metrics. Protected area size and tree basal area were also important in explaining variation in LCBD. SCBD was strongly related to naïve occupancy and relative abundance, but not to biological traits, such as body mass, trophic energy level, activity cycle, and taxonomic category. Local β-diversity was a result of species replacements and to a lesser extent differences in species richness. Our approach was useful in examining and comparing the ecological uniqueness among different sites, revealing the regional scale current status of mammal diversity. High LCBD values comprised sites embedded within smaller habitat extents, hosting lower tree basal areas, and harboring low species richness. SCBD showed that relatively ubiquitous species that occur at variable abundances across sites contributed most to β-diversity.
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Affiliation(s)
- Fernanda Santos
- Programa de Pós-graduação em Ecologia, Universidade Federal do Pará, Belém, Pará, Brazil; Departamento de Mastozoologia, Museu Paraense Emílio Goeldi, Belém, Pará, Brazil.
| | | | - Santiago Espinosa
- Facultad de Ciencias, Universidad Autónoma de San Luis Potosí, San Luis Potosí, Mexico; Escuela de Ciencias Biologicas, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Jorge A Ahumada
- Moore Center for Science, Conservation International, Arlington, VA, USA
| | - Patrick A Jansen
- Wildlife Ecology and Conservation Group, Wageningen University and Research, Wageningen, the Netherlands; Smithsonian Tropical Research Institute, Balboa, Ancon, Panama
| | - Wilson R Spironello
- Grupo de Pesquisa de Mamíferos Amazônicos, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
| | - Johanna Hurtado
- Independent consultant of Wildlife Management and Conservation, Heredia, Costa Rica
| | - Leandro Juen
- Laboratório de Ecologia e Conservação, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Carlos A Peres
- Centre for Ecology, Evolution and Conservation, School of Environmental Sciences, University of East Anglia, Norwich, UK
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10
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Singhal RK, Chauhan J, Jatav HS, Rajput VD, Singh GS, Bose B. Artificial night light alters ecosystem services provided by biotic components. Biol Futur 2021; 72:169-185. [PMID: 34554476 DOI: 10.1007/s42977-020-00065-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 12/28/2020] [Indexed: 12/14/2022]
Abstract
The global catastrophe of natural biodiversity and ecosystem services are expedited with the growing human population. Repercussions of artificial light at night ALAN are much wider, as it varies from unicellular to higher organism. Subsequently, hastened pollution and over exploitation of natural resources accelerate the expeditious transformation of climatic phenomenon and further cause global biodiversity losses. Moreover, it has a crucial role in global biodiversity and ecosystem services losses via influencing the ecosystem biodiversity by modulating abundance, number and aggregation at every levels as from individual to biome levels. Along with these affects, it disturbs the population, genetics and landscape structures by interfering inter- and intra-species interactions and landscape formation processes. Furthermore, alterations in normal light/dark (diurnal) signalling disrupt the stable physiological, biochemical, and molecular processes and modulate the regulating, cultural and provisioning ecosystem services and ultimately disorganize the stable ecosystem structure and functions. Moreover, ALAN reshapes the abiotic component of the ecosystem, and as a key component of global warming via producing greenhouse gases via emitting light. By taking together the above facts, this review highlights the impact of ALAN on the ecosystem and its living and non-living components, emphasizing to the terrestrial and aquatic ecosystem. Further, we summarize the means of minimizing strategies of ALAN in the environment, which are very crucial to reduce the further spread of night light contamination in the environment and can be useful to minimize the drastic impacts on the ecosystem.
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Affiliation(s)
- Rajesh K Singhal
- ICAR-Indian Grassland and Fodder Research Institute, Jhansi, U.P, 284003, India
| | - Jyoti Chauhan
- Department of Plant Physiology, Institute of Agriculture Sciences, Banaras Hindu University, Varanasi, U.P, 221005, India
| | - Hanuman S Jatav
- Sri Karan Narendra Agriculture University, Rajasthan, 303329, India.
- Department of Soil Science and Agricultural Chemistry, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, 221005, India.
| | | | - Gopal S Singh
- Institute of Environment & Sustainable Development, Banaras Hindu University, Varanasi, India
| | - Bandana Bose
- Department of Plant Physiology, Institute of Agriculture Sciences, Banaras Hindu University, Varanasi, U.P, 221005, India
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11
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Tammone MN, Lacey EA, Voglino D, Cuéllar Soto E, Pardiñas UFJ. Disentangling the complex alpha taxonomy of Andean populations of Ctenomys (Rodentia: Ctenomyidae) from northern Patagonia: the need for extensive sampling in heterogeneous landscapes. J Mammal 2021. [DOI: 10.1093/jmammal/gyab089] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
In the Andean portion of northern Patagonia, populations of Ctenomys are found from low-elevation plains to high-elevation meadows and valleys. Despite their prevalence, the taxonomy of these subterranean rodents remains poorly resolved. Using genetic and morphological data obtained from museum specimens and animals collected in the field, we examined the taxonomy of Ctenomys from southwestern Mendoza Province, Argentina. Our analyses suggest the presence of at least five species of Ctenomys within the study area. The highest, innermost portion of the Andes is occupied by C. maulinus. To the east, the mountains and foothills are inhabited by two forms associated with the “mendocinus” and the “magellanicus” lineages, respectively. The former appears to be a local variant of C. emilianus, while the latter is sister to C. pontifex. Although C. pontifex was not encountered during our field sampling, it remains a valid species that likely is restricted to the isolated Valle Hermoso in westernmost Mendoza Province. In addition, we report an undescribed form from Las Leñas Valley that is associated with the “mendocinus” lineage. This complex alpha taxonomic scenario occurs within less than one degree of latitude, thereby highlighting the need to conduct detailed field collections to improve our knowledge of the systematics of Ctenomys.
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Affiliation(s)
- Mauro N Tammone
- Instituto de Investigaciones en Biodiversidad y Medioambiente (CONICET-UNComahue), Quintral 1250, 8400 Bariloche, Río Negro, Argentina
- Parque Nacional Nahuel Huapi (CENAC-CONICET), 8400 Bariloche, Río Negro, Argentina
| | - Eileen A Lacey
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, 94720 Berkeley, California, USA
| | - Damián Voglino
- Museo de Ciencias Naturales Antonio Scasso, 2900 San Nicolás de los Arroyos, Buenos Aires, Argentina
| | - Erika Cuéllar Soto
- College of Science, Department of Biology, 123 Sultan Qaboos University, Muscat, Oman
| | - Ulyses F J Pardiñas
- Instituto de Diversidad y Evolución Austral (IDEAus-CONICET), Boulevard Brown 2915, 9120 Puerto Madryn, Chubut, Argentina
- Instituto Nacional de Biodiversidad, 170135 Quito, Ecuador
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12
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Ribeiro SE, de Almeida-Rocha JM, Weber MM, Kajin M, Lorini ML, Cerqueira R. Do anthropogenic matrix and life-history traits structure small mammal populations? A meta-analytical approach. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01352-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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13
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White HE, Clavel J, Tucker AS, Goswami A. A comparison of metrics for quantifying cranial suture complexity. J R Soc Interface 2020; 17:20200476. [PMID: 33023399 PMCID: PMC7653371 DOI: 10.1098/rsif.2020.0476] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 09/08/2020] [Indexed: 01/20/2023] Open
Abstract
Cranial sutures play critical roles in facilitating postnatal skull development and function. The diversity of function is reflected in the highly variable suture morphology and complexity. Suture complexity has seldom been studied, resulting in little consensus on the most appropriate approach for comparative, quantitative analyses. Here, we provide the first comprehensive comparison of current approaches for quantifying suture morphology, using a wide range of two-dimensional suture outlines across extinct and extant mammals (n = 79). Five complexity metrics (sinuosity index (SI), suture complexity index (SCI), fractal dimension (FD) box counting, FD madogram and a windowed short-time Fourier transform with power spectrum density (PSD) calculation) were compared with each other and with the shape variation in the dataset. Analyses of suture shape demonstrate that the primary axis of variation captured attributes other than complexity, supporting the use of a complexity metric over raw shape data for sutural complexity analyses. Each approach captured different aspects of complexity. PSD successfully discriminates different sutural features, such as looping patterns and interdigitation amplitude and number, while SCI best-captured variation in interdigitation number alone. Therefore, future studies should consider the relevant attributes for their question when selecting a metric for comparative analysis of suture variation, function and evolution.
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Affiliation(s)
- Heather E. White
- Department of Life Sciences, Natural History Museum, London SW7 5BD, UK
- Centre for Craniofacial and Regenerative Biology, King's College LondonSE1 9RT, UK
- Division of Biosciences, University College LondonWC1E 6DE, UK
| | - Julien Clavel
- Department of Life Sciences, Natural History Museum, London SW7 5BD, UK
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, F-69622, Villeurbanne, France
| | - Abigail S. Tucker
- Centre for Craniofacial and Regenerative Biology, King's College LondonSE1 9RT, UK
| | - Anjali Goswami
- Department of Life Sciences, Natural History Museum, London SW7 5BD, UK
- Division of Biosciences, University College LondonWC1E 6DE, UK
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Dáttilo W, Barrozo-Chávez N, Lira-Noriega A, Guevara R, Villalobos F, Santiago-Alarcon D, Neves FS, Izzo T, Ribeiro SP. Species-level drivers of mammalian ectoparasite faunas. J Anim Ecol 2020; 89:1754-1765. [PMID: 32198927 DOI: 10.1111/1365-2656.13216] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 02/27/2020] [Indexed: 12/15/2022]
Abstract
Traditionally, most studies have described the organization of host-parasite interaction networks by considering only few host groups at limited geographical extents. However, host-parasite relationships are merged within different taxonomic groups and factors shaping these interactions likely differ between host and parasite groups, making group-level differences important to better understand the ecological and evolutionary dynamics of these interactive communities. Here we used a dataset of 629 ectoparasite species and 251 species of terrestrial mammals, comprising 10 orders distributed across the Nearctic and Neotropical regions of Mexico to assess the species-level drivers of mammalian ectoparasite faunas. Specifically, we evaluated whether body weight, geographical range size and within-range mammal species richness (i.e. diversity field) predict mammal ectoparasite species richness (i.e. degree centrality) and their closeness centrality within the mammal-ectoparasite network. In addition, we also tested if the observed patterns differ among mammal orders and if taxonomic closely related host mammals could more likely share the same set of ectoparasites. We found that ectoparasite species richness of small mammals (mainly rodents) with large proportional range sizes was high compared to large-bodied mammals, whereas the diversity field of mammals had no predictive value (except for bats). We also observed that taxonomic proximity was a main determinant of the probability to share ectoparasite species. Specifically, the probability to share ectoparasites in congeneric species reached up to 90% and decreased exponentially as the taxonomic distance increased. Further, we also detected that some ectoparasites are generalists and capable to infect mammalian species across different orders and that rodents have a remarkable role in the network structure, being closely connected to many other taxa. Hence, because many rodent species have synanthropic habits they could act as undesired reservoirs of disease agents for humans and urban animals. Considering the reported worldwide phenomenon of the proliferation of rodents accompanying the demographic decrease or even local extinction of large-bodied mammal species, these organisms may already be an increasing health threat in many regions of the world.
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Affiliation(s)
- Wesley Dáttilo
- Red de Ecoetología, Instituto de Ecología A.C., Xalapa, Mexico
| | - Nathalia Barrozo-Chávez
- Programa de Pós-Graduação em Ecologia e Conservação da Biodiversidade, Universidade Federal de Mato Grosso, Cuiabá, Brazil
| | | | - Roger Guevara
- Red de Biología Evolutiva, Instituto de Ecología A.C., Xalapa, Mexico
| | | | - Diego Santiago-Alarcon
- Red de Biología y Conservación de Vertebrados, Instituto de Ecología A.C., Xalapa, Mexico
| | - Frederico Siqueira Neves
- Departamento de Genética, Ecología e Evoluçã, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Thiago Izzo
- Universidade Federal de Mato Grosso, Cuiabá, Brazil
| | - Sérvio Pontes Ribeiro
- Laboratório de Ecohealth, Ecologia de Insetos de Dossel e Sucessão Natural, Universidade Federal de Ouro Preto, Ouro Preto, Brazil
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15
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Dispersal and genetic structure in a tropical small mammal, the Bornean tree shrew (Tupaia longipes), in a fragmented landscape along the Kinabatangan River, Sabah, Malaysia. BMC Genet 2020; 21:43. [PMID: 32303177 PMCID: PMC7164274 DOI: 10.1186/s12863-020-00849-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 03/30/2020] [Indexed: 11/20/2022] Open
Abstract
Background Constraints in migratory capabilities, such as the disruption of gene flow and genetic connectivity caused by habitat fragmentation, are known to affect genetic diversity and the long-term persistence of populations. Although negative population trends due to ongoing forest loss are widespread, the consequence of habitat fragmentation on genetic diversity, gene flow and genetic structure has rarely been investigated in Bornean small mammals. To fill this gap in knowledge, we used nuclear and mitochondrial DNA markers to assess genetic diversity, gene flow and the genetic structure in the Bornean tree shrew, Tupaia longipes, that inhabits forest fragments of the Lower Kinabatangan Wildlife Sanctuary, Sabah. Furthermore, we used these markers to assess dispersal regimes in male and female T. longipes. Results In addition to the Kinabatangan River, a known barrier for dispersal in tree shrews, the heterogeneous landscape along the riverbanks affected the genetic structure in this species. Specifically, while in larger connected forest fragments along the northern riverbank genetic connectivity was relatively undisturbed, patterns of genetic differentiation and the distribution of mitochondrial haplotypes in a local scale indicated reduced migration on the strongly fragmented southern riverside. Especially, oil palm plantations seem to negatively affect dispersal in T. longipes. Clear sex-biased dispersal was not detected based on relatedness, assignment tests, and haplotype diversity. Conclusion This study revealed the importance of landscape connectivity to maintain migration and gene flow between fragmented populations, and to ensure the long-term persistence of species in anthropogenically disturbed landscapes.
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16
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Pereira AC, Bandeira V, Fonseca C, Cunha MV. Egyptian Mongoose ( Herpestes ichneumon) Gut Microbiota: Taxonomical and Functional Differences across Sex and Age Classes. Microorganisms 2020; 8:microorganisms8030392. [PMID: 32168965 PMCID: PMC7143146 DOI: 10.3390/microorganisms8030392] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 03/06/2020] [Accepted: 03/09/2020] [Indexed: 12/13/2022] Open
Abstract
The Egyptian mongoose (Herpestes ichneumon) is a medium-size carnivore that, in Europe, is restricted to Iberia. The bio-ecology of this species remains to be elucidated in several dimensions, including gut microbiota that is nowadays recognized as a fundamental component of mammals. In this work, we investigated the gut microbiota of this herpestid by single-molecule real-time sequencing of twenty paired male (n = 10) and female (n = 10) intestinal samples. This culture-independent approach enabled microbial profiling based on 16S rDNA and investigation of taxonomical and functional features. The core gut microbiome of the adult subpopulation was dominated by Firmicutes, Fusobacteria, Actinobacteria, and Proteobacteria. Eight genera were uniquely found in adults and five in non-adults. When comparing gut bacterial communities across sex, four genera were exclusive of females and six uniquely found in males. Despite these compositional distinctions, alpha- and beta-diversity analyses showed no statistically significant differences across sex or between adult and non-adult specimens. However, when function was inferred, males presented a significantly higher abundance of amino acid and citrate cycle metabolic pathways, compared to the significant overrepresentation in females of galactose metabolic pathways. Additionally, adults exhibited a significantly higher abundance of cationic antimicrobial peptide resistance pathways, while non-adults bared a significant overrepresentation of two-component systems associated with antibiotic synthesis, flagellin and biofilm production, and chemotaxis control. This study adds new insights into the mongoose bio-ecology palette, highlighting taxonomical and functional microbiome dissimilarities across sex and age classes, possibly related to primary production resources and life-history traits that impact on behavior and diet.
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Affiliation(s)
- André C. Pereira
- INIAV, IP- National Institute for Agrarian and Veterinary Research, 2780-157 Oeiras, Portugal;
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal
- Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Victor Bandeira
- Departamento de Biologia & CESAM, Universidade de Aveiro, 3810-193 Aveiro, Portugal; (V.B.)
| | - Carlos Fonseca
- Departamento de Biologia & CESAM, Universidade de Aveiro, 3810-193 Aveiro, Portugal; (V.B.)
| | - Mónica V. Cunha
- INIAV, IP- National Institute for Agrarian and Veterinary Research, 2780-157 Oeiras, Portugal;
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal
- Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal
- Correspondence: ; Tel.: +351-214-403-500
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17
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Rosario Carotenuto A, Guarracino F, Šumbera R, Fraldi M. Burrowing below ground: interaction between soil mechanics and evolution of subterranean mammals. J R Soc Interface 2020; 17:20190521. [PMID: 31910769 DOI: 10.1098/rsif.2019.0521] [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: 11/12/2022] Open
Abstract
The evolution of species is governed by complex phenomena in which biological and environmental features may interact dynamically. Subterranean mammals dig tunnels whose diameter minimizes energetic costs during excavations and display anatomical adaptations in order to burrow structurally stable tunnels according to specific features of the soil. These animals weight from less than 50 g up to 1-2 kg, and dig tunnels with diameters from 3 to 15 cm. The use of allometric laws has enabled these data to be correlated. However, since tunnels need to be stable with respect to the geomechanical characteristics of the resident soils, a mathematical treatment linking the admissible dimensions of tunnels to the environment here suggests a mechanically grounded correlation between the body mass of subterranean mammals and the maximum dimensions of tunnels. Remarkably, such theoretical findings reflect very well the empirical allometric relationship and contribute to explain the wide differences observed in body sizes of subterranean mammals. In this respect, a far from ancillary role of environmental mechanics on the morphological evolution of subterranean mammals can be hypothesized.
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Affiliation(s)
- Angelo Rosario Carotenuto
- Department of Structures for Engineering and Architecture, University of Napoli Federico II, Napoli, Italy
| | - Federico Guarracino
- Department of Structures for Engineering and Architecture, University of Napoli Federico II, Napoli, Italy
| | - Radim Šumbera
- Department of Zoology, Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
| | - Massimiliano Fraldi
- Department of Structures for Engineering and Architecture, University of Napoli Federico II, Napoli, Italy
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Abstract
Biological ageing and its mechanistic underpinnings are of immense biomedical and ecological significance. Ageing involves the decline of diverse biological functions and places a limit on a species’ maximum lifespan. Ageing is associated with epigenetic changes involving DNA methylation. Furthermore, an analysis of mammals showed that the density of CpG sites in gene promoters, which are targets for DNA methylation, is correlated with lifespan. Using 252 whole genomes and databases of animal age and promotor sequences, we show a pattern across vertebrates. We also derive a predictive lifespan clock based on CpG density in a selected set of promoters. The lifespan clock accurately predicts maximum lifespan in vertebrates (R2 = 0.76) from the density of CpG sites within only 42 selected promoters. Our lifespan clock provides a wholly new method for accurately estimating lifespan using genome sequences alone and enables estimation of this challenging parameter for both poorly understood and extinct species.
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19
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Morphological and genetic characterization of Mount Kenya brush-furred rats (Lophuromys Peters 1874); relevance to taxonomy and ecology. MAMMAL RES 2019. [DOI: 10.1007/s13364-019-00470-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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20
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Lee JB, Kim YK, Bae YS. A study of methods for monitoring wild mammals in Unmunsan, Korea. JOURNAL OF ASIA-PACIFIC BIODIVERSITY 2019. [DOI: 10.1016/j.japb.2019.04.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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21
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Mohammadi S, Ebrahimi E, Shahriari Moghadam M, Bosso L. Modelling current and future potential distributions of two desert jerboas under climate change in Iran. ECOL INFORM 2019. [DOI: 10.1016/j.ecoinf.2019.04.003] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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22
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López-Aguirre C, Hand SJ, Koyabu D, Son NT, Wilson LAB. Postcranial heterochrony, modularity, integration and disparity in the prenatal ossification in bats (Chiroptera). BMC Evol Biol 2019; 19:75. [PMID: 30866800 PMCID: PMC6417144 DOI: 10.1186/s12862-019-1396-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 02/21/2019] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Self-powered flight is one of the most energy-intensive types of locomotion found in vertebrates. It is also associated with a range of extreme morpho-physiological adaptations that evolved independently in three different vertebrate groups. Considering that development acts as a bridge between the genotype and phenotype on which selection acts, studying the ossification of the postcranium can potentially illuminate our understanding of bat flight evolution. However, the ontogenetic basis of vertebrate flight remains largely understudied. Advances in quantitative analysis of sequence heterochrony and morphogenetic growth have created novel approaches to study the developmental basis of diversification and the evolvability of skeletal morphogenesis. Assessing the presence of ontogenetic disparity, integration and modularity from an evolutionary approach allows assessing whether flight may have resulted in evolutionary differences in the magnitude and mode of development in bats. RESULTS We quantitatively compared the prenatal ossification of the postcranium (24 bones) between bats (14 species), non-volant mammals (11 species) and birds (14 species), combining for the first time prenatal sequence heterochrony and developmental growth data. Sequence heterochrony was found across groups, showing that bat postcranial development shares patterns found in other flying vertebrates but also those in non-volant mammals. In bats, modularity was found as an axial-appendicular partition, resembling a mammalian pattern of developmental modularity and suggesting flight did not repattern prenatal postcranial covariance in bats. CONCLUSIONS Combining prenatal data from 14 bat species, this study represents the most comprehensive quantitative analysis of chiropteran ossification to date. Heterochrony between the wing and leg in bats could reflect functional needs of the newborn, rather than ecological aspects of the adult. Bats share similarities with birds in the development of structures involved in flight (i.e. handwing and sternum), suggesting that flight altriciality and early ossification of pedal phalanges and sternum are common across flying vertebrates. These results indicate that the developmental modularity found in bats facilitates intramodular phenotypic diversification of the skeleton. Integration and disparity increased across developmental time in bats. We also found a delay in the ossification of highly adaptable and evolvable regions (e.g. handwing and sternum) that are directly associated with flight performance.
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Affiliation(s)
- Camilo López-Aguirre
- PANGEA Research Centre, School of Biological, Earth & Environmental Sciences, University of New South Wales, Sydney, NSW 2052 Australia
| | - Suzanne J. Hand
- PANGEA Research Centre, School of Biological, Earth & Environmental Sciences, University of New South Wales, Sydney, NSW 2052 Australia
| | - Daisuke Koyabu
- University Museum, University of Tokyo, Tokyo, Japan
- Department of Humanities and Sciences, Musashino Art University, Tokyo, Japan
| | - Nguyen Truong Son
- Department of Vertebrate Zoology, Institute of Ecology and Biological Resources, Vietnam Academy of Sciences and Technology, Hanoi, Vietnam
- Vietnam Academy of Science and Technology, Graduate University of Science and Technology, Hanoi, Vietnam
| | - Laura A. B. Wilson
- PANGEA Research Centre, School of Biological, Earth & Environmental Sciences, University of New South Wales, Sydney, NSW 2052 Australia
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Schnell IB, Bohmann K, Schultze SE, Richter SR, Murray DC, Sinding MHS, Bass D, Cadle JE, Campbell MJ, Dolch R, Edwards DP, Gray TNE, Hansen T, Hoa ANQ, Noer CL, Heise-Pavlov S, Sander Pedersen AF, Ramamonjisoa JC, Siddall ME, Tilker A, Traeholt C, Wilkinson N, Woodcock P, Yu DW, Bertelsen MF, Bunce M, Gilbert MTP. Debugging diversity - a pan-continental exploration of the potential of terrestrial blood-feeding leeches as a vertebrate monitoring tool. Mol Ecol Resour 2018; 18:1282-1298. [PMID: 29877042 DOI: 10.1111/1755-0998.12912] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 04/09/2018] [Accepted: 04/18/2018] [Indexed: 01/31/2023]
Abstract
The use of environmental DNA (eDNA) has become an applicable noninvasive tool with which to obtain information about biodiversity. A subdiscipline of eDNA is iDNA (invertebrate-derived DNA), where genetic material ingested by invertebrates is used to characterize the biodiversity of the species that served as hosts. While promising, these techniques are still in their infancy, as they have only been explored on limited numbers of samples from only a single or a few different locations. In this study, we investigate the suitability of iDNA extracted from more than 3,000 haematophagous terrestrial leeches as a tool for detecting a wide range of terrestrial vertebrates across five different geographical regions on three different continents. These regions cover almost the full geographical range of haematophagous terrestrial leeches, thus representing all parts of the world where this method might apply. We identify host taxa through metabarcoding coupled with high-throughput sequencing on Illumina and IonTorrent sequencing platforms to decrease economic costs and workload and thereby make the approach attractive for practitioners in conservation management. We identified hosts in four different taxonomic vertebrate classes: mammals, birds, reptiles and amphibians, belonging to at least 42 different taxonomic families. We find that vertebrate blood ingested by haematophagous terrestrial leeches throughout their distribution is a viable source of DNA with which to examine a wide range of vertebrates. Thus, this study provides encouraging support for the potential of haematophagous terrestrial leeches as a tool for detecting and monitoring terrestrial vertebrate biodiversity.
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Affiliation(s)
- Ida Baerholm Schnell
- Section for EvoGenomics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,Center for Zoo and Wild Animal Health, Copenhagen Zoo, Frederiksberg, Denmark
| | - Kristine Bohmann
- Section for EvoGenomics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Sebastian E Schultze
- Section for EvoGenomics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Stine R Richter
- Section for EvoGenomics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Dáithí C Murray
- Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, Perth, Western Australia, Australia
| | - Mikkel-Holger S Sinding
- Section for EvoGenomics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,Greenland Institute of Natural Resources, Nuuk, Greenland
| | - David Bass
- Department of Life Sciences, The Natural History Museum, London, UK.,Cefas, Weymouth, Dorset, UK
| | - John E Cadle
- Centre ValBio, Ranomafana, Ifanadiana, Fianarantsoa, Madagascar
| | - Mason J Campbell
- Centre for Tropical Environmental and Sustainability Science (TESS) and College of Science and Engineering, James Cook University, Cairns, Queensland, Australia
| | | | - David P Edwards
- Centre for Tropical Environmental and Sustainability Science (TESS) and College of Science and Engineering, James Cook University, Cairns, Queensland, Australia.,Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | | | - Teis Hansen
- Section for EvoGenomics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | | | - Christina Lehmkuhl Noer
- Section for EvoGenomics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,Center for Zoo and Wild Animal Health, Copenhagen Zoo, Frederiksberg, Denmark
| | - Sigrid Heise-Pavlov
- Centre for Rainforest Studies at the School for Field Studies, Yungaburra, Queensland, Australia
| | - Adam F Sander Pedersen
- Department of Immunology and Microbiology, Centre for Medical Parasitology, University of Copenhagen, Copenhagen, Denmark
| | | | - Mark E Siddall
- Division of Invertebrate Zoology, Sackler Institute of Comparative Genomics, American Museum of Natural History, New York, New York
| | - Andrew Tilker
- Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany.,Global Wildlife Conservation, Austin, Texas
| | - Carl Traeholt
- Center for Zoo and Wild Animal Health, Copenhagen Zoo, Frederiksberg, Denmark
| | | | | | - Douglas W Yu
- School of Biological Sciences, University of East Anglia, Norwich, UK.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | | | - Michael Bunce
- Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, Perth, Western Australia, Australia
| | - M Thomas P Gilbert
- Section for EvoGenomics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, Perth, Western Australia, Australia.,NTNU University Museum, Trondheim, Norway
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24
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Gainsbury AM, Tallowin OJS, Meiri S. An updated global data set for diet preferences in terrestrial mammals: testing the validity of extrapolation. Mamm Rev 2018. [DOI: 10.1111/mam.12119] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Alison M. Gainsbury
- Department of Biological Sciences; University of South Florida; 140 7th Ave S. St. Petersburg FL 33701 USA
| | | | - Shai Meiri
- Department of Zoology; Tel Aviv University; Tel Aviv 6997801 Israel
- Steinhardt Museum of Natural History Tel-Aviv University; 6997801 Tel Aviv Israel
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25
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Magintan D, Nor SM, Ean TP, Lechner AM, Azhar B. The conservation value of unlogged and logged forests for native mammals on the East Coast of Peninsular Malaysia. J Nat Conserv 2017. [DOI: 10.1016/j.jnc.2017.10.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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26
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Davidson AD, Shoemaker KT, Weinstein B, Costa GC, Brooks TM, Ceballos G, Radeloff VC, Rondinini C, Graham CH. Geography of current and future global mammal extinction risk. PLoS One 2017; 12:e0186934. [PMID: 29145486 PMCID: PMC5690607 DOI: 10.1371/journal.pone.0186934] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Accepted: 10/10/2017] [Indexed: 11/25/2022] Open
Abstract
Identifying which species are at greatest risk, what makes them vulnerable, and where they are distributed are central goals for conservation science. While knowledge of which factors influence extinction risk is increasingly available for some taxonomic groups, a deeper understanding of extinction correlates and the geography of risk remains lacking. Here, we develop a predictive random forest model using both geospatial and mammalian species' trait data to uncover the statistical and geographic distributions of extinction correlates. We also explore how this geography of risk may change under a rapidly warming climate. We found distinctive macroecological relationships between species-level risk and extinction correlates, including the intrinsic biological traits of geographic range size, body size and taxonomy, and extrinsic geographic settings such as seasonality, habitat type, land use and human population density. Each extinction correlate exhibited ranges of values that were especially associated with risk, and the importance of different risk factors was not geographically uniform across the globe. We also found that about 10% of mammals not currently recognized as at-risk have biological traits and occur in environments that predispose them towards extinction. Southeast Asia had the most actually and potentially threatened species, underscoring the urgent need for conservation in this region. Additionally, nearly 40% of currently threatened species were predicted to experience rapid climate change at 0.5 km/year or more. Biological and environmental correlates of mammalian extinction risk exhibit distinct statistical and geographic distributions. These results provide insight into species-level patterns and processes underlying geographic variation in extinction risk. They also offer guidance for future conservation research focused on specific geographic regions, or evaluating the degree to which species-level patterns mirror spatial variation in the pressures faced by populations within the ranges of individual species. The added impacts from climate change may increase the susceptibility of at-risk species to extinction and expand the regions where mammals are most vulnerable globally.
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Affiliation(s)
- Ana D. Davidson
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, United States of America
- NatureServe, Arlington, Virginia, United States of America
| | - Kevin T. Shoemaker
- Department of Natural Resources & Environmental Science, University of Nevada, Reno, Nevada, United States of America
| | - Ben Weinstein
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, United States of America
| | - Gabriel C. Costa
- Department of Biology, Auburn University at Montgomery, Montgomery, Alabama, United States of America
| | - Thomas M. Brooks
- International Union for Conservation of Nature, Gland, Switzerland
- World Agroforestry Center, University of the Philippines Los Baños, Laguna, Philippines
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia
| | - Gerardo Ceballos
- Instituto de Ecologia, Universidad Nacional Autonoma de Mexico, México D.F., México
| | - Volker C. Radeloff
- Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, Wisconsin, United States of America
| | - Carlo Rondinini
- Global Mammal Assessment program, Department of Biology and Biotechnologies, Sapienza University of Rome, Roma, Italy
| | - Catherine H. Graham
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, United States of America
- Unit of Biodiversity and Conservation, Swiss Federal Research Institute, Birmensdorf, Switzerland Unit of Biodiversity and Conservation, Swiss Federal Research Institute (WSL), Birmensdorf, Switzerland
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27
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Forest Fragmentation in the Lower Amazon Floodplain: Implications for Biodiversity and Ecosystem Service Provision to Riverine Populations. REMOTE SENSING 2016. [DOI: 10.3390/rs8110886] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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28
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Russo IRM, Sole CL, Barbato M, von Bramann U, Bruford MW. Landscape determinants of fine-scale genetic structure of a small rodent in a heterogeneous landscape (Hluhluwe-iMfolozi Park, South Africa). Sci Rep 2016; 6:29168. [PMID: 27406468 PMCID: PMC4942783 DOI: 10.1038/srep29168] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 06/13/2016] [Indexed: 12/05/2022] Open
Abstract
Small mammals provide ecosystem services, acting, for example, as pollinators and seed dispersers. In addition, they are also disease reservoirs that can be detrimental to human health and they can also act as crop pests. Knowledge of their dispersal preferences is therefore useful for population management and landscape planning. Genetic data were used alongside landscape data to examine the influence of the landscape on the demographic connectedness of the Natal multimammate mouse (Mastomys natalensis) and to identify landscape characteristics that influence the genetic structure of this species across a spatially and temporally varying environment. The most significant landscape features shaping gene flow were aspect, vegetation cover, topographic complexity (TC) and rivers, with western facing slopes, topographic complexity and rivers restricting gene flow. In general, thicket vegetation was correlated with increased gene flow. Identifying features of the landscape that facilitate movement/dispersal in M. natalensis potentially has application for other small mammals in similar ecosystems. As the primary reservoir host of the zoonotic Lassa virus, a landscape genetics approach may have applications in determining areas of high disease risk to humans. Identifying these landscape features may also be important in crop management due to damage by rodent pests.
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Affiliation(s)
- Isa-Rita M Russo
- Cardiff School of Biosciences, Sir Martin Evans Building, Cardiff University, Museum Avenue, Cardiff, CF10 3AX United Kingdom
| | - Catherine L Sole
- Department of Zoology and Entomology, University of Pretoria, Private Bag X20, Hatfield, 0028 South Africa
| | - Mario Barbato
- Cardiff School of Biosciences, Sir Martin Evans Building, Cardiff University, Museum Avenue, Cardiff, CF10 3AX United Kingdom
| | - Ullrich von Bramann
- Technische Universität Braunschweig, Institut für Geosysteme und Bioindikation, Langer Kamp 19c, Braunschweig, 38106 Germany
| | - Michael W Bruford
- Cardiff School of Biosciences, Sir Martin Evans Building, Cardiff University, Museum Avenue, Cardiff, CF10 3AX United Kingdom
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29
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Kluever BM, Gese EM, Dempsey SJ. The influence of wildlife water developments and vegetation on rodent abundance in the Great Basin Desert. J Mammal 2016. [DOI: 10.1093/jmammal/gyw077] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
Rodent communities have multiple functions including comprising a majority of the mammalian diversity within an ecosystem, providing a significant portion of the available biomass consumed by predators, and contributing to ecosystem services. Despite the importance of rodent communities, few investigations have explored the effects of increasing anthropogenic modifications to the landscape on rodents. Throughout the western United States, the construction of artificial water developments to benefit game species is commonplace. While benefits for certain species have been documented, several researchers recently hypothesized that these developments may cause unintentional negative effects to desert-adapted species and communities. To test this idea, we sampled rodents near to and distant from wildlife water developments over 4 consecutive summers. We employed an asymmetrical before-after-control-impact (BACI) design with sampling over 4 summers to determine if water developments influenced total rodent abundance. We performed an additional exploratory analysis to determine if factors other than free water influenced rodent abundance. We found no evidence that water developments impacted rodent abundance. Rodent abundance was primarily driven by vegetation type and year of sampling. Our findings suggested that water developments on our study area do not represent a significant disturbance to rodent abundance and that rodent abundance was influenced by the vegetative community and temporal factors linked to precipitation and primary plant production. Our findings represent one of the 1st efforts to determine the effects of an anthropogenic activity on the rodent community utilizing a manipulation design.
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30
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Jetz W, Freckleton RP. Towards a general framework for predicting threat status of data-deficient species from phylogenetic, spatial and environmental information. Philos Trans R Soc Lond B Biol Sci 2015; 370:20140016. [PMID: 25561677 DOI: 10.1098/rstb.2014.0016] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In taxon-wide assessments of threat status many species remain not included owing to lack of data. Here, we present a novel spatial-phylogenetic statistical framework that uses a small set of readily available or derivable characteristics, including phylogenetically imputed body mass and remotely sensed human encroachment, to provide initial baseline predictions of threat status for data-deficient species. Applied to assessed mammal species worldwide, the approach effectively identifies threatened species and predicts the geographical variation in threat. For the 483 data-deficient species, the models predict highly elevated threat, with 69% 'at-risk' species in this set, compared with 22% among assessed species. This results in 331 additional potentially threatened mammals, with elevated conservation importance in rodents, bats and shrews, and countries like Colombia, Sulawesi and the Philippines. These findings demonstrate the future potential for combining phylogenies and remotely sensed data with species distributions to identify species and regions of conservation concern.
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Affiliation(s)
- Walter Jetz
- Department of Ecology and Evolutionary Biology, Yale University, PO Box 208106, New Haven, CT 06520-8106, USA Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot, Berkshire SL5 7PY, UK
| | - Robert P Freckleton
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
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31
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Bland LM, Orme CDL, Bielby J, Collen B, Nicholson E, McCarthy MA. Cost-effective assessment of extinction risk with limited information. J Appl Ecol 2015. [DOI: 10.1111/1365-2664.12459] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Lucie M. Bland
- School of BioSciences; The University of Melbourne; Parkville Vic. 3010 Australia
- Division of Biology; Imperial College London; Silwood Park Ascot SL5 7PY UK
- Institute of Zoology; Zoological Society of London; Regent's Park London NW1 4RY UK
| | - C. David L. Orme
- Division of Biology; Imperial College London; Silwood Park Ascot SL5 7PY UK
| | - Jon Bielby
- Institute of Zoology; Zoological Society of London; Regent's Park London NW1 4RY UK
| | - Ben Collen
- Centre for Biodiversity and Environment Research; University College London; Gower Street London WC1 E6BT UK
| | - Emily Nicholson
- School of BioSciences; The University of Melbourne; Parkville Vic. 3010 Australia
- School of Life and Environmental Sciences; Deakin University; Burwood Vic. 3125 Australia
| | - Michael A. McCarthy
- School of BioSciences; The University of Melbourne; Parkville Vic. 3010 Australia
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32
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Abstract
Understanding the feeding behaviour of the species that make up any ecosystem is essential for designing further research. Mammals have been studied intensively, but the criteria used for classifying their diets are far from being standardized. We built a database summarizing the dietary preferences of terrestrial mammals using published data regarding their stomach contents. We performed multivariate analyses in order to set up a standardized classification scheme. Ideally, food consumption percentages should be used instead of qualitative classifications. However, when highly detailed information is not available we propose classifying animals based on their main feeding resources. They should be classified as generalists when none of the feeding resources constitute over 50% of the diet. The term ‘omnivore’ should be avoided because it does not communicate all the complexity inherent to food choice. Moreover, the so-called omnivore diets actually involve several distinctive adaptations. Our dataset shows that terrestrial mammals are generally highly specialized and that some degree of food mixing may even be required for most species.
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Affiliation(s)
- Silvia Pineda-Munoz
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - John Alroy
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
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33
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Kamilar JM, Beaudrot L, Reed KE. Climate and species richness predict the phylogenetic structure of African mammal communities. PLoS One 2015; 10:e0121808. [PMID: 25875361 PMCID: PMC4398448 DOI: 10.1371/journal.pone.0121808] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 02/04/2015] [Indexed: 11/18/2022] Open
Abstract
We have little knowledge of how climatic variation (and by proxy, habitat variation) influences the phylogenetic structure of tropical communities. Here, we quantified the phylogenetic structure of mammal communities in Africa to investigate how community structure varies with respect to climate and species richness variation across the continent. In addition, we investigated how phylogenetic patterns vary across carnivores, primates, and ungulates. We predicted that climate would differentially affect the structure of communities from different clades due to between-clade biological variation. We examined 203 communities using two metrics, the net relatedness (NRI) and nearest taxon (NTI) indices. We used simultaneous autoregressive models to predict community phylogenetic structure from climate variables and species richness. We found that most individual communities exhibited a phylogenetic structure consistent with a null model, but both climate and species richness significantly predicted variation in community phylogenetic metrics. Using NTI, species rich communities were composed of more distantly related taxa for all mammal communities, as well as for communities of carnivorans or ungulates. Temperature seasonality predicted the phylogenetic structure of mammal, carnivoran, and ungulate communities, and annual rainfall predicted primate community structure. Additional climate variables related to temperature and rainfall also predicted the phylogenetic structure of ungulate communities. We suggest that both past interspecific competition and habitat filtering have shaped variation in tropical mammal communities. The significant effect of climatic factors on community structure has important implications for the diversity of mammal communities given current models of future climate change.
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Affiliation(s)
- Jason M. Kamilar
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, United States of America
- Department of Anatomy, Arizona College of Osteopathic Medicine, Midwestern University, Glendale, Arizona, United States of America
- * E-mail:
| | - Lydia Beaudrot
- Graduate Group in Ecology, University of California Davis, Davis, California, United States of America
- Department of Anthropology, University of California Davis, Davis, California, United States of America
| | - Kaye E. Reed
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, United States of America
- Institute of Human Origins, Arizona State University, Tempe, Arizona, United States of America
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34
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Bland LM, Collen B, Orme CDL, Bielby J. Predicting the conservation status of data-deficient species. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2015; 29:250-9. [PMID: 25124400 DOI: 10.1111/cobi.12372] [Citation(s) in RCA: 124] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 05/12/2014] [Indexed: 05/19/2023]
Abstract
There is little appreciation of the level of extinction risk faced by one-sixth of the over 65,000 species assessed by the International Union for Conservation of Nature. Determining the status of these data-deficient (DD) species is essential to developing an accurate picture of global biodiversity and identifying potentially threatened DD species. To address this knowledge gap, we used predictive models incorporating species' life history, geography, and threat information to predict the conservation status of DD terrestrial mammals. We constructed the models with 7 machine learning (ML) tools trained on species of known status. The resultant models showed very high species classification accuracy (up to 92%) and ability to correctly identify centers of threatened species richness. Applying the best model to DD species, we predicted 313 of 493 DD species (64%) to be at risk of extinction, which increases the estimated proportion of threatened terrestrial mammals from 22% to 27%. Regions predicted to contain large numbers of threatened DD species are already conservation priorities, but species in these areas show considerably higher levels of risk than previously recognized. We conclude that unless directly targeted for monitoring, species classified as DD are likely to go extinct without notice. Taking into account information on DD species may therefore help alleviate data gaps in biodiversity indicators and conserve poorly known biodiversity.
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Affiliation(s)
- Lucie M Bland
- Institute of Zoology, Zoological Society of London, Regent's Park, London NW1 4RY, United Kingdom; Division of Biology, Imperial College London, Silwood Park, Ascot, SL5 7PY, United Kingdom.
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35
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Abstract
One of the fundamental challenges of conservation biology is gathering data on species distribution and abundance. And unless conservationists know where a species is found and in which numbers, it is very difficult to apply effective conservation efforts. In today's age of increasingly powerful monitoring tools, instant communication and online databases, one might be forgiven for thinking that such knowledge is easy to come by. However, of the approximately 5,400 terrestrial mammals on the IUCN Red List, no fewer than 789 (ca. 14%) are listed as 'Data Deficient' (IUCN 2012) – IUCN’s term for 'haven't got a clue'. Until recently, the only way to gather information of numbers and distribution of terrestrial mammals (and many other vertebrates) was through observational-based approaches such as visual records, the presence of tracks or spoor or even identification from bushmeat or hunters' trophies pinned to the walls in local villages. While recent technological developments have considerably improved the efficacy of such approaches, for example, using remote-sensing devices such as audio- or camera-traps or even remote drones (Koh & Wich 2012), there has been a growing realization of the power of molecular methods that identify mammals based on trace evidence. Suitable substrates include the obvious, such as faecal and hair samples (e.g. Vigilant et al. 2009), to the less obvious, including environmental DNA extracted from sediments, soil or water samples (e.g. Taberlet et al. 2012), and as recently demonstrated, the dietary content of blood-sucking invertebrates (Gariepy et al. 2012; Schnell et al. 2012). In this issue of Molecular Ecology, Calvignac-Spencer et al. (2013) present a potentially powerful development in this regard; diet analysis of carrion flies. With their near global distribution, and as most field biologists know, irritatingly high frequency in most terrestrial areas of conservation concern (which directly translates into ease of sampling them), the authors present extremely encouraging results that indicate how carnivorous flies may soon represent a strong weapon in the conservation arsenal.
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Affiliation(s)
- Kristine Bohmann
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
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36
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Calvignac-Spencer S, Merkel K, Kutzner N, Kühl H, Boesch C, Kappeler PM, Metzger S, Schubert G, Leendertz FH. Carrion fly-derived DNA as a tool for comprehensive and cost-effective assessment of mammalian biodiversity. Mol Ecol 2013; 22:915-24. [PMID: 23298293 DOI: 10.1111/mec.12183] [Citation(s) in RCA: 122] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Revised: 11/12/2012] [Accepted: 11/14/2012] [Indexed: 11/30/2022]
Abstract
Large-scale monitoring schemes are essential in assessing global mammalian biodiversity, and in this framework, leeches have recently been promoted as an indirect source of DNA from terrestrial mammal species. Carrion feeding flies are ubiquitous and can be expected to feed on many vertebrate carcasses. Hence, we tested whether fly-derived DNA analysis may also serve as a novel tool for mammalian diversity surveys. We screened DNA extracted from 201 carrion flies collected in tropical habitats of Côte d'Ivoire and Madagascar for mammal DNA using multiple PCR systems and retrieved DNA sequences from a diverse set of species (22 in Côte d'Ivoire, four in Madagascar) exploiting distinct forest strata and displaying a broad range of body sizes. Deep sequencing of amplicons generated from pools of flies performed equally well as individual sequencing approaches. We conclude that the analysis of fly-derived DNA can be implemented in a very rapid and cost-effective manner and will give a relatively unbiased picture of local mammal diversity. Carrion flies therefore represent an extraordinary and thus far unexploited resource of mammal DNA, which will probably prove useful for future inventories of wild mammal communities.
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37
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Monroe MJ, Bokma F. Mass extinctions do not explain skew in interspecific body size distributions. J ZOOL SYST EVOL RES 2012. [DOI: 10.1111/jzs.12002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Melanie J. Monroe
- Department of Ecology and Environmental Science; IceLab, Umeå University; Umeå Sweden
| | - Folmer Bokma
- Department of Ecology and Environmental Science; IceLab, Umeå University; Umeå Sweden
- IceLab, Umeå University; Umeå Sweden
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38
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Springer MS, Meredith RW, Janecka JE, Murphy WJ. The historical biogeography of Mammalia. Philos Trans R Soc Lond B Biol Sci 2011; 366:2478-502. [PMID: 21807730 DOI: 10.1098/rstb.2011.0023] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Palaeobiogeographic reconstructions are underpinned by phylogenies, divergence times and ancestral area reconstructions, which together yield ancestral area chronograms that provide a basis for proposing and testing hypotheses of dispersal and vicariance. Methods for area coding include multi-state coding with a single character, binary coding with multiple characters and string coding. Ancestral reconstruction methods are divided into parsimony versus Bayesian/likelihood approaches. We compared nine methods for reconstructing ancestral areas for placental mammals. Ambiguous reconstructions were a problem for all methods. Important differences resulted from coding areas based on the geographical ranges of extant species versus the geographical provenance of the oldest fossil for each lineage. Africa and South America were reconstructed as the ancestral areas for Afrotheria and Xenarthra, respectively. Most methods reconstructed Eurasia as the ancestral area for Boreoeutheria, Euarchontoglires and Laurasiatheria. The coincidence of molecular dates for the separation of Afrotheria and Xenarthra at approximately 100 Ma with the plate tectonic sundering of Africa and South America hints at the importance of vicariance in the early history of Placentalia. Dispersal has also been important including the origins of Madagascar's endemic mammal fauna. Further studies will benefit from increased taxon sampling and the application of new ancestral area reconstruction methods.
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Affiliation(s)
- Mark S Springer
- Department of Biology, University of California, Riverside, CA 92521, USA.
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39
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Jones KE, Blackburn TM, Isaac NJB. Can unified theories of biodiversity explain mammalian macroecological patterns? Philos Trans R Soc Lond B Biol Sci 2011; 366:2554-63. [PMID: 21807736 DOI: 10.1098/rstb.2011.0119] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The idea of a unifying theory of biodiversity linking the diverse array of macroecological patterns into a common theoretical framework is very appealing. We explore this idea to examine currently proposed unified theories of biodiversity (UTBs) and their predictions. Synthesizing the literature on the macroecological patterns of mammals, we critically evaluate the evidence to support these theories. We find general qualitative support for the UTBs' predictions within mammals, but rigorous testing is hampered by the types of data typically collected in studies of mammals. In particular, abundance is rarely estimated for entire mammalian communities or of individual species in multiple locations, reflecting the logistical challenges of studying wild mammal populations. By contrast, there are numerous macroecological patterns (especially allometric scaling relationships) that are extremely well characterized for mammals, but which fall outside the scope of current UTBs. We consider how these theories might be extended to explain mammalian biodiversity patterns more generally. Specifically, we suggest that UTBs need to incorporate the dimensions of geographical space, species' traits and time to reconcile theory with pattern.
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Affiliation(s)
- Kate E Jones
- Institute of Zoology, Zoological Society of London, Regent's Park, UK
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