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Campbell LI, Nwezeobi J, van Brunschot SL, Kaweesi T, Seal SE, Swamy RAR, Namuddu A, Maslen GL, Mugerwa H, Armean IM, Haggerty L, Martin FJ, Malka O, Santos-Garcia D, Juravel K, Morin S, Stephens ME, Muhindira PV, Kersey PJ, Maruthi MN, Omongo CA, Navas-Castillo J, Fiallo-Olivé E, Mohammed IU, Wang HL, Onyeka J, Alicai T, Colvin J. Comparative evolutionary analyses of eight whitefly Bemisia tabaci sensu lato genomes: cryptic species, agricultural pests and plant-virus vectors. BMC Genomics 2023; 24:408. [PMID: 37468834 DOI: 10.1186/s12864-023-09474-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 06/21/2023] [Indexed: 07/21/2023] Open
Abstract
BACKGROUND The group of > 40 cryptic whitefly species called Bemisia tabaci sensu lato are amongst the world's worst agricultural pests and plant-virus vectors. Outbreaks of B. tabaci s.l. and the associated plant-virus diseases continue to contribute to global food insecurity and social instability, particularly in sub-Saharan Africa and Asia. Published B. tabaci s.l. genomes have limited use for studying African cassava B. tabaci SSA1 species, due to the high genetic divergences between them. Genomic annotations presented here were performed using the 'Ensembl gene annotation system', to ensure that comparative analyses and conclusions reflect biological differences, as opposed to arising from different methodologies underpinning transcript model identification. RESULTS We present here six new B. tabaci s.l. genomes from Africa and Asia, and two re-annotated previously published genomes, to provide evolutionary insights into these globally distributed pests. Genome sizes ranged between 616-658 Mb and exhibited some of the highest coverage of transposable elements reported within Arthropoda. Many fewer total protein coding genes (PCG) were recovered compared to the previously published B. tabaci s.l. genomes and structural annotations generated via the uniform methodology strongly supported a repertoire of between 12.8-13.2 × 103 PCG. An integrative systematics approach incorporating phylogenomic analysis of nuclear and mitochondrial markers supported a monophyletic Aleyrodidae and the basal positioning of B. tabaci Uganda-1 to the sub-Saharan group of species. Reciprocal cross-mating data and the co-cladogenesis pattern of the primary obligate endosymbiont 'Candidatus Portiera aleyrodidarum' from 11 Bemisia genomes further supported the phylogenetic reconstruction to show that African cassava B. tabaci populations consist of just three biological species. We include comparative analyses of gene families related to detoxification, sugar metabolism, vector competency and evaluate the presence and function of horizontally transferred genes, essential for understanding the evolution and unique biology of constituent B. tabaci. s.l species. CONCLUSIONS These genomic resources have provided new and critical insights into the genetics underlying B. tabaci s.l. biology. They also provide a rich foundation for post-genomic research, including the selection of candidate gene-targets for innovative whitefly and virus-control strategies.
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Affiliation(s)
- Lahcen I Campbell
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
| | - Joachim Nwezeobi
- Natural Resources Institute, University of Greenwich, Chatham, Kent, UK.
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, Hinxton, UK.
| | - Sharon L van Brunschot
- Natural Resources Institute, University of Greenwich, Chatham, Kent, UK
- CSIRO Health and Biosecurity, Dutton Park, QLD, Australia
- School of Biological Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Tadeo Kaweesi
- Natural Resources Institute, University of Greenwich, Chatham, Kent, UK
- Rwebitaba Zonal Agricultural Research and Development Institute, Fort Portal, Uganda
| | - Susan E Seal
- Natural Resources Institute, University of Greenwich, Chatham, Kent, UK
| | - Rekha A R Swamy
- Natural Resources Institute, University of Greenwich, Chatham, Kent, UK
| | - Annet Namuddu
- Natural Resources Institute, University of Greenwich, Chatham, Kent, UK
- National Crops Resources Research Institute, Kampala, Uganda
| | - Gareth L Maslen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Imperial College London, South Kensington, London, UK
| | - Habibu Mugerwa
- Natural Resources Institute, University of Greenwich, Chatham, Kent, UK
- Department of Entomology, University of Georgia, Griffin, GA, USA
| | - Irina M Armean
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Leanne Haggerty
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Fergal J Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Osnat Malka
- Department of Entomology, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Diego Santos-Garcia
- CNRS, Laboratory of Biometry and Evolutionary Biology UMR 5558, University of Lyon, Villeurbanne, France
- Center for Biology and Management of Populations, INRAe UMR1062, Montferrier-sur-Lez, France
| | - Ksenia Juravel
- Department of Entomology, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Shai Morin
- Department of Entomology, The Hebrew University of Jerusalem, Rehovot, Israel
| | | | - Paul Visendi Muhindira
- Natural Resources Institute, University of Greenwich, Chatham, Kent, UK
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, Australia
| | - Paul J Kersey
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Royal Botanic Gardens, Kew, London, UK
| | - M N Maruthi
- Natural Resources Institute, University of Greenwich, Chatham, Kent, UK
| | | | - Jesús Navas-Castillo
- Instituto de Hortofruticultura Subtropical Y Mediterránea "La Mayora" (IHSM-UMA-CSIC), Consejo Superior de Investigaciones Científicas, Málaga, Algarrobo-Costa, Spain
| | - Elvira Fiallo-Olivé
- Instituto de Hortofruticultura Subtropical Y Mediterránea "La Mayora" (IHSM-UMA-CSIC), Consejo Superior de Investigaciones Científicas, Málaga, Algarrobo-Costa, Spain
| | | | - Hua-Ling Wang
- Natural Resources Institute, University of Greenwich, Chatham, Kent, UK
- College of Forestry, Hebei Agricultural University, Baoding, Hebei, China
| | - Joseph Onyeka
- National Root Crops Research Institute (NRCRI), Umudike, Nigeria
| | - Titus Alicai
- National Crops Resources Research Institute, Kampala, Uganda
| | - John Colvin
- Natural Resources Institute, University of Greenwich, Chatham, Kent, UK
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2
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Lambert JP, Zhang X, Shi K, Riordan P. The pikas of China: a review of current research priorities and challenges for conservation. Integr Zool 2023; 18:110-128. [PMID: 34937133 DOI: 10.1111/1749-4877.12615] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Of the approximately 30 extant species of pika (Ochotona; Ochotonidae; Lagomorpha), at least 23 occur in China. Of these, 8 are endemic, and 3 are classified as Endangered by the IUCN. Research into most Chinese species is scarce, and there is much to learn about basic aspects of their ecology. We reviewed the literature on the 23 Chinese Ochotona species, with the aim of highlighting knowledge gaps and biases in research allocation. Specifically, we identify (1) which pika species receive the most attention from researchers, (2) which topics are the most frequently studied, and (3) how well research satisfies conservation priorities. We covered a total of 879 articles, most of which were written in English or Chinese. Around 75% of all publications focused on the plateau pika Ochotona curzoniae. Seven species were represented by 10 or fewer publications each. Endangered and endemic species were particularly poorly represented. 204 papers treated pikas as a pest, while 13 studied conservation issues. Nine species were considered possible targets for pest control, including some poorly known endemics. We make some recommendations on how research into Chinese Ochotona could be improved, including: (1) recognizing that the current species-level taxonomy may be an ineffective way to prioritize conservation research in Ochotona, (2) directing more research toward threatened and endemic species, subspecies, and populations, (3) researching the ecosystem engineering effects of pikas, (4) collecting basic data on natural history of the many understudied species, and (5) researching threats, including climate change and pest control campaigns.
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Affiliation(s)
- Joseph P Lambert
- Wildlife Institute, School of Nature Conservation, Beijing Forestry University, Beijing, China
| | | | - Kun Shi
- Wildlife Institute, School of Nature Conservation, Beijing Forestry University, Beijing, China.,Eco-Bridge Continental, Haidian District, Beijing, China
| | - Philip Riordan
- Wildlife Institute, School of Nature Conservation, Beijing Forestry University, Beijing, China.,Marwell Wildlife, Winchester, Hampshire, UK
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3
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Tavares VDC, Gardner AL, Mcdonough MM, Maldonado JE, Gutiérrez EE, Velazco PM, Garbino GST. Historical DNA of rare yellow-eared bats Vampyressa Thomas, 1900 (Chiroptera, Phyllostomidae) clarifies phylogeny and species boundaries within the genus. SYST BIODIVERS 2022. [DOI: 10.1080/14772000.2022.2117247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Valéria da C. Tavares
- Instituto Tecnológico Vale (ITV), Belém, 66055-090, PA, Brazil
- Laboratório de Mamíferos, Departamento de Sistemática e Ecologia, Universidade Federal da Paraíba (UFPB), João Pessoa, 58059-900, PB, Brazil
| | - Alfred L. Gardner
- Division of Mammals, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Molly M. Mcdonough
- Department of Biological Sciences, Chicago State University, Chicago, IL, USA
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, USA
| | - Jesús E. Maldonado
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, USA
| | | | - Paúl M. Velazco
- Department of Biology, Arcadia University, Glenside, PA, USA
- Department of Mammalogy, American Museum of Natural History, New York, NY, USA
| | - Guilherme S. T. Garbino
- Museu de Zoologia João Moojen, Departamento de Biologia Animal, Universidade Federal de Viçosa, Viçosa, 36570-900, MG, Brazil
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4
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Wilson TC, Rossetto M, Bain D, Yap JS, Wilson PD, Stimpson ML, Weston PH, Croft L. A turn in species conservation for hairpin banksias: demonstration of oversplitting leads to better management of diversity. AMERICAN JOURNAL OF BOTANY 2022; 109:1652-1671. [PMID: 36164832 PMCID: PMC9828017 DOI: 10.1002/ajb2.16074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 08/29/2022] [Accepted: 08/30/2022] [Indexed: 06/16/2023]
Abstract
PREMISE Understanding evolutionary history and classifying discrete units of organisms remain overwhelming tasks, and lags in this workload concomitantly impede an accurate documentation of biodiversity and conservation management. Rapid advances and improved accessibility of sensitive high-throughput sequencing tools are fortunately quickening the resolution of morphological complexes and thereby improving the estimation of species diversity. The recently described and critically endangered Banksia vincentia is morphologically similar to the hairpin banksia complex (B. spinulosa s.l.), a group of eastern Australian flowering shrubs whose continuum of morphological diversity has been responsible for taxonomic controversy and possibly questionable conservation initiatives. METHODS To assist conservation while testing the current taxonomy of this group, we used high-throughput sequencing to infer a population-scale evolutionary scenario for a sample set that is comprehensive in its representation of morphological diversity and a 2500-km distribution. RESULTS Banksia spinulosa s.l. represents two clades, each with an internal genetic structure shaped through historical separation by biogeographic barriers. This structure conflicts with the existing taxonomy for the group. Corroboration between phylogeny and population statistics aligns with the hypothesis that B. collina, B. neoanglica, and B. vincentia should not be classified as species. CONCLUSIONS The pattern here supports how morphological diversity can be indicative of a locally expressed suite of traits rather than relationship. Oversplitting in the hairpin banksias is atypical since genomic analyses often reveal that species diversity is underestimated. However, we show that erring on overestimation can yield negative consequences, such as the disproportionate prioritization of a geographically anomalous population.
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Affiliation(s)
- Trevor C. Wilson
- Plant Discovery and Evolution, Australian Institute of Botanical ScienceRoyal Botanic Gardens and Domain TrustSydneyAustralia
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical ScienceThe Royal Botanic Garden SydneyAustralia
| | - Maurizio Rossetto
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical ScienceThe Royal Botanic Garden SydneyAustralia
| | - David Bain
- Ecosystems and Threatened Species, Biodiversity Conservation and ScienceNSW Department of Planning and EnvironmentWollongongAustralia
| | - Jia‐Yee S. Yap
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical ScienceThe Royal Botanic Garden SydneyAustralia
| | - Peter D. Wilson
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical ScienceThe Royal Botanic Garden SydneyAustralia
| | - Margaret L. Stimpson
- Botany, School of Environmental and Rural ScienceUniversity of New EnglandArmidaleNSW2351Australia
| | - Peter H. Weston
- Plant Discovery and Evolution, Australian Institute of Botanical ScienceRoyal Botanic Gardens and Domain TrustSydneyAustralia
| | - Larry Croft
- Centre of Integrative Ecology, School of Life and Environmental SciencesDeakin UniversityGeelong3125VictoriaAustralia
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5
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Stronen AV, Norman AJ, Vander Wal E, Paquet PC. The relevance of genetic structure in ecotype designation and conservation management. Evol Appl 2022; 15:185-202. [PMID: 35233242 PMCID: PMC8867706 DOI: 10.1111/eva.13339] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 12/02/2021] [Accepted: 12/20/2021] [Indexed: 11/28/2022] Open
Abstract
The concept of ecotypes is complex, partly because of its interdisciplinary nature, but the idea is intrinsically valuable for evolutionary biology and applied conservation. The complex nature of ecotypes has spurred some confusion and inconsistencies in the literature, thereby limiting broader theoretical development and practical application. We provide suggestions for how incorporating genetic analyses can ease confusion and help define ecotypes. We approach this by systematically reviewing 112 publications across taxa that simultaneously mention the terms ecotype, conservation and management, to examine the current use of the term in the context of conservation and management. We found that most ecotype studies involve fish, mammals and plants with a focus on habitat use, which at 60% was the most common criterion used for categorization of ecotypes. Only 53% of the studies incorporated genetic analyses, and major discrepancies in available genomic resources among taxa could have contributed to confusion about the role of genetic structure in delineating ecotypes. Our results show that the rapid advances in genetic methods, also for nonmodel organisms, can help clarify the spatiotemporal distribution of adaptive and neutral genetic variation and their relevance to ecotype designations. Genetic analyses can offer empirical support for the ecotype concept and provide a timely measure of evolutionary potential, especially in changing environmental conditions. Genetic variation that is often difficult to detect, including polygenic traits influenced by small contributions from several genes, can be vital for adaptation to rapidly changing environments. Emerging ecotypes may signal speciation in progress, and findings from genome‐enabled organisms can help clarify important selective factors driving ecotype development and persistence, and thereby improve preservation of interspecific genetic diversity. Incorporation of genetic analyses in ecotype studies will help connect evolutionary biology and applied conservation, including that of problematic groups such as natural hybrid organisms and urban or anthropogenic ecotypes.
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Affiliation(s)
- Astrid V. Stronen
- Department of Biology Biotechnical Faculty University of Ljubljana Ljubljana Slovenia
- Department of Biotechnology and Life Sciences Insubria University Varese Italy
- Department of Chemistry and Bioscience Aalborg University Aalborg Denmark
| | - Anita J. Norman
- Department of Fish, Wildlife and Environmental Studies Swedish University of Agricultural Sciences Umeå Sweden
| | - Eric Vander Wal
- Department of Biology Memorial University of Newfoundland St. John’s NL Canada
| | - Paul C. Paquet
- Department of Geography University of Victoria Victoria BC Canada
- Raincoast Conservation Foundation Sidney BC Canada
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6
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Kitchener AC, Hoffmann M, Yamaguchi N, Breitenmoser-Würsten C, Wilting A. A system for designating taxonomic certainty in mammals and other taxa. Mamm Biol 2022. [DOI: 10.1007/s42991-021-00205-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
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7
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Cardini A, de Jong YA, Butynski TM. Can morphotaxa be assessed with photographs? Estimating the accuracy of two-dimensional cranial geometric morphometrics for the study of threatened populations of African monkeys. Anat Rec (Hoboken) 2021; 305:1402-1434. [PMID: 34596361 PMCID: PMC9298422 DOI: 10.1002/ar.24787] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 08/23/2021] [Accepted: 08/26/2021] [Indexed: 11/09/2022]
Abstract
The classification of most mammalian orders and families is under debate and the number of species is likely greater than currently recognized. Improving taxonomic knowledge is crucial, as biodiversity is in rapid decline. Morphology is a source of taxonomic knowledge, and geometric morphometrics applied to two dimensional (2D) photographs of anatomical structures is commonly employed for quantifying differences within and among lineages. Photographs are informative, easy to obtain, and low cost. 2D analyses, however, introduce a large source of measurement error when applied to crania and other highly three dimensional (3D) structures. To explore the potential of 2D analyses for assessing taxonomic diversity, we use patas monkeys (Erythrocebus), a genus of large, semi-terrestrial, African guenons, as a case study. By applying a range of tests to compare ventral views of adult crania measured both in 2D and 3D, we show that, despite inaccuracies accounting for up to one-fourth of individual shape differences, results in 2D almost perfectly mirror those in 3D. This apparent paradox might be explained by the small strength of covariation in the component of shape variance related to measurement error. A rigorous standardization of photographic settings and the choice of almost coplanar landmarks are likely to further improve the correspondence of 2D to 3D shapes. 2D geometric morphometrics is, thus, appropriate for taxonomic comparisons of patas ventral crania. Although it is too early to generalize, our results corroborate similar findings from previous research in mammals, and suggest that 2D shape analyses are an effective heuristic tool for morphological investigation of small differences.
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Affiliation(s)
- Andrea Cardini
- Dipartimento di Scienze Chimiche e Geologiche, Università di Modena e Reggio Emilia, Modena, Italy.,School of Anatomy, Physiology and Human Biology, The University of Western Australia, Crawley, Western Australia, Australia
| | - Yvonne A de Jong
- Eastern Africa Primate Diversity and Conservation Program and Lolldaiga Hills Research Programme, Nanyuki, Kenya
| | - Thomas M Butynski
- Eastern Africa Primate Diversity and Conservation Program and Lolldaiga Hills Research Programme, Nanyuki, Kenya
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8
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Puckett EE, Murphy SM, Bradburd G. Phylogeographic analysis delimits three evolutionary significant units of least chipmunks in North America and identifies unique genetic diversity within the imperiled Peñasco population. Ecol Evol 2021; 11:12114-12128. [PMID: 34522364 PMCID: PMC8427584 DOI: 10.1002/ece3.7975] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 07/07/2021] [Accepted: 07/14/2021] [Indexed: 11/10/2022] Open
Abstract
Although least chipmunks (Neotamias minimus) are a widely distributed North American species of least concern, the southernmost population, N. m. atristriatus (Peñasco least chipmunk), is imperiled and a candidate for federal listing as a subspecies. We conducted a phylogeographic analysis across the N. minimus range to assess genomic differentiation and distinctiveness of the N. m. atristriatus population. Additionally, we leveraged the historical component of sampling to conduct a temporal analysis of N. minimus genetic diversity and also considered climate change effects on range persistence probability by projecting a species distribution model into the IPCC5 RCP 2.6 and 8.5 scenarios. We identified three geographically structured groups (West, North, and South) that were supported by both mitochondrial and nuclear data. N. m. atristriatus grouped within a unique South subclade but were not reciprocally monophyletic from N. m. operarius, and nuclear genome analyses did not separate N. m. atristriatus, N. m. caryi, and N. m. operarius. Thus, while least chipmunks in the Southwest represent an evolutionary significant unit, subspecies distinctions were not supported and listing of the Peñasco population as a Distinct Population Segment of N. m. operarius may be warranted. Our results also support consideration of populations with North and West mitogenomes as two additional evolutionary significant units. We found that N. minimus genetic diversity declined by ~87% over the last century, and our models predicted substantial future habitat contraction, including the loss of the full contemporary ranges of N. m. atristriatus, N. m. arizonensis, and N. m. chuskaensis.
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Affiliation(s)
- Emily E. Puckett
- Department of Biological SciencesUniversity of MemphisMemphisTennesseeUSA
| | - Sean M. Murphy
- Wildlife Management DivisionNew Mexico Department of Game & FishSanta FeNew MexicoUSA
- Present address:
Department of Forestry and Natural ResourcesUniversity of KentuckyLexingtonKentuckyUSA
| | - Gideon Bradburd
- Department of Integrative BiologyEcology, Evolution, and Behavior GroupMichigan State UniversityEast LansingMichiganUSA
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9
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Coimbra RTF, Winter S, Kumar V, Koepfli KP, Gooley RM, Dobrynin P, Fennessy J, Janke A. Whole-genome analysis of giraffe supports four distinct species. Curr Biol 2021; 31:2929-2938.e5. [PMID: 33957077 DOI: 10.1016/j.cub.2021.04.033] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 01/06/2021] [Accepted: 04/14/2021] [Indexed: 12/24/2022]
Abstract
Species is the fundamental taxonomic unit in biology and its delimitation has implications for conservation. In giraffe (Giraffa spp.), multiple taxonomic classifications have been proposed since the early 1900s.1 However, one species with nine subspecies has been generally accepted,2 likely due to limited in-depth assessments, subspecies hybridizing in captivity,3,4 and anecdotal reports of hybrids in the wild.5 Giraffe taxonomy received new attention after population genetic studies using traditional genetic markers suggested at least four species.6,7 This view has been met with controversy,8 setting the stage for debate.9,10 Genomics is significantly enhancing our understanding of biodiversity and speciation relative to traditional genetic approaches and thus has important implications for species delineation and conservation.11 We present a high-quality de novo genome assembly of the critically endangered Kordofan giraffe (G. camelopardalis antiquorum)12 and a comprehensive whole-genome analysis of 50 giraffe representing all traditionally recognized subspecies. Population structure and phylogenomic analyses support four separately evolving giraffe lineages, which diverged 230-370 ka ago. These lineages underwent distinct demographic histories and show different levels of heterozygosity and inbreeding. Our results strengthen previous findings of limited gene flow and admixture among putative giraffe species6,7,9 and establish a genomic foundation for recognizing four species and seven subspecies, the latter of which should be considered as evolutionary significant units. Achieving a consensus over the number of species and subspecies in giraffe is essential for adequately assessing their threat level and will improve conservation efforts for these iconic taxa.
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Affiliation(s)
- Raphael T F Coimbra
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt am Main, Germany; Institute for Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Straße 13, 60438 Frankfurt am Main, Germany.
| | - Sven Winter
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt am Main, Germany; Institute for Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Straße 13, 60438 Frankfurt am Main, Germany
| | - Vikas Kumar
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Klaus-Peter Koepfli
- Smithsonian-Mason School of Conservation, Front Royal, VA, 22630, USA; Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park, 3001 Connecticut Avenue NW, Washington, DC 20008, USA
| | - Rebecca M Gooley
- Smithsonian-Mason School of Conservation, Front Royal, VA, 22630, USA; Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park, 3001 Connecticut Avenue NW, Washington, DC 20008, USA
| | - Pavel Dobrynin
- Computer Technologies Laboratory, ITMO University, 49 Kronverkskiy Pr., Saint Petersburg 197101, Russia
| | - Julian Fennessy
- Giraffe Conservation Foundation, PO Box 86099, Eros, Windhoek, Namibia
| | - Axel Janke
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt am Main, Germany; Institute for Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Straße 13, 60438 Frankfurt am Main, Germany; LOEWE Centre for Translational Biodiversity Genomics, Senckenberganlage 25, 60325 Frankfurt am Main, Germany.
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10
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On the Misidentification of Species: Sampling Error in Primates and Other Mammals Using Geometric Morphometrics in More Than 4000 Individuals. Evol Biol 2021. [DOI: 10.1007/s11692-021-09531-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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11
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Sterner B, Elliott S, Upham N, Franz N. Bats, objectivity, and viral spillover risk. HISTORY AND PHILOSOPHY OF THE LIFE SCIENCES 2021; 43:7. [PMID: 33439354 PMCID: PMC7805256 DOI: 10.1007/s40656-021-00366-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 01/07/2021] [Indexed: 06/12/2023]
Abstract
What should the best practices be for modeling zoonotic disease risks, e.g. to anticipate the next pandemic, when background assumptions are unsettled or evolving rapidly? This challenge runs deeper than one might expect, all the way into how we model the robustness of contemporary phylogenetic inference and taxonomic classifications. Different and legitimate taxonomic assumptions can destabilize the putative objectivity of zoonotic risk assessments, thus potentially supporting inconsistent and overconfident policy decisions.
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Affiliation(s)
- Beckett Sterner
- School of Life Sciences, Arizona State University, Tempe, USA.
| | - Steve Elliott
- Center for Gender Equity in Science and Technology, Arizona State University, Tempe, USA
| | - Nate Upham
- School of Life Sciences, Arizona State University, Tempe, USA
| | - Nico Franz
- School of Life Sciences, Arizona State University, Tempe, USA
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12
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Padial JM, De la Riva I. A paradigm shift in our view of species drives current trends in biological classification. Biol Rev Camb Philos Soc 2020; 96:731-751. [PMID: 33368983 DOI: 10.1111/brv.12676] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 11/21/2020] [Accepted: 11/25/2020] [Indexed: 12/22/2022]
Abstract
Discontent about changes in species classifications has grown in recent years. Many of these changes are seen as arbitrary, stemming from unjustified conceptual and methodological grounds, or leading to species that are less distinct than those recognised in the past. We argue that current trends in species classification are the result of a paradigm shift toward which systematics and population genetics have converged and that regards species as the phylogenetic lineages that form the branches of the Tree of Life. Species delimitation now consists of determining which populations belong to which individual phylogenetic lineage. This requires inferences on the process of lineage splitting and divergence, a process to which we have only partial access through incidental evidence and assumptions that are themselves subject to refutation. This approach is not free of problems, as horizontal gene transfer, introgression, hybridisation, incorrect assumptions, sampling and methodological biases can mislead inferences of phylogenetic lineages. Increasing precision is demanded through the identification of both sister relationships and processes blurring or mimicking phylogeny, which has triggered, on the one hand, the development of methods that explicitly address such processes and, on the other hand, an increase in geographical and character data sampling necessary to infer/test such processes. Although our resolving power has increased, our knowledge of sister relationships - what we designate as species resolution - remains poor for many taxa and areas, which biases species limits and perceptions about how divergent species are or ought to be. We attribute to this conceptual shift the demise of trinominal nomenclature we are witnessing with the rise of subspecies to species or their rejection altogether; subspecies are raised to species if they are found to correspond to phylogenetic lineages, while they are rejected as fabricated taxa if they reflect arbitrary partitions of continuous or non-hereditary variation. Conservation strategies, if based on taxa, should emphasise species and reduce the use of subspecies to avoid preserving arbitrary partitions of continuous variation; local variation is best preserved by focusing on biological processes generating ecosystem resilience and diversity rather than by formally naming diagnosable units of any kind. Since many binomials still designate complexes of species rather than individual species, many species have been discovered but not named, geographical sampling is sparse, gene lineages have been mistaken for species, plenty of species limits remain untested, and many groups and areas lack adequate species resolution, we cannot avoid frequent changes to classifications as we address these problems. Changes will not only affect neglected taxa or areas, but also popular ones and regions where taxonomic research remained dormant for decades and old classifications were taken for granted.
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Affiliation(s)
- José M Padial
- Department of Herpetology, American Museum of Natural History, Central Park West & 79th St., New York, NY, 10024, U.S.A.,Department of Biology, Bronx Community College, City University of New York, 2155 University Avenue, Bronx, NY, 10453, U.S.A
| | - Ignacio De la Riva
- Museo Nacional de Ciencias Naturales-CSIC, José Gutiérrez Abascal 2, Madrid, 28006, Spain
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Miranda LS, Prestes BO, Aleixo A. Molecular systematics and phylogeography of a widespread Neotropical avian lineage: evidence for cryptic speciation with protracted gene flow throughout the Late Quaternary. Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Here we use an integrative approach, including coalescent-based methods, isolation–migration and species distribution models, to infer population structure, divergence times and diversification in the two species of the genus Cymbilaimus (Aves, Thamnophilidae). Our results support a recent and rapid diversification with both incomplete lineage sorting and gene flow shaping the evolutionary history of Cymbilaimus. The spatio-temporal pattern of cladogenesis suggests that Cymbilaimus originated in the north/western portion of cis-Andean South America and then diversified into the Brazilian Shield and Central America after consolidation of the modern Amazonian drainage and the Andean range. This evolutionary scenario is explained by cycles of range expansion and dispersal, followed by isolation, and recurrent gene flow, during the last 1.2 Myr. Our results agree with those recently reported for other closely related suboscine lineages, whereby the window of introgression between closely related taxa remains open for up to a few million years after their original split. In Cymbilaimus, introgression was recurrent between C. lineatus and C. sanctaemariae, even after they acquired vocal and ecological differentiation, supporting the claim that at least in Neotropical suboscines, full reproductive compatibility may take millions of years to evolve and cannot be interpreted as synonymous with a lack of speciation.
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Affiliation(s)
- Leonardo S Miranda
- Programa de Pós-graduação em Zoologia – Universidade Federal do Pará/Museu Paraense Emílio Goeldi, Belém, PA, Brazil
- Coordenação de Ciências da Terra e Ecologia, Museu Paraense Emílio Goeldi, Belém, PA, Brazil
| | - Bernardo O Prestes
- Programa de Pós-graduação em Zoologia – Universidade Federal do Pará/Museu Paraense Emílio Goeldi, Belém, PA, Brazil
| | - Alexandre Aleixo
- Programa de Pós-graduação em Zoologia – Universidade Federal do Pará/Museu Paraense Emílio Goeldi, Belém, PA, Brazil
- Coordenação de Zoologia, Museu Paraense Emílio Goeldi, Belém, PA, Brazil
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Raposo MA, Kirwan GM, Lourenço ACC, Sobral G, Bockmann FA, Stopiglia R. On the notions of taxonomic ‘impediment’, ‘gap’, ‘inflation’ and ‘anarchy’, and their effects on the field of conservation. SYST BIODIVERS 2020. [DOI: 10.1080/14772000.2020.1829157] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Marcos A. Raposo
- Setor de Ornitologia, Departamento de Vertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Quinta da Boa Vista, s/n, Rio de Janeiro, 20940–040, RJ, Brazil
- UMR 8590, IHPST–Institut d'Histoire et de Philosophie des Sciences et des Techniques, UMR 8590, Université Paris 1, Panthéon-Sorbonne & CNRS, 13 rue du Four, Paris, 75006, France
| | - Guy M. Kirwan
- Setor de Ornitologia, Departamento de Vertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Quinta da Boa Vista, s/n, Rio de Janeiro, 20940–040, RJ, Brazil
| | - Ana Carolina Calijorne Lourenço
- Departamento de Ciências Biológicas, Universidade do Estado de Minas Gerais, Campus Ubá, Av. Olegário Maciel, 1427, Ubá, 36502-000, MG, Brazil
| | - Gisela Sobral
- Departamento de Reprodução Animal, Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, Av. Prof. Dr. Orlando Marques de Paiva 87, São Paulo, 05508-270, SP, Brazil
| | - Flávio Alicino Bockmann
- Laboratório de Ictiologia de Ribeirão Preto, Departamento de Biologia, FFCLRP, Universidade de São Paulo, Av. dos Bandeirantes 3900, Ribeirão Preto, 14040–901, SP, Brazil
- Programa de Pós-Graduação em Biologia Comparada, FFCLRP, Universidade de São Paulo, Av. dos Bandeirantes 3900, Ribeirão Preto, Paris, 14040-901, SP, Brazil
| | - Renata Stopiglia
- Laboratório de Ictiologia de Ribeirão Preto, Departamento de Biologia, FFCLRP, Universidade de São Paulo, Av. dos Bandeirantes 3900, Ribeirão Preto, 14040–901, SP, Brazil
- Institut de Systématique, Évolution, Biodiversité, ISYEB, UMR 7205 – CNRS, MNHN, UPMC, EPHE, Muséum national d’Histoire naturelle, Sorbonne Universités, 57 rue Cuvier, CP 30, Paris, F-75005, France
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Quilodrán CS, Montoya-Burgos JI, Currat M. Harmonizing hybridization dissonance in conservation. Commun Biol 2020; 3:391. [PMID: 32694629 PMCID: PMC7374702 DOI: 10.1038/s42003-020-1116-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 06/25/2020] [Indexed: 12/24/2022] Open
Abstract
A dramatic increase in the hybridization between historically allopatric species has been induced by human activities. However, the notion of hybridization seems to lack consistency in two respects. On the one hand, it is inconsistent with the biological species concept, which does not allow for interbreeding between species, and on the other hand, it is considered either as an evolutionary process leading to the emergence of new biodiversity or as a cause of biodiversity loss, with conservation implications. In the first case, we argue that conservation biology should avoid the discussion around the species concept and delimit priorities of conservation units based on the impact on biodiversity if taxa are lost. In the second case, we show that this is not a paradox but an intrinsic property of hybridization, which should be considered in conservation programmes. We propose a novel view of conservation guidelines, in which human-induced hybridization may also be a tool to enhance the likelihood of adaptation to changing environmental conditions or to increase the genetic diversity of taxa affected by inbreeding depression. The conservation guidelines presented here represent a guide for the development of programmes aimed at protecting biodiversity as a dynamic evolutionary system.
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Affiliation(s)
- Claudio S Quilodrán
- Department of Zoology, University of Oxford, Oxford, United Kingdom.
- Laboratory of Anthropology, Genetics and Peopling History, Anthropology Unit, Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.
| | - Juan I Montoya-Burgos
- Laboratory of Vertebrate Evolution, Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (IGE3), Geneva, Switzerland
| | - Mathias Currat
- Laboratory of Anthropology, Genetics and Peopling History, Anthropology Unit, Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (IGE3), Geneva, Switzerland
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Abstract
Lists of species underpin many fields of human endeavour, but there are currently no universally accepted principles for deciding which biological species should be accepted when there are alternative taxonomic treatments (and, by extension, which scientific names should be applied to those species). As improvements in information technology make it easier to communicate, access, and aggregate biodiversity information, there is a need for a framework that helps taxonomists and the users of taxonomy decide which taxa and names should be used by society whilst continuing to encourage taxonomic research that leads to new species discoveries, new knowledge of species relationships, and the refinement of existing species concepts. Here, we present 10 principles that can underpin such a governance framework, namely (i) the species list must be based on science and free from nontaxonomic considerations and interference, (ii) governance of the species list must aim for community support and use, (iii) all decisions about list composition must be transparent, (iv) the governance of validated lists of species is separate from the governance of the names of taxa, (v) governance of lists of accepted species must not constrain academic freedom, (vi) the set of criteria considered sufficient to recognise species boundaries may appropriately vary between different taxonomic groups but should be consistent when possible, (vii) a global list must balance conflicting needs for currency and stability by having archived versions, (viii) contributors need appropriate recognition, (ix) list content should be traceable, and (x) a global listing process needs both to encompass global diversity and to accommodate local knowledge of that diversity. We conclude by outlining issues that must be resolved if such a system of taxonomic list governance and a unified list of accepted scientific names generated are to be universally adopted. Currently there are no rules on compiling lists of accepted names of species, meaning that many people use a variety of competing lists, which results in confusion and inefficiencies. This Perspective article provides principles for developing global lists of species that are needed if such lists are to be accepted by both taxonomists and users of taxonomy.
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Korshunova T, Malmberg K, Prkić J, Petani A, Fletcher K, Lundin K, Martynov A. Fine-scale species delimitation: speciation in process and periodic patterns in nudibranch diversity. Zookeys 2020; 917:15-50. [PMID: 32206016 PMCID: PMC7076062 DOI: 10.3897/zookeys.917.47444] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 01/02/2020] [Indexed: 11/12/2022] Open
Abstract
Using the nudibranch genus Amphorina as a model, ongoing speciation is demonstrated, as well as how periodic-like patterns in colouration can be included in an integrated method of fine-scale species delimitation. By combining several methods, including BPP analysis and the study of molecular, morphological, and ecological data from a large number of specimens within a broad geographic range from northern Europe to the Mediterranean, five species are recognised within the genus Amphorina, reviewed here for the first time. Two new species from the southwestern coast of Sweden are described, A. viriola sp. nov. and A. andra sp. nov. Evidence is provided of a recent speciation process between the two closely related, yet separate, species which inhabit the same geographic localities but demonstrate strict water depth differentiation, with one species inhabiting the shallow brackish top layer above the halocline and the other species inhabiting the underlying saltier water. The results presented here are of relevance for currently debated issues such as conservation in relation to speciation, fine species delimitation, and integration of molecular, morphological and ecological information in biodiversity studies. The periodic approach to biological taxonomy has considerable practical potential for various organismal groups.
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Affiliation(s)
- Tatiana Korshunova
- Koltzov Institute of Developmental Biology RAS, 26 Vavilova Str., 119334 Moscow, Russia Koltzov Institute of Developmental Biology RAS Moscow Russia.,Zoological Museum, Moscow State University, Bolshaya Nikitskaya Str. 6, 125009 Moscow, Russia Moscow State University Moscow Russia
| | - Klas Malmberg
- Aquatilis, Nostravägen 11, S-41743, Gothenburg, Sweden Aquatilis Gothenburgh Sweden
| | - Jakov Prkić
- Getaldiceva 11, C 21000 Split, Croatia Unaffiliated Split Croatia
| | - Alen Petani
- Put Kotlara 6, C 23000 Zadar, Croatia Unaffiliated Zadar Croatia
| | - Karin Fletcher
- Port Orchard, Washington, 98366, USA Unaffiliated Port Orchard United States of America
| | - Kennet Lundin
- Gothenburg Natural History Museum, Box 7283, SE-40235, Gothenburg, Sweden Gothenburg Natural History Museum Gothenburg Sweden.,Gothenburg Global Biodiversity Centre, Box 461, SE-40530, Gothenburg, Sweden Gothenburg Global Biodiversity Centre Gothenburg Sweden
| | - Alexander Martynov
- Zoological Museum, Moscow State University, Bolshaya Nikitskaya Str. 6, 125009 Moscow, Russia Moscow State University Moscow Russia
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Zachos FE, Christidis L, Garnett ST. Mammalian species and the twofold nature of taxonomy: a comment on Taylor et al. 2019. MAMMALIA 2019. [DOI: 10.1515/mammalia-2019-0009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Abstract
In a recently published paper, Taylor and colleagues discussed different approaches and interpretations of mammalian taxonomy and their bearing on more general issues such as conservation and evolutionary biology. We fully endorse the fundamental importance of taxonomy and its being grounded on scientific principles. However, we also deplore a lack of awareness in the literature of the fact that taxonomy is a twofold enterprise that encompasses not only (i) the scientific description and quantitative analysis of biodiversity but also (ii) an executive decision as to how the results of (i) are translated into names. This has serious ramifications for the conservation of our planet’s dwindling biodiversity and when taxonomic names are used as raw data for ecological and evolutionary analyses.
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Affiliation(s)
- Frank E. Zachos
- Natural History Museum Vienna , Mammal Collection , Burgring 7 , 1010 Vienna , Austria
- Department of Genetics , University of the Free State , PO Box 339 , Bloemfontein , South Africa
- Department of Integrative Zoology , University of Vienna , Althanstraße 14 , 1090 Vienna , Austria
| | - Les Christidis
- School of Environment, Science and Engineering , Southern Cross University , Coffs Harbour , NSW 2450 , Australia
| | - Stephen T. Garnett
- Research Institute for the Environment and Livelihoods , Charles Darwin University , Darwin , NT 0909 , Australia
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19
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Matrosova VA, Ivanova AD, Volodina EV, Volodin IA, Alexandrov DY, Sibiryakova OV, Ermakov OA. Phylogenetic relationship and variation of alarm call traits of populations of red-cheeked ground squirrels (Spermophilus erythrogenys sensu lato) suggest taxonomic delineation. Integr Zool 2019; 14:341-353. [PMID: 30688033 DOI: 10.1111/1749-4877.12383] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Distribution area and taxonomic borders within the species complex Spermophilus erythrogenys sensu lato remain questionable. Early evidence suggests that red-cheeked ground squirrels of Southeast Kazakhstan are remarkably different in terms of the acoustic structure of their alarm calls from the red-cheeked ground squirrels of the Kurgan region in Russia. In this study, we analyzed the differences in the acoustic structure of the alarm call and mitochondrial DNA (complete control region, 1005-1006 bp and complete cytochrome b gene, 1140 bp) in 3 populations of red-cheeked ground squirrels (Tara, Altyn-Emel and Balkhash), all located within areas isolated by geographical barriers in Southeast Kazakhstan. We found that the alarm call variables were similar between the 3 study populations and differed by the maximum fundamental frequency (8.46 ± 0.75 kHz) from the values (5.62 ± 0.06 kHz) reported for the red-cheeked ground squirrels from the Kurgan region of Russia. Variation in mtDNA control region was only 3% and variation in cytochrome b gene was only 2.5%. Phylogenetic trees based on cytochrome b gene polymorphism of 44 individuals from the study area and adjacent territories indicated 3 clades with high (98-100%) bootstrap support: "intermedius," "brevicauda" and "iliensis"). We conclude that the 3 study populations in Southeast Kazakhstan belong to the clade intermedius and suggest a taxonomical revision of the species complex Spermophilus erythrogenys sensu lato, including analyses of nuclear DNA and alarm calls for populations of the brevicauda and iliensis clades.
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Affiliation(s)
| | - Anastasia D Ivanova
- Engelhardt Institute of Molecular Biology, RAS, Moscow, Russia.,Lomonosov Moscow State University, Moscow, Russia
| | | | - Ilya A Volodin
- Lomonosov Moscow State University, Moscow, Russia.,Moscow Zoo, Moscow, Russia
| | | | | | - Oleg A Ermakov
- Department of Zoology and Ecology, Penza State University, Penza, Russia
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20
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Mori E, Nerva L, Lovari S. Reclassification of the serows and gorals: the end of a neverending story? Mamm Rev 2019. [DOI: 10.1111/mam.12154] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Emiliano Mori
- Dipartimento di Scienze della VitaUniversità degli Studi di Siena Via P.A. Mattioli 4 53100 Siena Italy
| | - Luca Nerva
- Research Centre for Viticulture and EnologyCREA Via XXVIII Aprile 26 31015 Conegliano (Treviso) Italy
- Institute for Sustainable Plant Protection Strada delle Cacce 73 10135 Torino Italy
| | - Sandro Lovari
- Dipartimento di Scienze della VitaUniversità degli Studi di Siena Via P.A. Mattioli 4 53100 Siena Italy
- Museo di Storia Naturale della Maremma Strada Corsini 5 58100 Grosseto Italy
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22
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Rutting roars in native Pannonian red deer of Southern Hungary and the evidence of acoustic divergence of male sexual vocalization between Eastern and Western European red deer (Cervus elaphus). Mamm Biol 2019. [DOI: 10.1016/j.mambio.2018.10.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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24
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25
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Powell DM. Collection planning for the next 100 years: What will we commit to save in zoos and aquariums? Zoo Biol 2018; 38:139-148. [PMID: 30465724 PMCID: PMC7380042 DOI: 10.1002/zoo.21453] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 08/27/2018] [Accepted: 10/09/2018] [Indexed: 11/07/2022]
Abstract
The "sustainability crisis" in zoos and aquariums has been a sobering reminder of how limited our resources are for maintaining viable populations of species threatened with extinction. This, combined with increasing concern among the public about the value of zoos and aquariums, suggests that the zoological profession should engage in a thorough re-examination of our guiding principles, philosophies, and practices with regard to collection planning at global, regional, and institutional scales. An analysis of AZA cooperative breeding programs reveals that in order to make these populations viable, many more founders and tens of thousands more spaces for animals, either in existing facilities or new ones, are necessary if we want to maintain all of the species that are covered by cooperative breeding programs currently. Regional zoological associations and their associated cooperative breeding programs must be more strategic and make more scientifically defensible decisions about which species to try and safeguard in zoos and aquariums. This would enable the zoological profession to give society a "Promise List" of species that we will commit to save from total extinction. Developing such a list will require a collaborative, inclusive process that transcends zoological regions. Regional association leaders, zoo & aquarium directors, and curators must make commitments to safeguard the species on the Promise List regardless of other interests. As our profession re-examines its philosophies and practices and finds ways to increase its capacity to provide refuge for species facing extinction in the wild, it may be possible to expand the Promise List.
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Affiliation(s)
- David M. Powell
- Department of Reproductive and Behavioral SciencesSaint Louis ZooSaint LouisMissouri
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Iacolina L, Corlatti L, Buzan E, Safner T, Šprem N. Hybridisation in European ungulates: an overview of the current status, causes, and consequences. Mamm Rev 2018. [DOI: 10.1111/mam.12140] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Laura Iacolina
- Department of Chemistry and Bioscience; Aalborg University; Frederik Bajers Vej 7H 9220 Aalborg Denmark
- Aalborg Zoo; Mølleparkvej 63 9000 Aalborg Denmark
| | - Luca Corlatti
- Wildlife Ecology and Management; University of Freiburg; Tennenbacher Straße 4 79106 Freiburg Germany
- Institute of Wildlife Biology and Game Management; University of Natural Resources and Life Sciences Vienna; Gregor-Mendel-Straße 33 1180 Vienna Austria
| | - Elena Buzan
- Department of Biodiversity; Faculty of Mathematics, Natural Sciences and Information Technologies; University of Primorska; Glagoljaška 8 6000 Koper Slovenia
| | - Toni Safner
- Faculty of Agriculture; Department of Plant Breeding, Genetics and Biometrics; University of Zagreb; Svetošimunska cesta 25 10000 Zagreb Croatia
| | - Nikica Šprem
- Faculty of Agriculture; Department of Fisheries, Beekeeping, Game Management and Special Zoology; University of Zagreb; Svetošimunska cesta 25 10000 Zagreb Croatia
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Werhahn G, Senn H, Ghazali M, Karmacharya D, Sherchan AM, Joshi J, Kusi N, López-Bao JV, Rosen T, Kachel S, Sillero-Zubiri C, Macdonald DW. The unique genetic adaptation of the Himalayan wolf to high-altitudes and consequences for conservation. Glob Ecol Conserv 2018. [DOI: 10.1016/j.gecco.2018.e00455] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
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28
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Zachos FE. (New) Species concepts, species delimitation and the inherent limitations of taxonomy. J Genet 2018. [DOI: 10.1007/s12041-018-0965-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Ricci M, Peona V, Guichard E, Taccioli C, Boattini A. Transposable Elements Activity is Positively Related to Rate of Speciation in Mammals. J Mol Evol 2018; 86:303-310. [PMID: 29855654 PMCID: PMC6028844 DOI: 10.1007/s00239-018-9847-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Accepted: 05/24/2018] [Indexed: 02/05/2023]
Abstract
Transposable elements (TEs) play an essential role in shaping eukaryotic genomes and generating variability. Speciation and TE activity bursts could be strongly related in mammals, in which simple gradualistic models of differentiation do not account for the currently observed species variability. In order to test this hypothesis, we designed two parameters: the Density of insertion (DI) and the Relative rate of speciation (RRS). DI is the ratio between the number of TE insertions in a genome and its size, whereas the RRS is a conditional parameter designed to identify potential speciation bursts. Thus, by analyzing TE insertions in mammals, we defined the genomes as “hot” (high DI) and “cold” (low DI). Then, comparing TE activity among 29 taxonomical families of the whole Mammalia class, 16 intra-order pairs of mammalian species, and four superorders of Eutheria, we showed that taxa with high rates of speciation are associated with “hot” genomes, whereas taxa with low ones are associated with “cold” genomes. These results suggest a remarkable correlation between TE activity and speciation, also being consistent with patterns describing variable rates of differentiation and accounting for the different time frames of the speciation bursts.
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Affiliation(s)
- Marco Ricci
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy.
| | - Valentina Peona
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
- Department of Ecology and Genetics, University of Uppsala, Uppsala, Sweden
| | - Etienne Guichard
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy.
| | - Cristian Taccioli
- Department of Animal Medicine, Health and Production, University of Padova, Padova, Italy
| | - Alessio Boattini
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
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