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Schmid S, Bachmann Salvy M, Garcia Jimenez A, Bertrand JAM, Cortesi F, Heim S, Huyghe F, Litsios G, Marcionetti A, O'Donnell JL, Riginos C, Tettamanti V, Salamin N. Gene flow throughout the evolutionary history of a colour polymorphic and generalist clownfish. Mol Ecol 2024; 33:e17436. [PMID: 38872589 DOI: 10.1111/mec.17436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 05/12/2024] [Accepted: 05/17/2024] [Indexed: 06/15/2024]
Abstract
Even seemingly homogeneous on the surface, the oceans display high environmental heterogeneity across space and time. Indeed, different soft barriers structure the marine environment, which offers an appealing opportunity to study various evolutionary processes such as population differentiation and speciation. Here, we focus on Amphiprion clarkii (Actinopterygii; Perciformes), the most widespread of clownfishes that exhibits the highest colour polymorphism. Clownfishes can only disperse during a short pelagic larval phase before their sedentary adult lifestyle, which might limit connectivity among populations, thus facilitating speciation events. Consequently, the taxonomic status of A. clarkii has been under debate. We used whole-genome resequencing data of 67 A. clarkii specimens spread across the Indian and Pacific Oceans to characterize the species' population structure, demographic history and colour polymorphism. We found that A. clarkii spread from the Indo-Pacific Ocean to the Pacific and Indian Oceans following a stepping-stone dispersal and that gene flow was pervasive throughout its demographic history. Interestingly, colour patterns differed noticeably among the Indonesian populations and the two populations at the extreme of the sampling distribution (i.e. Maldives and New Caledonia), which exhibited more comparable colour patterns despite their geographic and genetic distances. Our study emphasizes how whole-genome studies can uncover the intricate evolutionary past of wide-ranging species with diverse phenotypes, shedding light on the complex nature of the species concept paradigm.
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Affiliation(s)
- Sarah Schmid
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | | | | | - Joris A M Bertrand
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Fabio Cortesi
- Queensland Brain Institute, the University of Queensland, Brisbane, Queensland, Australia
- School of the Environment, The University of Queensland, Brisbane, Queensland, Australia
| | - Sara Heim
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Filip Huyghe
- Marine Biology Laboratory, Department of Ecology and Biodiversity, Vrije Universiteit Brussel, Brussel, Belgium
| | - Glenn Litsios
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Anna Marcionetti
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - James L O'Donnell
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, California, USA
| | - Cynthia Riginos
- School of the Environment, The University of Queensland, Brisbane, Queensland, Australia
| | - Valerio Tettamanti
- Queensland Brain Institute, the University of Queensland, Brisbane, Queensland, Australia
| | - Nicolas Salamin
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
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2
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Vences M, Patmanidis S, Schmidt JC, Matschiner M, Miralles A, Renner SS. Hapsolutely: a user-friendly tool integrating haplotype phasing, network construction, and haploweb calculation. BIOINFORMATICS ADVANCES 2024; 4:vbae083. [PMID: 38895561 PMCID: PMC11184345 DOI: 10.1093/bioadv/vbae083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 05/15/2024] [Accepted: 06/04/2024] [Indexed: 06/21/2024]
Abstract
Motivation Haplotype networks are a routine approach to visualize relationships among alleles. Such visual analysis of single-locus data is still of importance, especially in species diagnosis and delimitation, where a limited amount of sequence data usually are available and sufficient, along with other datasets in the framework of integrative taxonomy. In diploid organisms, this often requires separating (phasing) sequences with heterozygotic positions, and typically separate programs are required for phasing, reformatting of input files, and haplotype network construction. We therefore developed Hapsolutely, a user-friendly program with an ergonomic graphical user interface that integrates haplotype phasing from single-locus sequences with five approaches for network/genealogy reconstruction. Results Among the novel options implemented, Hapsolutely integrates phasing and graphical reconstruction steps of haplotype networks, supports input of species partition data in the common SPART and SPART-XML formats, and calculates and visualizes haplowebs and fields for recombination, thus allowing graphical comparison of allele distribution and allele sharing among subsets for the purpose of species delimitation. The new tool has been specifically developed with a focus on the workflow in alpha-taxonomy, where exploring fields for recombination across alternative species partitions may help species delimitation. Availability and implementation Hapsolutely is written in Python, and integrates code from Phase, SeqPHASE, and PopART in C++ and Haxe. Compiled stand-alone executables for MS Windows and Mac OS along with a detailed manual can be downloaded from https://www.itaxotools.org; the source code is openly available on GitHub (https://github.com/iTaxoTools/Hapsolutely).
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Affiliation(s)
- Miguel Vences
- Division of Evolutionary Biology, Zoological Institute, Technische Universität Braunschweig, 38106 Braunschweig, Germany
| | - Stefanos Patmanidis
- Department of Computer Science, School of Electrical and Computer Engineering, National Technical University of Athens, 15780 Athens, Greece
| | - Jan-Christopher Schmidt
- Division of Evolutionary Biology, Zoological Institute, Technische Universität Braunschweig, 38106 Braunschweig, Germany
| | | | - Aurélien Miralles
- Division of Evolutionary Biology, Zoological Institute, Technische Universität Braunschweig, 38106 Braunschweig, Germany
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, CNRS, Sorbonne Université, EPHE, 75005 Paris, France
| | - Susanne S Renner
- Department of Biology, Washington University, Saint Louis, MO 63130, United States
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3
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Koepfli KP. Evolution: Genomes reveal the reticulated history of giraffes. Curr Biol 2024; 34:R533-R536. [PMID: 38834025 DOI: 10.1016/j.cub.2024.04.045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
The diversification and taxonomy of modern giraffe lineages have been a riddle for more than 200 years. A new genomic study shows that divergence with gene flow has played a significant role in the history of this zoological icon.
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Affiliation(s)
- Klaus-Peter Koepfli
- Smithsonian-Mason School of Conservation, George Mason University, 1500 Remount Road, Front Royal, VA 22630, USA.
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4
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Bertola LD, Quinn L, Hanghøj K, Garcia-Erill G, Rasmussen MS, Balboa RF, Meisner J, Bøggild T, Wang X, Lin L, Nursyifa C, Liu X, Li Z, Chege M, Moodley Y, Brüniche-Olsen A, Kuja J, Schubert M, Agaba M, Santander CG, Sinding MHS, Muwanika V, Masembe C, Siegismund HR, Moltke I, Albrechtsen A, Heller R. Giraffe lineages are shaped by major ancient admixture events. Curr Biol 2024; 34:1576-1586.e5. [PMID: 38479386 DOI: 10.1016/j.cub.2024.02.051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 09/29/2023] [Accepted: 02/21/2024] [Indexed: 04/11/2024]
Abstract
Strong genetic structure has prompted discussion regarding giraffe taxonomy,1,2,3 including a suggestion to split the giraffe into four species: Northern (Giraffa c. camelopardalis), Reticulated (G. c. reticulata), Masai (G. c. tippelskirchi), and Southern giraffes (G. c. giraffa).4,5,6 However, their evolutionary history is not yet fully resolved, as previous studies used a simple bifurcating model and did not explore the presence or extent of gene flow between lineages. We therefore inferred a model that incorporates various evolutionary processes to assess the drivers of contemporary giraffe diversity. We analyzed whole-genome sequencing data from 90 wild giraffes from 29 localities across their current distribution. The most basal divergence was dated to 280 kya. Genetic differentiation, FST, among major lineages ranged between 0.28 and 0.62, and we found significant levels of ancient gene flow between them. In particular, several analyses suggested that the Reticulated lineage evolved through admixture, with almost equal contribution from the Northern lineage and an ancestral lineage related to Masai and Southern giraffes. These new results highlight a scenario of strong differentiation despite gene flow, providing further context for the interpretation of giraffe diversity and the process of speciation in general. They also illustrate that conservation measures need to target various lineages and sublineages and that separate management strategies are needed to conserve giraffe diversity effectively. Given local extinctions and recent dramatic declines in many giraffe populations, this improved understanding of giraffe evolutionary history is relevant for conservation interventions, including reintroductions and reinforcements of existing populations.
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Affiliation(s)
- Laura D Bertola
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Liam Quinn
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kristian Hanghøj
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Renzo F Balboa
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jonas Meisner
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Bøggild
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Xi Wang
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Long Lin
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Casia Nursyifa
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Xiaodong Liu
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Zilong Li
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Mumbi Chege
- Institute of Environmental Sciences (CML), Leiden University, Leiden, The Netherlands; Wildlife Research and Training Institute, Naivasha, Kenya
| | - Yoshan Moodley
- Department of Biological Sciences, University of Venda, Private Bag X5050, Thohoyandou 0950, Republic of South Africa
| | | | - Josiah Kuja
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Mikkel Schubert
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Morris Agaba
- School of Life Sciences and Bioengineering, Nelson Mandela African Institution of Science and Technology, Nelson Mandela Road, Arusha, Tanzania
| | - Cindy G Santander
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Vincent Muwanika
- College of Agricultural and Environmental Sciences, Makerere University, P.O. Box 7062, Kampala, Uganda
| | - Charles Masembe
- College of Natural Sciences, Makerere University, P O. Box 7062, Kampala, Uganda
| | - Hans R Siegismund
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Ida Moltke
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | | | - Rasmus Heller
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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5
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Opatova V, Bourguignon K, Bond JE. Species delimitation with limited sampling: An example from rare trapdoor spider genus Cyclocosmia (Mygalomorphae, Halonoproctidae). Mol Ecol Resour 2024; 24:e13894. [PMID: 37971187 DOI: 10.1111/1755-0998.13894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 10/24/2023] [Accepted: 10/31/2023] [Indexed: 11/19/2023]
Abstract
The outcome of species delimitation depends on many factors, including conceptual framework, study design, data availability, methodology employed and subjective decision making. Obtaining sufficient taxon sampling in endangered or rare taxa might be difficult, particularly when non-lethal tissue collection cannot be utilized. The need to avoid overexploitation of the natural populations may thus limit methodological framework available for downstream data analyses and bias the results. We test species boundaries in rare North American trapdoor spider genus Cyclocosmia Ausserer (1871) inhabiting the Southern Coastal Plain biodiversity hotspot with the use of genomic data and two multispecies coalescent model methods. We evaluate the performance of each methodology within a limited sampling framework. To mitigate the risk of species over splitting, common in taxa with highly structured populations, we subsequently implement a species validation step via genealogical diversification index (gdi), which accounts for both genetic isolation and gene flow. We delimited eight geographically restricted lineages within sampled North American Cyclocosmia, suggesting that major river drainages in the region are likely barriers to dispersal. Our results suggest that utilizing BPP in the species discovery step might be a good option for datasets comprising hundreds of loci, but fewer individuals, which may be a common scenario for rare taxa. However, we also show that such results should be validated via gdi, in order to avoid over splitting.
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Affiliation(s)
- Vera Opatova
- Department of Zoology, Faculty of Sciences, Charles University, Prague 2, Czech Republic
| | - Kellie Bourguignon
- Department of Biological Sciences, Auburn University, Auburn, Alabama, USA
| | - Jason E Bond
- Department of Entomology and Nematology, University of California, Davis, California, USA
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6
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Balboa RF, Bertola LD, Brüniche-Olsen A, Rasmussen MS, Liu X, Besnard G, Salmona J, Santander CG, He S, Zinner D, Pedrono M, Muwanika V, Masembe C, Schubert M, Kuja J, Quinn L, Garcia-Erill G, Stæger FF, Rakotoarivony R, Henrique M, Lin L, Wang X, Heaton MP, Smith TPL, Hanghøj K, Sinding MHS, Atickem A, Chikhi L, Roos C, Gaubert P, Siegismund HR, Moltke I, Albrechtsen A, Heller R. African bushpigs exhibit porous species boundaries and appeared in Madagascar concurrently with human arrival. Nat Commun 2024; 15:172. [PMID: 38172616 PMCID: PMC10764920 DOI: 10.1038/s41467-023-44105-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 11/30/2023] [Indexed: 01/05/2024] Open
Abstract
Several African mammals exhibit a phylogeographic pattern where closely related taxa are split between West/Central and East/Southern Africa, but their evolutionary relationships and histories remain controversial. Bushpigs (Potamochoerus larvatus) and red river hogs (P. porcus) are recognised as separate species due to morphological distinctions, a perceived lack of interbreeding at contact, and putatively old divergence times, but historically, they were considered conspecific. Moreover, the presence of Malagasy bushpigs as the sole large terrestrial mammal shared with the African mainland raises intriguing questions about its origin and arrival in Madagascar. Analyses of 67 whole genomes revealed a genetic continuum between the two species, with putative signatures of historical gene flow, variable FST values, and a recent divergence time (<500,000 years). Thus, our study challenges key arguments for splitting Potamochoerus into two species and suggests their speciation might be incomplete. Our findings also indicate that Malagasy bushpigs diverged from southern African populations and underwent a limited bottleneck 1000-5000 years ago, concurrent with human arrival in Madagascar. These results shed light on the evolutionary history of an iconic and widespread African mammal and provide insight into the longstanding biogeographic puzzle surrounding the bushpig's presence in Madagascar.
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Affiliation(s)
- Renzo F Balboa
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Laura D Bertola
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Xiaodong Liu
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Guillaume Besnard
- Laboratoire Evolution et Diversité Biologique (EDB), UMR 5174, CNRS, IRD, Université Toulouse Paul Sabatier, 31062, Toulouse, France
| | - Jordi Salmona
- Laboratoire Evolution et Diversité Biologique (EDB), UMR 5174, CNRS, IRD, Université Toulouse Paul Sabatier, 31062, Toulouse, France
| | - Cindy G Santander
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Shixu He
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Dietmar Zinner
- Cognitive Ecology Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077, Göttingen, Germany
- Department of Primate Cognition, Georg-August-Universität Göttingen, 37077, Göttingen, Germany
- Leibniz Science Campus Primate Cognition, 37077, Göttingen, Germany
| | - Miguel Pedrono
- UMR ASTRE, CIRAD, Campus International de Baillarguet, Montpellier, France
| | - Vincent Muwanika
- College of Agricultural and Environmental Sciences, Makerere University, Kampala, Uganda
| | - Charles Masembe
- College of Natural Sciences, Makerere University, Kampala, Uganda
| | - Mikkel Schubert
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Josiah Kuja
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Liam Quinn
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | | | | | | | - Long Lin
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Xi Wang
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Kristian Hanghøj
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Anagaw Atickem
- Department of Zoological Sciences, Addis Ababa University, PO Box 1176, Addis Ababa, Ethiopia
| | - Lounès Chikhi
- Laboratoire Evolution et Diversité Biologique (EDB), UMR 5174, CNRS, IRD, Université Toulouse Paul Sabatier, 31062, Toulouse, France
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077, Göttingen, Germany
| | - Philippe Gaubert
- Laboratoire Evolution et Diversité Biologique (EDB), UMR 5174, CNRS, IRD, Université Toulouse Paul Sabatier, 31062, Toulouse, France
- Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR), Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208, Porto, Portugal
| | - Hans R Siegismund
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Ida Moltke
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | | | - Rasmus Heller
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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7
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Coimbra RTF, Winter S, Muneza A, Fennessy S, Otiende M, Mijele D, Masiaine S, Stacy-Dawes J, Fennessy J, Janke A. Genomic analysis reveals limited hybridization among three giraffe species in Kenya. BMC Biol 2023; 21:215. [PMID: 37833744 PMCID: PMC10576358 DOI: 10.1186/s12915-023-01722-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 10/02/2023] [Indexed: 10/15/2023] Open
Abstract
BACKGROUND In the speciation continuum, the strength of reproductive isolation varies, and species boundaries are blurred by gene flow. Interbreeding among giraffe (Giraffa spp.) in captivity is known, and anecdotal reports of natural hybrids exist. In Kenya, Nubian (G. camelopardalis camelopardalis), reticulated (G. reticulata), and Masai giraffe sensu stricto (G. tippelskirchi tippelskirchi) are parapatric, and thus, the country might be a melting pot for these taxa. We analyzed 128 genomes of wild giraffe, 113 newly sequenced, representing these three taxa. RESULTS We found varying levels of Nubian ancestry in 13 reticulated giraffe sampled across the Laikipia Plateau most likely reflecting historical gene flow between these two lineages. Although comparatively weaker signs of ancestral gene flow and potential mitochondrial introgression from reticulated into Masai giraffe were also detected, estimated admixture levels between these two lineages are minimal. Importantly, contemporary gene flow between East African giraffe lineages was not statistically significant. Effective population sizes have declined since the Late Pleistocene, more severely for Nubian and reticulated giraffe. CONCLUSIONS Despite historically hybridizing, these three giraffe lineages have maintained their overall genomic integrity suggesting effective reproductive isolation, consistent with the previous classification of giraffe into four species.
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Affiliation(s)
- Raphael T F Coimbra
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt, Germany.
- Institute for Ecology, Evolution and Diversity, Goethe University, Frankfurt, Germany.
| | - Sven Winter
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt, Germany
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Vienna, Austria
| | | | | | | | | | | | | | - Julian Fennessy
- Giraffe Conservation Foundation, Windhoek, Namibia
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Axel Janke
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt, Germany.
- Institute for Ecology, Evolution and Diversity, Goethe University, Frankfurt, Germany.
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt, Germany.
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8
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Dufresnes C, Poyarkov N, Jablonski D. Acknowledging more biodiversity without more species. Proc Natl Acad Sci U S A 2023; 120:e2302424120. [PMID: 37748058 PMCID: PMC10556632 DOI: 10.1073/pnas.2302424120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023] Open
Abstract
Delimiting and naming biodiversity is a vital step toward wildlife conservation and research. However, species delimitation must be consistent across biota so that the limited resources available for nature protection can be spent effectively and objectively. To date, newly discovered lineages typically are either left undescribed and thus remain unprotected or are being erroneously proposed as new species despite mixed evidence for completed speciation, in turn contributing to the emerging problem of taxonomic inflation. Inspired by recent conceptual and methodological progress, we propose a standardized workflow for species delimitation that combines phylogenetic and hybrid zone analyses of genomic datasets ("genomic taxonomy"), in which phylogeographic lineages that do not freely admix are ranked as species, while those that have remained fully genetically compatible are ranked as subspecies. In both cases, we encourage their formal taxonomic naming, diagnosis, and description to promote social awareness toward biodiversity. The use of loci throughout the genome overcomes the unreliability of widely used barcoding genes when phylogeographic patterns are complex, while the evaluation of divergence and reproductive isolation unifies the long-opposed concepts of lineage species and biological species. We suggest that a shift in conservation assessments from a single level (species) toward a two-level hierarchy (species and subspecies) will lead to a more balanced perception of biodiversity in which both intraspecific and interspecific diversity are valued and more adequately protected.
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Affiliation(s)
- Christophe Dufresnes
- Laboratory of Amphibian Systematics and Evolutionary Research, College of Biology and Environment, Nanjing Forestry University, Nanjing210037, People’s Republic of China
| | - Nikolay Poyarkov
- Joint Russian-Vietnamese Tropical Research and Technological Center, Hanoi122000, Vietnam
- Department of Vertebrate Zoology, Lomonosov Moscow State University, Moscow119234, Russia
| | - Daniel Jablonski
- Department of Zoology, Comenius University in Bratislava, Bratislava84215, Slovakia
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9
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Bogdanov A, Tambovtseva V, Matveevsky S, Bakloushinskaya I. Speciation on the Roof of the World: Parallel Fast Evolution of Cryptic Mole Vole Species in the Pamir-Alay-Tien Shan Region. Life (Basel) 2023; 13:1751. [PMID: 37629608 PMCID: PMC10455883 DOI: 10.3390/life13081751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/03/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023] Open
Abstract
Speciation is not always accompanied by morphological changes; numerous cryptic closely related species were revealed using genetic methods. In natural populations of Ellobius tancrei (2n = 54-30) and E. alaicus (2n = 52-48) of the Pamir-Alay and Tien Shan, the chromosomal variability due to Robertsonian translocations has been revealed. Here, by comprehensive genetic analysis (karyological analyses as well as sequencing of mitochondrial genes, cytb and COI, and nuclear genes, XIST and IRBP) of E. alaicus and E. tancrei samples from the Inner Tien Shan, the Alay Valley, and the Pamir-Alay, we demonstrated fast and independent diversification of these species. We described an incompletely consistent polymorphism of the mitochondrial and nuclear markers, which arose presumably because of habitat fragmentation in the highlands, rapid karyotype changes, and hybridization of different intraspecific varieties and species. The most intriguing results are a low level of genetic distances calculated from mitochondrial and nuclear genes between some phylogenetic lines of E. tancrei and E. alaicus, as well significant species-specific chromosome variability in both species. The chromosomal rearrangements are what most clearly define species specificity and provide further diversification. The "mosaicism" and inconsistency in polymorphism patterns are evidence of rapid speciation in these mammals.
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Affiliation(s)
- Aleksey Bogdanov
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 119334 Moscow, Russia;
| | - Valentina Tambovtseva
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 119334 Moscow, Russia;
| | - Sergey Matveevsky
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia;
| | - Irina Bakloushinskaya
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 119334 Moscow, Russia;
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10
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Dong X, Zhang H, Zhu X, Wang K, Xue H, Ye Z, Zheng C, Bu W. Mitochondrial introgression and mito-nuclear discordance obscured the closely related species boundaries in Cletus Stål from China (Heteroptera: Coreidae). Mol Phylogenet Evol 2023; 184:107802. [PMID: 37221926 DOI: 10.1016/j.ympev.2023.107802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 04/07/2023] [Accepted: 04/18/2023] [Indexed: 05/25/2023]
Abstract
Accurate taxonomy and delimitation are of great importance for pest control strategies and management programs. Here, we focus on Cletus (Insecta: Hemiptera: Coreidae), which includes many crop pests. The species boundaries still conflict and only cytochrome c oxidase subunit I (COI) barcoding has been previously used for molecular studies. We generated new mitochondrial genome and nuclear genome-wide SNPs to explore the species boundaries of 46 Cletus samples from China using multiple species delimitation approaches. All results recovered a monophyly with high support, except for two closely related species in clade I - C. punctiger and C. graminis. Mitochondrial data demonstrated admixture in clade I, while genome-wide SNPs unambiguously identified two separate species, which were confirmed by morphological classification. Inconsistent nuclear and mitochondrial data indicated mito-nuclear discordance. Mitochondrial introgression is the most likely explanation, and more extensive sampling and more comprehensive data are needed to ascertain a pattern. Accurate species delimitation will shed light on species status; thus, an accurate taxonomy is of particular concern, as there is a pressing need to implement precise control of agricultural pests and to perform further research on diversification.
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Affiliation(s)
- Xue Dong
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Haiguang Zhang
- College of Life Science, Linyi University, Linyi 276000, China
| | - Xiuxiu Zhu
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Kaibin Wang
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Huaijun Xue
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Zhen Ye
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China.
| | - Chenguang Zheng
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China.
| | - Wenjun Bu
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China.
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Tukhbatullin A, Ermakov O, Kapustina S, Starikov V, Tambovtseva V, Titov S, Brandler O. Surrounded by Kindred: Spermophilus major Hybridization with Other Spermophilus Species in Space and Time. BIOLOGY 2023; 12:880. [PMID: 37372163 DOI: 10.3390/biology12060880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/05/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023]
Abstract
Among the numerous described cases of hybridization in mammals, the most intriguing are (a) cases of introgressive hybridization deeply affecting the evolutionary history of species, and (b) models involving not a pair of species but a multi-species complex. Therefore, the hybridization history of the russet ground squirrel Spermophilus major, whose range has repeatedly changed due to climatic fluctuations and now borders the ranges of four related species, is of great interest. The main aims of this study were to determine the direction and intensity of gene introgression, the spatial depth of the infiltration of extraneous genes into the S. major range, and to refine the hypothesis of the hybridogenic replacement of mitochondrial genomes in the studied group. Using phylogenetic analysis of the variability of mitochondrial (CR, cytb) and nuclear (SmcY, BGN, PRKCI, c-myc, i6p53) markers, we determined the contribution of neighboring species to the S. major genome. We showed that 36% of S. major individuals had extraneous alleles. All peripheral species that were in contact with S. major contributed towards its genetic variability. We also proposed a hypothesis for the sequence and localization of serial hybridization events. Our assessment of the S. major genome implications of introgression highlights the importance of implementing conservation measures to protect this species.
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Affiliation(s)
- Andrey Tukhbatullin
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Vavilova Str. 26, Moscow 119334, Russia
| | - Oleg Ermakov
- Faculty of Physics, Mathematics and Natural Sciences, Belinsky Institute of Teacher Education, Penza State University, Lermontov Str. 37, Penza 440026, Russia
| | - Svetlana Kapustina
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Vavilova Str. 26, Moscow 119334, Russia
| | - Vladimir Starikov
- Department of Biology and Biotechnology, Institute of Natural and Technical Sciences, Surgut State University, Lenin Avenue 1, Surgut 628412, Russia
| | - Valentina Tambovtseva
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Vavilova Str. 26, Moscow 119334, Russia
| | - Sergey Titov
- Faculty of Physics, Mathematics and Natural Sciences, Belinsky Institute of Teacher Education, Penza State University, Lermontov Str. 37, Penza 440026, Russia
| | - Oleg Brandler
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Vavilova Str. 26, Moscow 119334, Russia
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12
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Lohay GG, Lee DE, Wu‐Cavener L, Pearce DL, Hou X, Bond ML, Cavener DR. Genetic evidence of population subdivision among Masai giraffes separated by the Gregory Rift Valley in Tanzania. Ecol Evol 2023; 13:e10160. [PMID: 37313272 PMCID: PMC10259769 DOI: 10.1002/ece3.10160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 05/17/2023] [Accepted: 05/22/2023] [Indexed: 06/15/2023] Open
Abstract
The Masai giraffe has experienced a population decline from 70,000 to 35,000 in the past three decades and was declared an endangered subspecies by the IUCN in 2019. The remaining number of Masai giraffe are geographically separated by the steep cliffs of the Gregory Rift escarpments (GRE) in Tanzania and Kenya dividing them into two populations, one west and one east of the GRE. The cliffs of the GRE are formidable barriers to east-west dispersal and gene flow and the few remaining natural corridors through the GRE are occupied by human settlements. To assess the impact of the GRE on Masai giraffe gene flow, we examined whole genome sequences of nuclear and mitochondrial DNA (mtDNA) variation in populations located east (Tarangire ecosystem) and west (Serengeti ecosystem) of the GRE in northern Tanzania. Evidence from mtDNA variation, which measures female-mediated gene flow, suggests that females have not migrated across the GRE between populations in the Serengeti and Tarangire ecosystems in the past ~289,000 years. The analysis of nuclear DNA variation compared to mtDNA DNA variation suggests that male-mediated gene flow across the GRE has occurred more recently but stopped a few thousand years ago. Our findings show that Masai giraffes are split into two populations and fulfill the criteria for designation as distinct evolutionary significant units (ESUs), which we denote as western Masai giraffe and eastern Masai giraffe. While establishing giraffe dispersal corridors across the GRE is impractical, conservation efforts should be focused on maintaining connectivity among populations within each of these two populations. The importance of these efforts is heightened by our finding that the inbreeding coefficients are high in some of these Masai giraffe populations, which could result in inbreeding depression in the small and fragmented populations.
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Affiliation(s)
- George G. Lohay
- Biology DepartmentPenn State UniversityUniversity ParkPennsylvaniaUSA
- Research Innovation for the Serengeti Ecosystem, Grumeti FundMaraTanzania
| | - Derek E. Lee
- Biology DepartmentPenn State UniversityUniversity ParkPennsylvaniaUSA
- Wild Nature InstituteConcordNew HampshireUSA
| | - Lan Wu‐Cavener
- Biology DepartmentPenn State UniversityUniversity ParkPennsylvaniaUSA
| | - David L. Pearce
- Department of Ecosystem Science and ManagementPenn State UniversityUniversity ParkPennsylvaniaUSA
| | - Xiaoyi Hou
- Biology DepartmentPenn State UniversityUniversity ParkPennsylvaniaUSA
| | - Monica L. Bond
- Biology DepartmentPenn State UniversityUniversity ParkPennsylvaniaUSA
- Wild Nature InstituteConcordNew HampshireUSA
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZurichSwitzerland
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13
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Sabroux R, Corbari L, Hassanin A. Phylogeny of sea spiders (Arthropoda: Pycnogonida) inferred from mitochondrial genome and 18S ribosomal RNA gene sequences. Mol Phylogenet Evol 2023; 182:107726. [PMID: 36754337 DOI: 10.1016/j.ympev.2023.107726] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 01/20/2023] [Accepted: 02/03/2023] [Indexed: 02/10/2023]
Abstract
The phylogeny of sea spiders has been debated for more than a century. Despite several molecular studies in the last twenty years, interfamilial relationships remain uncertain. In the present study, relationships within Pycnogonida are examined in the light of a new dataset composed of 160 mitochondrial genomes (including 152 new sequences) and 130 18S rRNA gene sequences (including 120 new sequences), from 141 sea spider morphospecies representing 26 genera and 9 families. Node congruence between mitochondrial and nuclear markers was analysed to identify the most reliable relationships. We also reanalysed a multilocus dataset previously published and showed that the high percentages of missing data make phylogenetic conclusions difficult and uncertain. Our results support the monophyly of most families currently accepted, except Callipallenidae and Nymphonidae, the monophyly of the superfamilies Ammotheoidea (Ammotheidae + Pallenopsidae), Nymphonoidea (Nymphonidae + Callipallenidae), Phoxichilidioidea (Phoxichilidiidae + Endeidae) and Colossendeoidea (Colossendeidae + Pycnogonidae + Rhynchothoracidae), and the sister-group relationship between Ammotheoidea and Phoxichilidioidea. We discuss the morphological evolution of sea spiders, identifying homoplastic characters and possible synapomorphies. We also discuss the palaeontological and phylogenetic arguments supporting either a radiation of sea spiders prior to Jurassic or a progressive diversification from Ordovician or Cambrian.
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Affiliation(s)
- Romain Sabroux
- Institut Systématique Evolution Biodiversité (ISYEB), Sorbonne Université, MNHN, CNRS, EPHE, UA, 57 rue Cuvier, CP 51, 75005 Paris, France
| | - Laure Corbari
- Institut Systématique Evolution Biodiversité (ISYEB), Sorbonne Université, MNHN, CNRS, EPHE, UA, 57 rue Cuvier, CP 51, 75005 Paris, France
| | - Alexandre Hassanin
- Institut Systématique Evolution Biodiversité (ISYEB), Sorbonne Université, MNHN, CNRS, EPHE, UA, 57 rue Cuvier, CP 51, 75005 Paris, France.
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14
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Bernstein-Kurtycz LM, Dunham NT, Evenhuis J, Brown MB, Muneza AB, Fennessy J, Dennis PM, Lukas KE. Evaluating the effects of giraffe skin disease and wire snare wounds on the gaits of free-ranging Nubian giraffe. Sci Rep 2023; 13:1959. [PMID: 36737637 PMCID: PMC9898309 DOI: 10.1038/s41598-023-28677-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 01/23/2023] [Indexed: 02/05/2023] Open
Abstract
Giraffe skin disease (GSD), a condition that results in superficial lesions in certain giraffe (Giraffa spp.) populations, has emerged as a potential conservation threat. Preliminary findings suggested that individuals with GSD lesions move with greater difficulty which may in turn reduce their foraging efficiency or make them more vulnerable to predation. A current known threat to some giraffe populations is their mortality associated with entrapment in wire snares, and the morbidity and potential locomotor deficiencies associated with wounds acquired from snares. The goal of our study was to quantify the locomotor kinematics of free-ranging Nubian giraffe (G. camelopardalis camelopardalis) in Murchison Falls National Park (MFNP), Uganda, and compare spatiotemporal limb and neck angle kinematics of healthy giraffe to those of giraffe with GSD lesions, snare wounds, and both GSD lesions and snare wounds. The presence of GSD lesions did not significantly affect spatiotemporal limb kinematic parameters. This finding is potentially because lesions were located primarily on the necks of Nubian giraffe in MFNP. The kinematic parameters of individuals with snare wounds differed from those of healthy individuals, resulting in significantly shorter stride lengths, reduced speed, lower limb phase values, and increased gait asymmetry. Neck angle kinematic parameters did not differ among giraffe categories, which suggests that GSD neck lesions do not impair normal neck movements and range of motion during walking. Overall, MFNP giraffe locomotor patterns are largely conservative between healthy individuals and those with GSD, while individuals with snare wounds showed more discernible kinematic adjustments consistent with unilateral limb injuries. Additional studies are recommended to assess spatiotemporal limb kinematics of giraffe at sites where lesions are found predominantly on the limbs to better assess the potential significance of GSD on their locomotion.
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Affiliation(s)
- L M Bernstein-Kurtycz
- Division of Conservation and Science, Cleveland Metroparks Zoo, 4200 Wildlife Way, Cleveland, OH, 44109, USA.,Department of Biology, Case Western Reserve University, Cleveland, OH, USA.,Little Rock Zoo, Little Rock, AR, USA
| | - N T Dunham
- Division of Conservation and Science, Cleveland Metroparks Zoo, 4200 Wildlife Way, Cleveland, OH, 44109, USA. .,Department of Biology, Case Western Reserve University, Cleveland, OH, USA.
| | - J Evenhuis
- Department of Biology, Case Western Reserve University, Cleveland, OH, USA.,College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - M B Brown
- Giraffe Conservation Foundation, P.O. Box 86099, Eros, Namibia.,Smithsonian National Zoo and Conservation Biology Institute, Front Royal, VA, 22630, USA.,Department of Biological Sciences Program in Ecology, Evolution, Ecosystems, and Society, Dartmouth College, Hanover, NH, USA
| | - A B Muneza
- Giraffe Conservation Foundation, P.O. Box 86099, Eros, Namibia
| | - J Fennessy
- Giraffe Conservation Foundation, P.O. Box 86099, Eros, Namibia
| | - P M Dennis
- Division of Conservation and Science, Cleveland Metroparks Zoo, 4200 Wildlife Way, Cleveland, OH, 44109, USA.,Department of Biology, Case Western Reserve University, Cleveland, OH, USA.,Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, OH, USA
| | - K E Lukas
- Division of Conservation and Science, Cleveland Metroparks Zoo, 4200 Wildlife Way, Cleveland, OH, 44109, USA.,Department of Biology, Case Western Reserve University, Cleveland, OH, USA
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15
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Using spot pattern recognition to examine population biology, evolutionary ecology, sociality, and movements of giraffes: a 70-year retrospective. Mamm Biol 2022. [DOI: 10.1007/s42991-022-00261-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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16
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Morandi K, Lindholm AK, Lee DE, Bond ML. Phenotypic matching by spot pattern potentially mediates female giraffe social associations. J Zool (1987) 2022. [DOI: 10.1111/jzo.13009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- K. Morandi
- Department of Evolutionary Biology and Environmental Studies University of Zurich Zurich Switzerland
| | - A. K. Lindholm
- Department of Evolutionary Biology and Environmental Studies University of Zurich Zurich Switzerland
| | - D. E. Lee
- Wild Nature Institute Concord NH USA
- Department of Biology Pennsylvania State University University Park PA USA
| | - M. L. Bond
- Department of Evolutionary Biology and Environmental Studies University of Zurich Zurich Switzerland
- Wild Nature Institute Concord NH USA
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17
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Geographic Mosaic of Extensive Genetic Variations in Subterranean Mole Voles Ellobius alaicus as a Consequence of Habitat Fragmentation and Hybridization. Life (Basel) 2022; 12:life12050728. [PMID: 35629395 PMCID: PMC9146075 DOI: 10.3390/life12050728] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 05/03/2022] [Accepted: 05/11/2022] [Indexed: 11/17/2022] Open
Abstract
Restricted mobility, sociality, and high inbreeding—characteristic for subterranean mammals—lead to rapid changes in their genome structure. Up to now, the Alay mole vole Ellobius alaicus was a data-deficient species; its spatial and phylogenetic relationships with a sibling species, E. tancrei, were not clarified. We carried out a genetic analysis including differential G-banding of chromosomes and mitochondrial (cytb) and nuclear gene (XIST and IRBP) sequencing. The phylogenetic reconstruction based on cytb represented the expected phylogenetic relationships of two species. Using the XIST, we revealed two new lineages among E. alaicus from the Alay Valley (Southern Kyrgyzstan). Analysis of IRBP demonstrated presence of the specific genotype in most of E. alaicus specimens, but also revealed the haplotype, typical for E. tancrei, in some Alay mole voles. The results may be explained as persistence of ancestral gene polymorphism in E. alaicus or limited interspecific hybridization with E. tancrei. Several chromosomal forms were revealed in E. alaicus in the Alay Valley. We propose that ‘mosaic’ genetic polymorphism might appear in E. alaicus due to fragmentation of their habitats in highlands of the Alay Valley, Tien Shan, and Pamir-Alay as well as due to hybridization with E. tancrei or persistence of ancestral polymorphisms.
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18
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Phylogeography and evolutionary history of the Panamic Clingfish Gobiesox adustus in the Tropical Eastern Pacific. Mol Phylogenet Evol 2022; 173:107496. [PMID: 35569809 DOI: 10.1016/j.ympev.2022.107496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 02/26/2022] [Accepted: 04/18/2022] [Indexed: 11/20/2022]
Abstract
The Panamic Clingfish Gobiesox adustus is widely distributed in the Tropical Eastern Pacific (TEP), from the central Gulf of California, Mexico to Ecuador, including the oceanic Revillagigedo Archipelago, and Isla del Coco. This cryptobenthic species is restricted to very shallow rocky-reef habitats. Here, we used one mitochondrial and three nuclear DNA markers from 155 individuals collected across the distribution range of the species in order to evaluate if geographically structured populations exist and to elucidate its evolutionary history. Phylogenetic analyses recovered a monophyletic group, with four well-supported, allopatric subgroups. Each subgroup corresponded to one of the following well-known biogeographic regions/provinces: 1) the Revillagigedo Archipelago, 2) the Cortez + Mexican provinces (Mexico), 3) the Panamic province (from El Salvador to Ecuador), and 4) Isla del Coco. A molecular-clock analysis showed a mean date for the divergence between clade I (the Revillagigedos and Cortez + Mexican provinces) and clade II (Panamic province and Isla del Coco) in the Pliocene, at ca. 5.33 Mya. Within clade I, the segregation between the Revillagigedos and Cortez + Mexican province populations was dated at ca. 1.18 Mya, during the Pleistocene. Within clade II, the segregation between samples of Isla del Coco and the Panamic province samples was dated at ca. 0.77 Mya, during the Pleistocene. The species tree, Bayesian species delimitation tests (BPP and STACEY), the ΦST, AMOVA, and the substantial genetic distances that exist between those four subgroups, indicate that they are independent evolutionary units. These cladogenetic events seem to be related to habitat discontinuities, and oceanographic and geological processes that produce barriers to gene flow for G. adustus, effects of which are enhanced by the intrinsic ecological characteristics of this species.
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19
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Marsh CJ, Sica YV, Burgin CJ, Dorman WA, Anderson RC, del Toro Mijares I, Vigneron JG, Barve V, Dombrowik VL, Duong M, Guralnick R, Hart JA, Maypole JK, McCall K, Ranipeta A, Schuerkmann A, Torselli MA, Lacher T, Mittermeier RA, Rylands AB, Sechrest W, Wilson DE, Abba AM, Aguirre LF, Arroyo‐Cabrales J, Astúa D, Baker AM, Braulik G, Braun JK, Brito J, Busher PE, Burneo SF, Camacho MA, Cavallini P, de Almeida Chiquito E, Cook JA, Cserkész T, Csorba G, Cuéllar Soto E, da Cunha Tavares V, Davenport TRB, Deméré T, Denys C, Dickman CR, Eldridge MDB, Fernandez‐Duque E, Francis CM, Frankham G, Franklin WL, Freitas T, Friend JA, Gadsby EL, Garbino GST, Gaubert P, Giannini N, Giarla T, Gilchrist JS, Gongora J, Goodman SM, Gursky‐Doyen S, Hackländer K, Hafner MS, Hawkins M, Helgen KM, Heritage S, Hinckley A, Hintsche S, Holden M, Holekamp KE, Honeycutt RL, Huffman BA, Humle T, Hutterer R, Ibáñez Ulargui C, Jackson SM, Janecka J, Janecka M, Jenkins P, Juškaitis R, Juste J, Kays R, Kilpatrick CW, Kingston T, Koprowski JL, Kryštufek B, Lavery T, Lee TE, Leite YLR, Novaes RLM, Lim BK, Lissovsky A, López‐Antoñanzas R, López‐Baucells A, MacLeod CD, Maisels FG, Mares MA, Marsh H, Mattioli S, Meijaard E, Monadjem A, Morton FB, Musser G, Nadler T, Norris RW, Ojeda A, Ordóñez‐Garza N, Pardiñas UFJ, Patterson BD, Pavan A, Pennay M, Pereira C, Prado J, Queiroz HL, Richardson M, Riley EP, Rossiter SJ, Rubenstein DI, Ruelas D, Salazar‐Bravo J, Schai‐Braun S, Schank CJ, Schwitzer C, Sheeran LK, Shekelle M, Shenbrot G, Soisook P, Solari S, Southgate R, Superina M, Taber AB, Talebi M, Taylor P, Vu Dinh T, Ting N, Tirira DG, Tsang S, Turvey ST, Valdez R, Van Cakenberghe V, Veron G, Wallis J, Wells R, Whittaker D, Williamson EA, Wittemyer G, Woinarski J, Zinner D, Upham NS, Jetz W. Expert range maps of global mammal distributions harmonised to three taxonomic authorities. JOURNAL OF BIOGEOGRAPHY 2022; 49:979-992. [PMID: 35506011 PMCID: PMC9060555 DOI: 10.1111/jbi.14330] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 01/05/2022] [Accepted: 01/13/2022] [Indexed: 06/01/2023]
Abstract
AIM Comprehensive, global information on species' occurrences is an essential biodiversity variable and central to a range of applications in ecology, evolution, biogeography and conservation. Expert range maps often represent a species' only available distributional information and play an increasing role in conservation assessments and macroecology. We provide global range maps for the native ranges of all extant mammal species harmonised to the taxonomy of the Mammal Diversity Database (MDD) mobilised from two sources, the Handbook of the Mammals of the World (HMW) and the Illustrated Checklist of the Mammals of the World (CMW). LOCATION Global. TAXON All extant mammal species. METHODS Range maps were digitally interpreted, georeferenced, error-checked and subsequently taxonomically aligned between the HMW (6253 species), the CMW (6431 species) and the MDD taxonomies (6362 species). RESULTS Range maps can be evaluated and visualised in an online map browser at Map of Life (mol.org) and accessed for individual or batch download for non-commercial use. MAIN CONCLUSION Expert maps of species' global distributions are limited in their spatial detail and temporal specificity, but form a useful basis for broad-scale characterizations and model-based integration with other data. We provide georeferenced range maps for the native ranges of all extant mammal species as shapefiles, with species-level metadata and source information packaged together in geodatabase format. Across the three taxonomic sources our maps entail, there are 1784 taxonomic name differences compared to the maps currently available on the IUCN Red List website. The expert maps provided here are harmonised to the MDD taxonomic authority and linked to a community of online tools that will enable transparent future updates and version control.
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Affiliation(s)
- Charles J. Marsh
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenConnecticutUSA
- Center for Biodiversity and Global ChangeYale UniversityNew HavenConnecticutUSA
| | - Yanina V. Sica
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenConnecticutUSA
- Center for Biodiversity and Global ChangeYale UniversityNew HavenConnecticutUSA
| | - Connor J. Burgin
- Department of BiologyUniversity of New MexicoAlbuquerqueNew MexicoUSA
| | - Wendy A. Dorman
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenConnecticutUSA
- Center for Biodiversity and Global ChangeYale UniversityNew HavenConnecticutUSA
| | - Robert C. Anderson
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenConnecticutUSA
- Center for Biodiversity and Global ChangeYale UniversityNew HavenConnecticutUSA
| | - Isabel del Toro Mijares
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenConnecticutUSA
- Center for Biodiversity and Global ChangeYale UniversityNew HavenConnecticutUSA
| | - Jessica G. Vigneron
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenConnecticutUSA
- Center for Biodiversity and Global ChangeYale UniversityNew HavenConnecticutUSA
| | - Vijay Barve
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFloridaUSA
| | - Victoria L. Dombrowik
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenConnecticutUSA
- Center for Biodiversity and Global ChangeYale UniversityNew HavenConnecticutUSA
| | - Michelle Duong
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenConnecticutUSA
- Center for Biodiversity and Global ChangeYale UniversityNew HavenConnecticutUSA
| | - Robert Guralnick
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFloridaUSA
| | - Julie A. Hart
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenConnecticutUSA
- Center for Biodiversity and Global ChangeYale UniversityNew HavenConnecticutUSA
- New York Natural Heritage ProgramState University of New York College of Environmental Science and ForestryAlbanyNew YorkUSA
| | - J. Krish Maypole
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenConnecticutUSA
- Center for Biodiversity and Global ChangeYale UniversityNew HavenConnecticutUSA
| | - Kira McCall
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenConnecticutUSA
- Center for Biodiversity and Global ChangeYale UniversityNew HavenConnecticutUSA
| | - Ajay Ranipeta
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenConnecticutUSA
- Center for Biodiversity and Global ChangeYale UniversityNew HavenConnecticutUSA
| | - Anna Schuerkmann
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenConnecticutUSA
- Center for Biodiversity and Global ChangeYale UniversityNew HavenConnecticutUSA
| | - Michael A. Torselli
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenConnecticutUSA
- Center for Biodiversity and Global ChangeYale UniversityNew HavenConnecticutUSA
| | - Thomas Lacher
- Department of Ecology and Conservation BiologyTexas A&M UniversityCollege StationTexasUSA
- Re:wildAustinTexasUSA
| | | | | | | | - Don E. Wilson
- National Museum of Natural HistorySmithsonian InstitutionWashingtonDistrict of ColumbiaUSA
| | - Agustín M. Abba
- Centro de Estudios Parasitológicos y de Vectores (CEPAVE‐UNLP‐CONICET)La Plata, Buenos AiresArgentina
| | - Luis F. Aguirre
- Centro de Biodiversidad y GenéticaUniversidad Mayor de San SimónCochabambaBolivia
| | | | - Diego Astúa
- Departamento de ZoologiaUniversidade Federal de PernambucoRecifePernambucoBrazil
| | - Andrew M. Baker
- School of Biology and Environmental Science, Faculty of ScienceQueensland University of TechnologyBrisbaneQueenslandAustralia
- Biodiversity and Geosciences ProgramQueensland MuseumBrisbaneQueenslandAustralia
| | - Gill Braulik
- School of BiologyUniversity of St. AndrewsSt. Andrews, FifeUK
| | | | - Jorge Brito
- Instituto Nacional de Biodiversidad (INABIO)QuitoEcuador
| | - Peter E. Busher
- College of General StudiesBoston UniversityBostonMassachusettsUSA
| | - Santiago F. Burneo
- Sección Mastozoología, Museo de Zoología, Facultad de Ciencias Exactas y NaturalesPontificia Universidad Católica del EcuadorQuitoEcuador
| | - M. Alejandra Camacho
- Sección Mastozoología, Museo de Zoología, Facultad de Ciencias Exactas y NaturalesPontificia Universidad Católica del EcuadorQuitoEcuador
| | | | | | - Joseph A. Cook
- Museum of Southwestern Biology and Department of BiologyUniversity of New MexicoAlbuquerqueNew MexicoUSA
| | - Tamás Cserkész
- Department of ZoologyHungarian Natural History MuseumBudapestHungary
| | - Gábor Csorba
- Department of ZoologyHungarian Natural History MuseumBudapestHungary
| | | | - Valeria da Cunha Tavares
- Vale Technological InstituteBelémParáBrazil
- Laboratório de Mamíferos, Departamento de Sistemática e Ecologia, CCEN/DSEUniversidade Federal da ParaíbaJoão PessoaPBBrazil
| | - Tim R. B. Davenport
- Species Conservation & Science (Africa)Wildlife Conservation Society (WCS)ArushaTanzania
| | | | - Christiane Denys
- Institut de Systématique, Evolution, Biodiversité (ISYEB)Muséum national d'Histoire naturelle (CNRS)ParisFrance
| | - Christopher R. Dickman
- Desert Ecology Research Group, School of Life and Environmental SciencesThe University of SydneySydneyNew South WalesAustralia
| | - Mark D. B. Eldridge
- Australian Museum Research InstituteAustralian MuseumSydneyNew South WalesAustralia
| | - Eduardo Fernandez‐Duque
- Department of Anthropology and School of the EnvironmentYale UniversityNew HavenConnecticutUSA
| | - Charles M. Francis
- Canadian Wildlife ServiceEnvironment and Climate Change CanadaOttawaOntarioCanada
| | - Greta Frankham
- Australian Museum Research InstituteAustralian MuseumSydneyNew South WalesAustralia
| | - William L. Franklin
- Deparment of Natural Resource Ecology and EnvironmentIowa State UniversityAmesIowaUSA
| | - Thales Freitas
- Departamento de GenéticaUniversidade Federal do Rio Grande do SulPorto AlegreRio Grande do SulBrazil
| | - J. Anthony Friend
- Department of BiodiversityConservation and AttractionsAlbanyWestern AustraliaAustralia
| | | | | | - Philippe Gaubert
- Laboratoire Évolution & Diversité BiologiqueUniversité Toulouse III Paul SabatierToulouseFrance
| | - Norberto Giannini
- Unidad Ejecutora LilloCONICET ‐ Fundación Miguel LilloSan Miguel de Tucumán, TucumánArgentina
| | - Thomas Giarla
- Department of BiologySiena CollegeLoudonvilleNew YorkUSA
| | | | - Jaime Gongora
- Sydney School of Veterinary Science, Faculty of ScienceThe University of SydneySydneyNew South WalesAustralia
| | - Steven M. Goodman
- Negaunee Integrative Research Center, Field Museum of Natural HistoryChicagoIllinoisUSA
| | | | - Klaus Hackländer
- Institute of Wildlife Biology and Game ManagementUniversity of Natural Resources and Life SciencesWienAustria
| | - Mark S. Hafner
- Museum of Natural ScienceLouisiana State UniversityBaton RougeLouisianaUSA
| | - Melissa Hawkins
- National Museum of Natural HistorySmithsonian InstitutionWashingtonDistrict of ColumbiaUSA
| | - Kristofer M. Helgen
- Australian Museum Research InstituteAustralian MuseumSydneyNew South WalesAustralia
| | - Steven Heritage
- Duke Lemur Center, Museum of Natural HistoryDuke UniversityDurhamNorth CarolinaUSA
| | | | | | - Mary Holden
- Department of MammalogyAmerican Museum of Natural HistoryNew YorkNew YorkUSA
| | - Kay E. Holekamp
- Department of Integrative BiologyMichigan State UniversityEast LansingMichiganUSA
| | | | | | - Tatyana Humle
- Durrell Institute of Conservation and EcologySchool of Anthropology and Conservation, University of KentCanterburyUK
| | | | | | | | - Jan Janecka
- Department of Biological SciencesDuquesne UniversityPittsburghPennsylvaniaUSA
| | - Mary Janecka
- Department of Biological SciencesUniversity of PittsburghPittsburghPennsylvaniaUSA
| | - Paula Jenkins
- Mammal Group, Vertebrates DivisionDepartment of Life Sciences, The Natural History MuseumLondonUK
| | | | | | - Roland Kays
- North Carolina Museum of Natural SciencesRaleighNorth CarolinaUSA
| | | | - Tigga Kingston
- Department of Biological SciencesTexas Tech UniversityLubbockTexasUSA
| | | | | | - Tyrone Lavery
- Fenner School of Environment and SocietyThe Australian National UniversityActonAustralian Capital TerritoryAustralia
| | - Thomas E. Lee
- Department of BiologyAbilene Christian UniversityAbileneTexasUSA
| | - Yuri L. R. Leite
- Departamento de Ciências BiológicasUniversidade Federal do Espírito SantoVitóriaEspiríto SantoBrazil
| | | | - Burton K. Lim
- Department of Natural HistoryRoyal Ontario MuseumTorontoOntarioCanada
| | | | - Raquel López‐Antoñanzas
- Institut des Sciences de l'Évolution de Montpellier (ISE‐M, UMR 5554, UM/CNRS/IRD/EPHE)MontpellierFrance
| | | | | | - Fiona G. Maisels
- Wildlife Conservation SocietyGlobal Conservation ProgramNew YorkNew YorkUSA
- Faculty of Natural SciencesUniversity of StirlingStirlingUK
| | | | - Helene Marsh
- Division of Tropical Environments and SocietiesCentre for Tropical Water and Aquatic Ecosystem Research, James Cook UniversityTownsvilleQueenslandAustralia
| | - Stefano Mattioli
- Research Unit of Behavioural Ecology, Ethology and Wildlife Management, Department of Life SciencesUniversity of SienaSienaItaly
| | - Erik Meijaard
- Borneo FuturesBandar Seri BegawanBABrunei Darussalam
| | - Ara Monadjem
- Department of Biological SciencesUniversity of EswatiniKwaluseniEswatini
- Department of Zoology & Entomology, Mammal Research InstituteUniversity of PretoriaPretoriaSouth Africa
| | | | - Grace Musser
- Jackson School of GeosciencesUniversity of Texas at AustinAustinTexasUSA
| | - Tilo Nadler
- Cuc Phuong CommuneNho Quan DistrictNinh BInh, ProvinceVietnam
| | - Ryan W. Norris
- Evolution, Ecology and Organismal BiologyThe Ohio State UniversityLimaOhioUSA
| | - Agustina Ojeda
- Instituto Argentino de Zonas Áridas (IADIZA)‐CCT Mendoza‐CONICETMendozaArgentina
| | | | | | - Bruce D. Patterson
- Negaunee Integrative Research Center, Field Museum of Natural HistoryChicagoIllinoisUSA
| | - Ana Pavan
- Universidade de São PauloSão PauloBrazil
| | - Michael Pennay
- NSW National Parks and Wildlife ServiceQueanbeyanNew South WalesAustralia
| | | | | | - Helder L. Queiroz
- Instituto de Desenvolvimento Sustentável Mamirauá – IDSMTeféAmazonasBrazil
| | | | - Erin P. Riley
- Department of AnthropologySan Diego State UniversitySan DiegoCaliforniaUSA
| | - Stephen J. Rossiter
- School of Biological and Chemical SciencesQueen Mary University of LondonLondonUK
| | - Daniel I. Rubenstein
- Department of Ecology and Evolutionary BiologyPrinceton UniversityPrincetonNew JerseyUSA
| | - Dennisse Ruelas
- Museo de Historia NaturalUniversidad Nacional Mayor de San Marcos, LimaLimaPeru
- Institut des Sciences de l'Evolution (ISEM, UMR 5554 CNRS‐IRD‐UM)Université de MontpellierMontpellier Cedex 5France
| | | | - Stéphanie Schai‐Braun
- Institute of Wildlife Biology and Game ManagementUniversity of Natural Resources and Life SciencesViennaAustria
| | - Cody J. Schank
- Re:wildAustinTexasUSA
- Department of Geography and the EnvironmentThe University of Texas at AustinAustinTexasUSA
| | | | - Lori K. Sheeran
- Department of Anthropology and Museum StudiesCentral Washington UniversityEllensburgWAUSA
| | - Myron Shekelle
- Department of AnthropologyWestern Washington UniversityBellinghamWAUSA
| | - Georgy Shenbrot
- Mitrani Department of Desert EcologyJacob Blaustein Institutes for Desert ResearchBen‐Gurion University of the NegevMidreshet Ben‐GurionIsrael
| | - Pipat Soisook
- Princess Maha Chakri Sirindhorn Natural History MuseumPrince of Songkhla UniversityHatyai, SongkhlaThailand
| | - Sergio Solari
- Instituto de BiologíaUniversidad de AntioquiaMedellínColombia
| | | | - Mariella Superina
- IMBECU, CCT CONICET Mendoza – UNCuyoParque Gral. San MartínMendozaArgentina
| | - Andrew B. Taber
- Forestry DivisionFood and Agriculture Organization of the United NationsRomeItaly
| | - Maurício Talebi
- Laboratório de Ecologia e Conservação da NaturezaDeptartamento de Ciências AmbientaisUniversidade Federal de São Paulo (UNIFESP) ‐ Campus Diadema, DiademaSão PauloBrazil
| | | | - Thong Vu Dinh
- Institute of Ecology and Biological ResourcesVietnam Academy of Science and TechnologyHanoiVietnam
| | - Nelson Ting
- Department of AnthropologyUniversity of OregonEugeneOregonUSA
| | | | - Susan Tsang
- Department of MammalogyAmerican Museum of Natural HistoryNew YorkNew YorkUSA
| | | | - Raul Valdez
- Department of Fish, Wildlife, and Conservation EcologyNew Mexico State UniversityLas CrucesNew MexicoUSA
| | - Victor Van Cakenberghe
- Laboratory for Functional Morphology, Biology DepartmentUniversity of Antwerp, Campus Drie EikenAntwerpen (Wilrijk)Belgium
| | - Geraldine Veron
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRSSorbonne Université, EPHE, Université des AntillesParisFrance
| | | | - Rod Wells
- Biological Sciences, College of Science and EngineeringFlinders UniversityAdelaideSouth AustraliaAustralia
| | - Danielle Whittaker
- BEACON Center for the Study of Evolution in ActionMichigan State UniversityEast LansingMichiganUSA
| | | | - George Wittemyer
- Department of Fish, Wildlife and Conservation BiologyColorado State UniversityFort CollinsColoradoUSA
| | - John Woinarski
- Research Institute for the Environment and LivelihoodsCharles Darwin UniversityCasuarinaNorthern TerritoryAustralia
| | - Dietmar Zinner
- German Primate Center (DPZ)Leibniz Institute for Primate ResearchGöttingenGermany
| | - Nathan S. Upham
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenConnecticutUSA
- Center for Biodiversity and Global ChangeYale UniversityNew HavenConnecticutUSA
- School of Life SciencesArizona State UniversityTempeArizonaUSA
| | - Walter Jetz
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenConnecticutUSA
- Center for Biodiversity and Global ChangeYale UniversityNew HavenConnecticutUSA
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20
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Cryopreservation of Giraffe Epidydimal Spermatozoa Using Different Extenders and Cryoprotectants. Animals (Basel) 2022; 12:ani12070857. [PMID: 35405846 PMCID: PMC8997136 DOI: 10.3390/ani12070857] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/23/2022] [Accepted: 03/25/2022] [Indexed: 01/04/2023] Open
Abstract
Simple Summary Giraffe numbers have been plummeting over the last 30 years by 30–40%. As such, efforts to manage in situ and ex situ populations are increasing. Assisted reproduction techniques such as sperm cryopreservation can help preserve the genetic diversity of giraffe subspecies or enhance genetic exchange between populations. However, to date, the post-thaw motility of recovered sperm has been variable. In this study, spermatozoa were collected from the epididymides of seven giraffes to investigate whether an alternative cryoprotectant could improve sperm motility following conventional cryopreservation. For this, we compared the motility and viability of sperm prior to and after freezing in three different extenders: a commercial equine extender (BotuCrio®; Nidacon, Moedal, Schweden), a commercial bovine extender (Steridyl, Minitube, Tiefenbach, Germany), and an in-house “made” bovine egg yolk extender (TEY). Each was further supplemented with either glycerol or a mix of glycerol and methylformamide cryoprotectants. The results show that spermatozoa frozen with a mix of two cryoprotectants had significantly higher post-thaw motility compared to glycerol alone. Specifically, spermatozoa frozen in TEY and a mix of cryoprotectants achieved post-thaw sperm motility of 57 ± 3%. These results might serve as a blueprint for an improved protocol for giraffe sperm cryopreservation. Abstract Giraffe numbers have plummeted over the last 30 years by 30–40%. Thus, their conservation status has been raised from least concern to vulnerable. Efforts to manage in situ and ex situ populations are increasing. Assisted reproduction techniques (ART) such as sperm cryopreservation could help preserve the genetic diversity of giraffe subspecies and, when used for artificial inseminations, enhance genetic exchange between isolated populations. However, to date, the post-thaw motility of recovered sperm has been low and inconsistent. In this study, epididymal sperm collected from the testes of giraffes (n = 7) was frozen in three different extenders, namely, BotuCrio, Steridyl, and test egg yolk (TEY), each supplemented with one of two different cryoprotectants (5% glycerol or a mix of 1% glycerol and 4% methylformamide) and frozen over liquid nitrogen vapor. Across all three extenders, sperm showed significantly better post-thaw results when frozen with a mix of glycerol and methylformamide compared with glycerol alone. Sperm frozen with TEY and a mix of glycerol and methylformamide achieved superior post-thaw total and progressive sperm motility of 57 ± 3% and 45 ± 3%, respectively. These results show the benefit of using alternative cryoprotectants for freezing giraffe spermatozoa and could aid in the application of ARTs for giraffe subspecies or the closely related endangered Okapi.
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21
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Conservation Genomics of Two Threatened Subspecies of Northern Giraffe: The West African and the Kordofan Giraffe. Genes (Basel) 2022; 13:genes13020221. [PMID: 35205265 PMCID: PMC8872558 DOI: 10.3390/genes13020221] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/22/2022] [Accepted: 01/23/2022] [Indexed: 11/17/2022] Open
Abstract
Three of the four species of giraffe are threatened, particularly the northern giraffe (Giraffa camelopardalis), which collectively have the smallest known wild population estimates. Among the three subspecies of the northern giraffe, the West African giraffe (Giraffa camelopardalis peralta) had declined to 49 individuals by 1996 and only recovered due to conservation efforts undertaken in the past 25 years, while the Kordofan giraffe (Giraffa camelopardalis antiquorum) remains at <2300 individuals distributed in small, isolated populations over a large geographical range in Central Africa. These combined factors could lead to genetically depauperated populations. We analyzed 119 mitochondrial sequences and 26 whole genomes of northern giraffe individuals to investigate their population structure and assess the recent demographic history and current genomic diversity of West African and Kordofan giraffe. Phylogenetic and population structure analyses separate the three subspecies of northern giraffe and suggest genetic differentiation between populations from eastern and western areas of the Kordofan giraffe’s range. Both West African and Kordofan giraffe show a gradual decline in effective population size over the last 10 ka and have moderate genome-wide heterozygosity compared to other giraffe species. Recent inbreeding levels are higher in the West African giraffe and in Kordofan giraffe from Garamba National Park, Democratic Republic of Congo. Although numbers for both West African and some populations of Kordofan giraffe have increased in recent years, the threat of habitat loss, climate change impacts, and illegal hunting persists. Thus, future conservation actions should consider close genetic monitoring of populations to detect and, where practical, counteract negative trends that might develop.
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22
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Torres-Hernández E, Betancourt-Resendes I, Angulo A, Robertson DR, Barraza E, Espinoza E, Díaz-Jaimes P, Domínguez-Domínguez O. A multi-locus approach to elucidating the evolutionary history of the clingfish Tomicodon petersii (Gobiesocidae) in the Tropical Eastern Pacific. Mol Phylogenet Evol 2021; 166:107316. [PMID: 34537324 DOI: 10.1016/j.ympev.2021.107316] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 09/07/2021] [Accepted: 09/14/2021] [Indexed: 10/20/2022]
Abstract
Marine species that are widely distributed in the Tropical Eastern Pacific (TEP) has served as a model for studying biogeographic patterns resulting from the effects of intraregional habitat discontinuities and oceanographic processes on the diversification and evolution of cryptobenthic reef fishes. Tomicodon petersii, a clingfish (Gobiesocidae) endemic to the TEP, is found on very shallow rocky reefs from central Mexico to northern Peru, and in the Cocos and Galapagos islands. We evaluated the effect of likely biogeographic barriers in different parts of the TEP on the diversification process of this species. We used one mitochondrial and three nuclear DNA markers from 112 individuals collected across the distribution range of T. petersii. Our phylogenetic results showed the samples constituted a monophyletic group, with three well-supported, allopatric subgroups: in the Mexican province, the Panamic province (from El Salvador to Ecuador), and the Galapagos Islands. The split between the Mexican and more southerly clades was estimated to occur at the end of the Miocene ca. 5.74 Mya, and the subsequent cladogenetic event separating the Galapagos population from the Panamic population at the junction of the Pliocene and Pleistocene, ca. 2.85 Mya. The species tree, Bayesian species delimitation tests (BPP), STACEY, and substantial genetic distances separating these three populations indicate that these three independent evolutionary units likely include two unnamed species. The cladogenetic events that promoted the formation of those genetically differentiated groups are consistent with disruptive effects on gene flow of habitat discontinuities and oceanographic processes along the mainland shoreline in the TEP and of ocean-island isolation, in conjunction with the species intrinsic life-history characteristics.
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Affiliation(s)
- Eloísa Torres-Hernández
- Posgrado en Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Av. Ciudad Universitaria 3000, C.P. 04510, Coyoacán, Ciudad de México, Mexico; Instituto Nacional de Biodiversidad (INABIO), Colección de Peces Calle Rumipamba 341, Av. De los Shyris, Parque "La Carolina", Quito, Ecuador.
| | - Isai Betancourt-Resendes
- CONACYT-Laboratorio de Zoología, Facultad de Ciencias Naturales, Universidad Autónoma de Querétaro, Av. De las Ciencias s/n, Juriquilla, C.P 76230, Delegación Santa Rosa Jáuregui, Santiago de Querétaro, Mexico.
| | - Arturo Angulo
- Museo de Zoología/ Centro de Investigación en Biodiversidad y Ecología Tropical (CIBET) y Centro de Investigación en Ciencias del Mar y Limnología (CIMAR), Universidad de Costa Rica, San Pedro de Montes de Oca, 11501-2060 San José, Costa Rica.
| | - D Ross Robertson
- Naos Marine Laboratory, Smithsonian Tropical Research Institute, Balboa, Panama.
| | - Enrique Barraza
- Universidad Francisco Gavidia, Instituto de Ciencia, Tecnología e Inovación, Segundo Nivel, Calle El Progreso N°2748, San Salvador, El Salvador.
| | - Eduardo Espinoza
- Dirección del Parque Nacional Galápagos, Puerto Ayora, Islas Galápagos, Ecuador.
| | - Píndaro Díaz-Jaimes
- Unidad de Ecología y Biodiversidad Acuática, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Av. Ciudad Universitaria 3000, C.P. 04510, Coyoacán, Ciudad de México, Mexico.
| | - Omar Domínguez-Domínguez
- Instituto Nacional de Biodiversidad (INABIO), Colección de Peces Calle Rumipamba 341, Av. De los Shyris, Parque "La Carolina", Quito, Ecuador; Laboratorio de Biología Acuática, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Edificio "R" Planta Baja, Ciudad Universitaria, Morelia, Michoacán 58030, Mexico.
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Abstract
Ecotourism can fuel an important source of financial income for African countries and can therefore help biodiversity policies in the continent. Translocations can be a powerful tool to spread economic benefits among countries and communities; yet, to be positive for biodiversity conservation, they require a basic knowledge of conservation units through appropriate taxonomic research. This is not always the case, as taxonomy was considered an outdated discipline for almost a century, and some plurality in taxonomic approaches is incorrectly considered as a disadvantage for conservation work. As an example, diversity of the genus Giraffa and its recent taxonomic history illustrate the importance of such knowledge for a sound conservation policy that includes translocations. We argue that a fine-grained conservation perspective that prioritizes all remaining populations along the Nile Basin is needed. Translocations are important tools for giraffe diversity conservation, but more discussion is needed, especially for moving new giraffes to regions where the autochthonous taxa/populations are no longer existent. As the current discussion about the giraffe taxonomy is too focused on the number of giraffe species, we argue that the plurality of taxonomic and conservation approaches might be beneficial, i.e., for defining the number of units requiring separate management using a (majority) consensus across different concepts (e.g., MU—management unit, ESU—evolutionary significant unit, and ECU—elemental conservation unit). The taxonomically sensitive translocation policy/strategy would be important for the preservation of current diversity, while also supporting the ecological restoration of some regions within rewilding. A summary table of the main translocation operations of African mammals that have underlying problems is included. Therefore, we call for increased attention toward the taxonomy of African mammals not only as the basis for sound conservation but also as a further opportunity to enlarge the geographic scope of ecotourism in Africa.
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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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25
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Curaudeau M, Rozzi R, Hassanin A. The genome of the lowland anoa (Bubalus depressicornis) illuminates the origin of river and swamp buffalo. Mol Phylogenet Evol 2021; 161:107170. [PMID: 33798669 DOI: 10.1016/j.ympev.2021.107170] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 03/12/2021] [Accepted: 03/25/2021] [Indexed: 10/21/2022]
Abstract
Two types of domestic water buffalo are currently recognized: the river buffalo from the Indian subcontinent and Mediterranean countries and the swamp buffalo from China and Southeast Asia. To test the hypothesis of two separate species of water buffalo, we sequenced the genome of the lowland anoa, Bubalus depressicornis, which is a dwarf wild buffalo endemic to Sulawesi, and two genomes of swamp buffalo, and made comparisons with 12 additional genomes. Three genomic data sets were constructed to infer phylogenetic relationships: the mitochondrial genome (15,468 bp; maternal transmission), two concatenated Y-chromosomal genes, AMELY and DDX3Y (20,036 bp; paternal transmission), and a selection of 30 nuclear genes representing all cattle chromosomes (364,887 bp; biparental transmission). The comparisons between our 30 nuclear gene sequences obtained by read mapping and those directly extracted from Bos taurus and Bubalus bubalis genome assemblies show that the mapping approach revealed higher levels of heterozygosity at both nucleotide sites and indels (insertions and deletions) (0.09-0.15%), as well as several sequence errors (0.07%). Our phylogenetic and molecular dating analyses provide strong evidence that the lowland anoa, river buffalo, and swamp buffalo are three distinct taxa which separated rapidly from each other during the Pleistocene epoch. We therefore conclude that two species of domestic water buffalo should be distinguished: Bubalus bubalis for the river buffalo and Bubalus kerabau for the swamp buffalo. The new classification can have deep implications for understanding the evolution and selection of domesticated forms and for the conservation and management of wild buffalo populations in South and Southeast Asia.
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Affiliation(s)
- Manon Curaudeau
- Institut Systématique Evolution Biodiversité (ISYEB), Sorbonne Université, MNHN, CNRS, EPHE, UA, 57 rue Cuvier, CP 51, 75005 Paris, France
| | - Roberto Rozzi
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Synthesis Centre for Biodiversity Sciences (sDiv), Puschstr. 4, D-04103 Leipzig, Germany; Museum für Naturkunde, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, 10115 Berlin, Germany
| | - Alexandre Hassanin
- Institut Systématique Evolution Biodiversité (ISYEB), Sorbonne Université, MNHN, CNRS, EPHE, UA, 57 rue Cuvier, CP 51, 75005 Paris, France.
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26
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Hassanin A, Veron G, Ropiquet A, Jansen van Vuuren B, Lécu A, Goodman SM, Haider J, Nguyen TT. Evolutionary history of Carnivora (Mammalia, Laurasiatheria) inferred from mitochondrial genomes. PLoS One 2021; 16:e0240770. [PMID: 33591975 PMCID: PMC7886153 DOI: 10.1371/journal.pone.0240770] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 01/06/2021] [Indexed: 11/18/2022] Open
Abstract
The order Carnivora, which currently includes 296 species classified into 16 families, is distributed across all continents. The phylogeny and the timing of diversification of members of the order are still a matter of debate. Here, complete mitochondrial genomes were analysed to reconstruct the phylogenetic relationships and to estimate divergence times among species of Carnivora. We assembled 51 new mitogenomes from 13 families, and aligned them with available mitogenomes by selecting only those showing more than 1% of nucleotide divergence and excluding those suspected to be of low-quality or from misidentified taxa. Our final alignment included 220 taxa representing 2,442 mitogenomes. Our analyses led to a robust resolution of suprafamilial and intrafamilial relationships. We identified 21 fossil calibration points to estimate a molecular timescale for carnivorans. According to our divergence time estimates, crown carnivorans appeared during or just after the Early Eocene Climatic Optimum; all major groups of Caniformia (Cynoidea/Arctoidea; Ursidae; Musteloidea/Pinnipedia) diverged from each other during the Eocene, while all major groups of Feliformia (Nandiniidae; Feloidea; Viverroidea) diversified more recently during the Oligocene, with a basal divergence of Nandinia at the Eocene/Oligocene transition; intrafamilial divergences occurred during the Miocene, except for the Procyonidae, as Potos separated from other genera during the Oligocene.
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Affiliation(s)
- Alexandre Hassanin
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Sorbonne Université, MNHN, CNRS, EPHE, UA, Paris, France
| | - Géraldine Veron
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Sorbonne Université, MNHN, CNRS, EPHE, UA, Paris, France
| | - Anne Ropiquet
- Faculty of Science and Technology, Department of Natural Sciences, Middlesex University, London, United Kingdom
| | - Bettine Jansen van Vuuren
- Department of Zoology, Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Johannesburg, South Africa
| | - Alexis Lécu
- Parc zoologique de Paris, Muséum national d’Histoire naturelle, Paris, France
| | - Steven M. Goodman
- Field Museum of Natural History, Chicago, IL, United States of America
| | - Jibran Haider
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Sorbonne Université, MNHN, CNRS, EPHE, UA, Paris, France
- Department of Wildlife Management, Pir Mehr Ali Shah, Arid Agriculture University Rawalpindi, Rawalpindi, Pakistan
- Forest Parks & Wildlife Department Gilgit-Baltistan, Skardu, Pakistan
| | - Trung Thanh Nguyen
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Sorbonne Université, MNHN, CNRS, EPHE, UA, Paris, France
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27
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Spöri Y, Flot J. HaplowebMaker and CoMa: Two web tools to delimit species using haplowebs and conspecificity matrices. Methods Ecol Evol 2020. [DOI: 10.1111/2041-210x.13454] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yann Spöri
- Evolutionary Biology & Ecology Université libre de Bruxelles (ULB) Brussels Belgium
- Interuniversity Institute of Bioinformatics in Brussels – (IB)2 Brussels Belgium
| | - Jean‐François Flot
- Evolutionary Biology & Ecology Université libre de Bruxelles (ULB) Brussels Belgium
- Interuniversity Institute of Bioinformatics in Brussels – (IB)2 Brussels Belgium
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28
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Affiliation(s)
- Fred B. Bercovitch
- Save The Giraffes San Antonio TX USA
- Wildlife Research Center Kyoto University Kyoto Japan
- Department of Animal, Wildlife, and Grassland Sciences University of the Free State Bloemfontein South Africa
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Vitali F, Kariuki EK, Mijele D, Kaitho T, Faustini M, Preziosi R, Gakuya F, Ravasio G. Etorphine-Azaperone Immobilisation for Translocation of Free-Ranging Masai Giraffes ( Giraffa Camelopardalis Tippelskirchi): A Pilot Study. Animals (Basel) 2020; 10:ani10020322. [PMID: 32085568 PMCID: PMC7070639 DOI: 10.3390/ani10020322] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 02/12/2020] [Accepted: 02/14/2020] [Indexed: 12/18/2022] Open
Abstract
Simple Summary Due to their peculiar anatomy and sensitivity to drugs, giraffes are among the most challenging mammals to immobilise. Masai giraffes have recently been listed as endangered. Hence, their conservation needs actions that require veterinary capture such as translocations. In this study, we evaluated a new protocol of immobilisation for translocation of free-ranging Masai giraffes. The hypothesis is that, by combining a potent opioid with a tranquiliser, it is possible to mitigate the capture stress, which is a major cause of disastrous homeostatic consequences, including capture myopathy and death. The combination produced, in all individuals, smooth and quick inductions and reliable immobilisations. Although hypoxaemia in a few individuals and acidosis were seen, the overall cardiorespiratory function was adequate. Whereas the initial stress to the capture was limited in the individuals, likely due to tourism-related habituation, the opioid-related excitement and resulting increased exertion was responsible for worse immobilisation and physiological derangement. A low dose of an antagonist was used and evaluated and, in the two-week boma follow-up, it proved to be efficient in providing safe recoveries and transport. At the investigated doses, the combination provided partially reversed immobilisation that allowed uneventful translocation in free-ranging Masai giraffes. Abstract Etorphine-azaperone immobilisation was evaluated for translocation of Masai giraffes. Nine giraffes were darted with 0.012 ± 0.001 mg/kg etorphine and 0.07 ± 0.01 mg/kg azaperone. Once ataxic, giraffes were roped for recumbency and restrained manually. Naltrexone (3 mg/mg etorphine) was immediately given intravenously to reverse etorphine-related side effects. Protocol evaluation included physiological monitoring, blood-gas analyses, anaesthetic times, and quality scores (1 = excellent, 4 = poor). Sedation onset and recumbency were achieved in 2.6 ± 0.8 and 5.6 ± 1.4 min. Cardio-respiratory function (HR = 70 ± 16, RR = 32 ± 8, MAP = 132 ± 16) and temperature (37.8 ± 0.5) were stable. Arterial gas analysis showed hypoxaemia in some individuals (PaO2 = 67 ± 8 mmHg) and metabolic acidosis (pH = 7.23 ± 0.05, PaCO2 = 34 ± 4 mmHg, HCO3− = 12.9 ± 1.2 mmol/l). Minor startle response occurred, while higher induction-induced excitement correlated to longer inductions, worse restraint, and decreased HCO3−. After 19 ± 3.5 min of restraint, giraffes were allowed to stand and were loaded onto a chariot. Immobilisations were good and scored 2 (1–3). Inductions and recoveries were smooth and scored 1 (1–2). Translocations were uneventful and no complications occurred in 14-days boma follow-up.
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Affiliation(s)
- Francesca Vitali
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Via dell’Università 6, 26900 Lodi, Italy; (M.F.); (G.R.)
- Correspondence: ; Tel.: +39-348-714-6920
| | - Edward K. Kariuki
- Department of Veterinary Services, Kenya Wildlife Service, P.O. Box 40241-00100 Nairobi, Kenya; (E.K.K.); (D.M.); (T.K.); (F.G.)
| | - Domnic Mijele
- Department of Veterinary Services, Kenya Wildlife Service, P.O. Box 40241-00100 Nairobi, Kenya; (E.K.K.); (D.M.); (T.K.); (F.G.)
| | - Titus Kaitho
- Department of Veterinary Services, Kenya Wildlife Service, P.O. Box 40241-00100 Nairobi, Kenya; (E.K.K.); (D.M.); (T.K.); (F.G.)
| | - Massimo Faustini
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Via dell’Università 6, 26900 Lodi, Italy; (M.F.); (G.R.)
| | - Richard Preziosi
- Ecology and Environment Research Centre, Department of Natural Sciences, Faculty of Science and Engineering, Manchester Metropolitan University, Manchester M1 5GD, UK;
| | - Francis Gakuya
- Department of Veterinary Services, Kenya Wildlife Service, P.O. Box 40241-00100 Nairobi, Kenya; (E.K.K.); (D.M.); (T.K.); (F.G.)
| | - Giuliano Ravasio
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Via dell’Università 6, 26900 Lodi, Italy; (M.F.); (G.R.)
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