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Burroughs RW, Parham JF, Stuart BL, Smits PD, Angielczyk KD. Morphological Species Delimitation in The Western Pond Turtle ( Actinemys): Can Machine Learning Methods Aid in Cryptic Species Identification? Integr Org Biol 2024; 6:obae010. [PMID: 38689939 PMCID: PMC11058871 DOI: 10.1093/iob/obae010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/29/2024] [Indexed: 05/02/2024] Open
Abstract
As the discovery of cryptic species has increased in frequency, there has been an interest in whether geometric morphometric data can detect fine-scale patterns of variation that can be used to morphologically diagnose such species. We used a combination of geometric morphometric data and an ensemble of five supervised machine learning methods (MLMs) to investigate whether plastron shape can differentiate two putative cryptic turtle species, Actinemys marmorata and Actinemys pallida. Actinemys has been the focus of considerable research due to its biogeographic distribution and conservation status. Despite this work, reliable morphological diagnoses for its two species are still lacking. We validated our approach on two datasets, one consisting of eight morphologically disparate emydid species, the other consisting of two subspecies of Trachemys (T. scripta scripta, T. scripta elegans). The validation tests returned near-perfect classification rates, demonstrating that plastron shape is an effective means for distinguishing taxonomic groups of emydids via MLMs. In contrast, the same methods did not return high classification rates for a set of alternative phylogeographic and morphological binning schemes in Actinemys. All classification hypotheses performed poorly relative to the validation datasets and no single hypothesis was unequivocally supported for Actinemys. Two hypotheses had machine learning performance that was marginally better than our remaining hypotheses. In both cases, those hypotheses favored a two-species split between A. marmorata and A. pallida specimens, lending tentative morphological support to the hypothesis of two Actinemys species. However, the machine learning results also underscore that Actinemys as a whole has lower levels of plastral variation than other turtles within Emydidae, but the reason for this morphological conservatism is unclear.
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Affiliation(s)
- R W Burroughs
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794, USA
- Center for Inclusive Education, Stony Brook University, Stony Brook, NY 11794, USA
| | - J F Parham
- Department of Geological Sciences, California State University, Fullerton, CA 92834, USA
| | - B L Stuart
- Section of Research and Collections, NC Museum of Natural Sciences, Raleigh, NC 27601, USA
| | - P D Smits
- 952 NW 60th St., Seattle, Washington, WA 98107, USA
| | - K D Angielczyk
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, IL 60605, USA
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2
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Alexander Pyron R. Unsupervised machine learning for species delimitation, integrative taxonomy, and biodiversity conservation. Mol Phylogenet Evol 2023; 189:107939. [PMID: 37804960 DOI: 10.1016/j.ympev.2023.107939] [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: 06/12/2023] [Revised: 09/25/2023] [Accepted: 10/04/2023] [Indexed: 10/09/2023]
Abstract
Integrative taxonomy, combining data from multiple axes of biologically relevant variation, is a major goal of systematics. Ideally, such taxonomies will derive from similarly integrative species-delimitation analyses. Yet, most current methods rely solely or primarily on molecular data, with other layers often incorporated only in a post hoc qualitative or comparative manner. A major limitation is the difficulty of devising quantitative parametric models linking different datasets in a unified ecological and evolutionary framework. Machine Learning (ML) methods offer flexibility in this arena by easily learning high-dimensional associations between observations (e.g., individual specimens) across a wide array of input features (e.g., genetics, geography, environment, and phenotype) to delimit statistically meaningful clusters. Here, I implement an unsupervised method using Self-Organizing (or "Kohonen") Maps (SOMs) for such purposes. Recent extensions called "SuperSOMs" can integrate multiple layers, each of which exerts independent influence on a two-dimensional output grid via empirically estimated weights. The grid cells are then delimited into K distinct units that can be interpreted as species or other entities. I show empirical examples in salamanders (Desmognathus) and snakes (Storeria) with layers representing alleles, space, climate, and traits. Simulations reveal that the SuperSOM approach can detect K = 1, tends not to over-split, reflects contributions from all layers, and limits large layers (e.g., genetic matrices) from overwhelming other datasets, desirable properties addressing major concerns from previous studies. Finally, I suggest that these and similar methods could integrate conservation-relevant layers such as population trends and human encroachment to delimit management units from an explicitly quantitative framework grounded in the ecology and evolution of species limits and boundaries.
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Affiliation(s)
- R Alexander Pyron
- Department of Biological Sciences, The George Washington University, Washington, DC 20052 USA.
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3
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Cook CN, Redford KH, Schwartz MW. Species conservation in the era of genomic science. Bioscience 2023; 73:885-890. [PMID: 38162573 PMCID: PMC10755706 DOI: 10.1093/biosci/biad098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 10/11/2023] [Accepted: 10/20/2023] [Indexed: 01/03/2024] Open
Abstract
The exponential increase in the availability of genomic data, derived from sequencing thousands of loci or whole genomes, provides exciting new insights into the diversity of life. However, it can also challenge established species concepts and existing management regimes derived from these concepts. Genomic data can help inform decisions about how to manage genetic diversity, but policies that protect identified taxonomic entities can generate conflicting recommendations that create challenges for practitioners. We outline three dimensions of management concern that arise when facing new and potentially conflicting interpretations of genomic data: defining conservation entities, deciding how to manage diversity, and evaluating the risks and benefits of management actions. We highlight the often-underappreciated role of values in influencing management choices made by individuals, scientists, practitioners, the public, and other stakeholders. Such values influence choices through mechanisms such as the Rashomon effect, whereby management decisions are complicated by conflicting perceptions of the causes and consequences of the conservation problem. To illustrate how this might operate, we offer a hypothetical example of this effect for the interpretation of genomic data and its implications for conservation management. Such value-based decisions can be challenged by the rigidity of existing management regimes, making it difficult to achieve the necessary flexibility to match the changing biological understanding. We finish by recommending that both conservation geneticists and practitioners reflect on their respective values, responsibilities, and roles in building a more robust system of species management. This includes embracing the inclusion of stakeholders in decision-making because, as in many cases, there are not objectively defensible right or wrong decisions.
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Affiliation(s)
- Carly N Cook
- Monash University's School of Biological Sciences, Melbourne, Australia
| | - Kent H Redford
- University of New England's Department of Environmental Studies, Biddeford, Maine, United States
| | - Mark W Schwartz
- Department of Environmental Science and Policy, University of California, Davis, Davis, California, United States
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4
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Powell DM. Losing the forest for the tree? On the wisdom of subpopulation management. Zoo Biol 2023; 42:591-604. [PMID: 37218348 DOI: 10.1002/zoo.21776] [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: 07/19/2022] [Revised: 03/24/2023] [Accepted: 04/26/2023] [Indexed: 05/24/2023]
Abstract
Animal habitats are changing around the world in many ways, presenting challenges to the survival of species. Zoo animal populations are also challenged by small population sizes and limited genetic diversity. Some ex situ populations are managed as subpopulations based on presumed subspecies or geographic locality and related concerns over genetic purity or taxonomic integrity. However, these decisions can accelerate the loss of genetic diversity and increase the likelihood of population extinction. Here I challenge the wisdom of subpopulation management, pointing out significant concerns in the literature with delineation of species, subspecies, and evolutionarily significant units. I also review literature demonstrating the value of gene flow for preserving adaptive potential, the often-misunderstood role of hybridization in evolution, and the likely overstated concerns about outbreeding depression, and preservation of local adaptations. I argue that the most effective way to manage animal populations for the long term be they in human care, in the wild, or if a captive population is being managed for reintroduction, is to manage for maximum genetic diversity rather than managing subpopulations focusing on taxonomic integrity, genetic purity, or geographic locale because selection in the future, rather than the past, will determine what genotypes and phenotypes are the most fit. Several case studies are presented to challenge the wisdom of subpopulation management and stimulate thinking about the preservation of genomes rather than species, subspecies, or lineages because those units evolved in habitats that are likely very different from those habitats today and in the future.
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Affiliation(s)
- David M Powell
- Department of Reproductive & Behavioral Sciences, Saint Louis Zoo, Saint Louis, Missouri, USA
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5
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Wootton LM, Forest F, Verboom GA. Consilience Across Multiple, Independent Genomic Data Sets Reveals Species in a Complex with Limited Phenotypic Variation. Syst Biol 2023; 72:753-766. [PMID: 37098166 DOI: 10.1093/sysbio/syad024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/18/2023] [Accepted: 04/20/2023] [Indexed: 04/27/2023] Open
Abstract
Species delimitation in the genomic era has focused predominantly on the application of multiple analytical methodologies to a single massive parallel sequencing (MPS) data set, rather than leveraging the unique but complementary insights provided by different classes of MPS data. In this study, we demonstrate how the use of two independent MPS data sets, a sequence capture data set and a single-nucleotide polymorphism (SNP) data set generated via genotyping-by-sequencing, enables the resolution of species in three complexes belonging to the grass genus Ehrharta, whose strong population structure and subtle morphological variation limit the effectiveness of traditional species delimitation approaches. Sequence capture data are used to construct a comprehensive phylogenetic tree of Ehrharta and to resolve population relationships within the focal clades, while SNP data are used to detect patterns of gene pool sharing across populations, using a novel approach that visualizes multiple values of K. Given that the two genomic data sets are independent, the strong congruence in the clusters they resolve provides powerful ratification of species boundaries in all three complexes studied. Our approach is also able to resolve a number of single-population species and a probable hybrid species, both of which would be difficult to detect and characterize using a single MPS data set. Overall, the data reveal the existence of 11 and five species in the E. setacea and E. rehmannii complexes, with the E. ramosa complex requiring further sampling before species limits are finalized. Despite phenotypic differentiation being generally subtle, true crypsis is limited to just a few species pairs and triplets. We conclude that, in the absence of strong morphological differentiation, the use of multiple, independent genomic data sets is necessary in order to provide the cross-data set corroboration that is foundational to an integrative taxonomic approach. [Species delimitation; genotyping-by-sequencing; population structure; integrative taxonomy; cryptic species; Ehrharta (Poaceae).].
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Affiliation(s)
- Lara M Wootton
- Department of Biological Sciences and Bolus Herbarium, University of Cape Town, 7701, Rondebosch, South Africa
- Laboratoire d'Ecologie Alpine, Université Grenoble Alpes, FR-38000 Grenoble, France
| | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
| | - G Anthony Verboom
- Department of Biological Sciences and Bolus Herbarium, University of Cape Town, 7701, Rondebosch, South Africa
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6
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Gallego-García N, Ihlow F, Ettmar S, Iverson JB, Fritz U. Where to set the bar? Recent descriptions inflate species number in South American toad-headed turtles (Mesoclemmys). Zootaxa 2023; 5263:566-574. [PMID: 37044968 DOI: 10.11646/zootaxa.5263.4.8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Indexed: 04/14/2023]
Affiliation(s)
- Natalia Gallego-García
- Department of Ecology and Evolutionary Biology; University of California; Los Angeles; CA; 90095; USA.
| | - Flora Ihlow
- Computational Landscape Ecology; Institute of Geography; Technische Universität Dresden; Helmholtzstraße 10; 01069 Dresden; Germany.
| | - Stephan Ettmar
- Museum of Zoology; Senckenberg Dresden; A.B. Meyer Building; 01109 Dresden; Germany.
| | - John B Iverson
- ZooCon-Zoological Consulting; Schönbergerweg 4; 7201 Neudörfl; Austria.
| | - Uwe Fritz
- Department of Biology; Earlham College; 801 National Road West; Richmond; IN; 47374; USA.
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7
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Molinari J. A bare-bones scheme to choose between the species, subspecies, and ‘evolutionarily significant unit’ categories in taxonomy and conservation. J Nat Conserv 2023. [DOI: 10.1016/j.jnc.2023.126335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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8
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Kelly TS, Martin RA, Ronez C, Cañón C, Pardiñas UFJ. Morphology and genetics of grasshopper mice revisited in a paleontological framework: reinstatement of Onychomyini (Rodentia, Cricetidae). J Mammal 2022. [DOI: 10.1093/jmammal/gyac093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Abstract
Grasshopper mice of the genus Onychomys, represented by three living species in North America, have a long and controversial taxonomic history. Usually allocated to either the cricetine or neotomine cricetids, they also have been considered to represent a distinct tribe. Since the discovery and description of the extinct grasshopper mouse relative Acrolophomys rhodopetros from the late Miocene of the upper Dove Spring Formation of California, dated at 9.3–8.8 Ma, it has become apparent that the grasshopper mouse clade has a long, distinct evolutionary history. Using a combination of morphological (including paleontological material) and molecular data, we reassessed the phylogenetic position of grasshopper mice. A morphological phylogenetic analysis was done on fossil and modern specimens of all recognized neotomine tribes, including craniodental, phallic, and soft tissue characters. A DNA-based matrix was constructed including 72 species representing all known living genera of Neotominae and 13 outgroup taxa belonging mostly to cricetid subfamilies. DNA sampling covered the mitochondrial protein-coding gene cytochrome-b (Cytb), and seven nuclear loci. The morphological analysis yielded a single most parsimonious tree of 42 steps, placing Ochrotomys (Ochrotomyini), Baiomys (Baiomyini), Reithrodontomys (Reithrodontomyini), and an Onychomys–Acrolophomys clade as successive sister clades to a Peromyscus clade, respectively. The molecular phylogenetic analyses recovered seven major clades: (1) a clade including Habromys, Megadontomys, Neotomodon, Osgoodomys, Podomys, and a paraphyletic Peromyscus clade, sister to (2) a second clade containing extant Onychomys species, (3) a Reithrodontomys clade, (4) an Isthmomys clade, (5) a clade including Baiomys and Scotinomys, (6) an Ochrotomys clade, and (7) a well-supported clade containing Hodomys, Neotoma, and Xenomys. A Bayesian combined morphological and molecular analysis recovered the same major phylogenetic associations as the molecular analyses. The sum of molecular markers and morphological traits expressed by Acrolophomys and Onychomys leads to a phylogenetic position supporting their recognition as a distinct tribe.
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Affiliation(s)
- Thomas S Kelly
- Vertebrate Paleontology Department, Natural History Museum of Los Angeles County , 900 Exposition Boulevard, Los Angeles, California 90007 , USA
| | - Robert A Martin
- Department of Biological Sciences, Murray State University , 102 Curris Center, Murray, Kentucky 42071 , USA
| | - Christophe Ronez
- Instituto de Diversidad y Evolución Austral (IDEAus-CONICET) , Boulevard Almirante Brown 2915, Puerto Madryn 9120, Chubut , Argentina
| | - Carola Cañón
- Departamento de Ecosistemas y Medio Ambiente, Pontificia Universidad Católica de Chile , Vicuña Mackenna 4860, Macul 7820436, Santiago , Chile
| | - Ulyses F J Pardiñas
- Instituto de Diversidad y Evolución Austral (IDEAus-CONICET) , Boulevard Almirante Brown 2915, Puerto Madryn 9120, Chubut , Argentina
- Instituto Nacional de Biodiversidad (INABIO) , Pasaje Rumipamba y Av. Shyris, Quito 170135 , Ecuador
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9
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Creighton MJA, Luo AQ, Reader SM, Mooers AØ. Predictors of taxonomic splitting and its role in primate conservation. Anim Conserv 2022. [DOI: 10.1111/acv.12825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - A. Q. Luo
- Department of Biology McGill University Montreal Quebec Canada
| | - S. M. Reader
- Department of Biology McGill University Montreal Quebec Canada
| | - A. Ø. Mooers
- Department of Biological Sciences Simon Fraser University Burnaby British Columbia Canada
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10
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Mitogenome selection in the evolution of key ecological strategies in the ancient hexapod class Collembola. Sci Rep 2022; 12:14810. [PMID: 36045215 PMCID: PMC9433435 DOI: 10.1038/s41598-022-18407-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 08/10/2022] [Indexed: 11/09/2022] Open
Abstract
A longstanding question in evolutionary biology is how natural selection and environmental pressures shape the mitochondrial genomic architectures of organisms. Mitochondria play a pivotal role in cellular respiration and aerobic metabolism, making their genomes functionally highly constrained. Evaluating selective pressures on mitochondrial genes can provide functional and ecological insights into the evolution of organisms. Collembola (springtails) are an ancient hexapod group that includes the oldest terrestrial arthropods in the fossil record, and that are closely associated with soil environments. Of interest is the diversity of habitat stratification preferences (life forms) exhibited by different species within the group. To understand whether signals of positive selection are linked to the evolution of life forms, we analysed 32 published Collembola mitogenomes in a phylomitogenomic framework. We found no evidence that signatures of selection are correlated with the evolution of novel life forms, but rather that mutations have accumulated as a function of time. Our results highlight the importance of nuclear-mitochondrial interactions in the evolution of collembolan life forms and that mitochondrial genomic data should be interpreted with caution, as complex selection signals may complicate evolutionary inferences.
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İbiş O, Koepfli KP, Özcan S, Tez C. Whole mitogenomes of Turkish white-toothed shrews, genus Crocidura (Eulipotyphla: Soricidae), with new insights into the phylogenetic positions of Crocidura leucodon and the Crocidura suaveolens group. ORG DIVERS EVOL 2022. [DOI: 10.1007/s13127-022-00579-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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12
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Janiak MC, Silva FE, Beck RMD, de Vries D, Kuderna LFK, Torosin NS, Melin AD, Marquès‐Bonet T, Goodhead IB, Messias M, da Silva MNF, Sampaio I, Farias IP, Rossi R, de Melo FR, Valsecchi J, Hrbek T, Boubli JP. Two hundred and five newly assembled mitogenomes provide mixed evidence for rivers as drivers of speciation for Amazonian primates. Mol Ecol 2022; 31:3888-3902. [PMID: 35638312 PMCID: PMC9546496 DOI: 10.1111/mec.16554] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 05/06/2022] [Accepted: 05/20/2022] [Indexed: 12/02/2022]
Abstract
Mitochondrial DNA remains a cornerstone for molecular ecology, especially for study species from which high-quality tissue samples cannot be easily obtained. Methods using mitochondrial markers are usually reliant on reference databases, but these are often incomplete. Furthermore, available mitochondrial genomes often lack crucial metadata, such as sampling location, limiting their utility for many analyses. Here, we assembled 205 new mitochondrial genomes for platyrrhine primates, most from the Amazon and with known sampling locations. We present a dated mitogenomic phylogeny based on these samples along with additional published platyrrhine mitogenomes, and use this to assess support for the long-standing riverine barrier hypothesis (RBH), which proposes that river formation was a major driver of speciation in Amazonian primates. Along the Amazon, Negro, and Madeira rivers, we found mixed support for the RBH. While we identified divergences that coincide with a river barrier, only some occur synchronously and also overlap with the proposed dates of river formation. The most compelling evidence is for the Amazon river potentially driving speciation within bearded saki monkeys (Chiropotes spp.) and within the smallest extant platyrrhines, the marmosets and tamarins. However, we also found that even large rivers do not appear to be barriers for some primates, including howler monkeys (Alouatta spp.), uakaris (Cacajao spp.), sakis (Pithecia spp.), and robust capuchins (Sapajus spp.). Our results support a more nuanced, clade-specific effect of riverine barriers and suggest that other evolutionary mechanisms, besides the RBH and allopatric speciation, may have played an important role in the diversification of platyrrhines.
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Affiliation(s)
- Mareike C. Janiak
- School of Science, Engineering & EnvironmentUniversity of SalfordSalfordUK
| | - Felipe E. Silva
- Research Group on Primate Biology and ConservationMamirauá Institute for Sustainable DevelopmentTeféAMBrazil
- Unit of Evolutionary Biology and Ecology (EBE), Département de Biologie des OrganismesUniversité Libre de BruxellesBrusselsBelgium
| | - Robin M. D. Beck
- School of Science, Engineering & EnvironmentUniversity of SalfordSalfordUK
| | - Dorien de Vries
- School of Science, Engineering & EnvironmentUniversity of SalfordSalfordUK
| | - Lukas F. K. Kuderna
- Institute of Evolutionary Biology (UPF‐CSIC)BarcelonaUSA
- Present address:
Illumina Artificial Intelligence LaboratoryIllumina Inc.San DiegoCAUSA
| | - Nicole S. Torosin
- Department of GeneticsHuman Genetics Institute of New JerseyRutgers UniversityPiscatawayNew JerseyUSA
| | - Amanda D. Melin
- Department of Anthropology & Archaeology and Department of Medical GeneticsUniversity of CalgaryCalgaryAlbertaCanada
- Alberta Children's Hospital Research InstituteCalgaryAlbertaCanada
| | - Tomàs Marquès‐Bonet
- Institute of Evolutionary Biology (UPF‐CSIC)BarcelonaUSA
- Catalan Institution of Research and Advanced Studies (ICREA)BarcelonaSpain
- CNAG‐CRG, Centre for Genomic Regulation (CRG)Barcelona Institute of Science and Technology (BIST)BarcelonaSpain
- Institut Català de Paleontologia Miquel CrusafontUniversitat Autònoma de Barcelona, Edifici ICTA‐ICPCerdanyola del Vallès, BarcelonaSpain
| | - Ian B. Goodhead
- School of Science, Engineering & EnvironmentUniversity of SalfordSalfordUK
| | - Mariluce Messias
- Department of BiologyUniversidade Federal de RondôniaPorto VelhoROBrazil
| | | | | | - Izeni P. Farias
- Laboratory of Evolution and Animal GeneticsUniversidade Federal do AmazonasManausAMBrazil
| | - Rogerio Rossi
- Instituto de BiociênciasUniversidade Federal do Mato GrossoCuiabáMTBrazil
| | - Fabiano R. de Melo
- Department of Forestry EngineeringUniversidade Federal de ViçosaViçosaMGBrazil
| | - João Valsecchi
- Research Group on Primate Biology and ConservationMamirauá Institute for Sustainable DevelopmentTeféAMBrazil
| | - Tomas Hrbek
- Department of BiologyTrinity UniversitySan AntonioTexasUSA
| | - Jean P. Boubli
- School of Science, Engineering & EnvironmentUniversity of SalfordSalfordUK
- Coleção de MamíferosInstituto Nacional de Pesquisas da AmazôniaManausAMBrazil
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13
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Conservation Genetics of Mediterranean Brown Trout in Central Italy (Latium): A Multi-Marker Approach. WATER 2022. [DOI: 10.3390/w14060937] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Brown trout is considered a complex of incipient species, including several phylogenetic lineages, whose natural distribution in the Mediterranean area has been altered, since the beginning of the 1900s, by massive introductions of domestic strains of Atlantic origin to support fisheries. Introduced trout naturalize in new suitable environments and extensively hybridize with native populations. Here, we characterized putatively neutral and adaptive genetic variability and population structure of Mediterranean brown trout from six river catchments in central peninsular Italy, as revealed by both mitochondrial (Control Region) and nuclear (microsatellites, LDH-C1, major histocompatibility complex) markers. We quantified the admixture of wild populations with hatchery strains and evaluated the effects of domestic trout introductions on shaping population genetics. Our analyses indicated: (1) a composite picture of genetic variability in the area, with the presence of all native Mediterranean trout mitochondrial lineages (“Adriatic”, “Mediterranean”, “marmoratus”), various frequencies of allochthonous genotypes and different rates of introgression among sampling sites; (2) asymmetric mito-nuclear introgression; (3) increasing nuclear marker diversity with increasing levels of admixture across populations; (4) strong population structure coupled with relatively low effective population size. Data allowed the identification of five management units and we propose specific actions to support ongoing and future conservation strategies within the examined area.
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14
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Kitchener AC, Hoffmann M, Yamaguchi N, Breitenmoser-Würsten C, Wilting A. A system for designating taxonomic certainty in mammals and other taxa. Mamm Biol 2022. [DOI: 10.1007/s42991-021-00205-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
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15
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Chiozzi G, De Marchi G, Fasola M, Ibrahim KM, Bardelli G, Hagos F, Rocca F, Masseti M. Insular gazelles of the circum-Arabian seas: origin, distribution, dwarfism and taxonomy. Mamm Biol 2021. [DOI: 10.1007/s42991-021-00186-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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16
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Mahmoudi A, Kryštufek B, Sludsky A, Schmid BV, DE Almeida AMP, Lei X, Ramasindrazana B, Bertherat E, Yeszhanov A, Stenseth NC, Mostafavi E. Plague reservoir species throughout the world. Integr Zool 2021; 16:820-833. [PMID: 33264458 DOI: 10.1111/1749-4877.12511] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Plague has been known since ancient times as a re-emerging infectious disease, causing considerable socioeconomic burden in regional hotspots. To better understand the epidemiological cycle of the causative agent of the plague, its potential occurrence, and possible future dispersion, one must carefully consider the taxonomy, distribution, and ecological requirements of reservoir-species in relation either to natural or human-driven changes (e.g. climate change or urbanization). In recent years, the depth of knowledge on species taxonomy and species composition in different landscapes has undergone a dramatic expansion, driven by modern taxonomic methods such as synthetic surveys that take into consideration morphology, genetics, and the ecological setting of captured animals to establish their species identities. Here, we consider the recent taxonomic changes of the rodent species in known plague reservoirs and detail their distribution across the world, with a particular focus on those rodents considered to be keystone host species. A complete checklist of all known plague-infectable vertebrates living in plague foci is provided as a Supporting Information table.
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Affiliation(s)
- Ahmad Mahmoudi
- Department of Biology, Faculty of Science, Urmia University, Iran
- Department of Epidemiology and Biostatistics, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran
| | | | - Alexander Sludsky
- Russian Research Anti-Plague Institute «Microbe», Saratov, Russian Federation
| | - Boris V Schmid
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | | | - Xu Lei
- State Key Laboratory of Integrated Management on Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | | | - Eric Bertherat
- Department of Infectious Hazard Management, Health Emergencies Programme, WHO, Geneva, Switzerland
| | - Aidyn Yeszhanov
- M.Aikimbaev's National Scientific Center for Especially Dangerous Infections, Almaty, Kazakhstan
| | - Nils Chr Stenseth
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Ehsan Mostafavi
- Department of Epidemiology and Biostatistics, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran
- National Reference Laboratory for Plague, Tularemia and Q fever, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Akanlu, Kabudar Ahang, Hamadan, Iran
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Lücking R, Leavitt SD, Hawksworth DL. Species in lichen-forming fungi: balancing between conceptual and practical considerations, and between phenotype and phylogenomics. FUNGAL DIVERS 2021. [DOI: 10.1007/s13225-021-00477-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
AbstractLichens are symbiotic associations resulting from interactions among fungi (primary and secondary mycobionts), algae and/or cyanobacteria (primary and secondary photobionts), and specific elements of the bacterial microbiome associated with the lichen thallus. The question of what is a species, both concerning the lichen as a whole and its main fungal component, the primary mycobiont, has faced many challenges throughout history and has reached new dimensions with the advent of molecular phylogenetics and phylogenomics. In this paper, we briefly revise the definition of lichens and the scientific and vernacular naming conventions, concluding that the scientific, Latinized name usually associated with lichens invariably refers to the primary mycobiont, whereas the vernacular name encompasses the entire lichen. Although the same lichen mycobiont may produce different phenotypes when associating with different photobionts or growing in axenic culture, this discrete variation does not warrant the application of different scientific names, but must follow the principle "one fungus = one name". Instead, broadly agreed informal designations should be used for such discrete morphologies, such as chloromorph and cyanomorph for lichens formed by the same mycobiont but with either green algae or cyanobacteria. The taxonomic recognition of species in lichen-forming fungi is not different from other fungi and conceptual and nomenclatural approaches follow the same principles. We identify a number of current challenges and provide recommendations to address these. Species delimitation in lichen-forming fungi should not be tailored to particular species concepts but instead be derived from empirical evidence, applying one or several of the following principles in what we call the LPR approach: lineage (L) coherence vs. divergence (phylogenetic component), phenotype (P) coherence vs. divergence (morphological component), and/or reproductive (R) compatibility vs. isolation (biological component). Species hypotheses can be established based on either L or P, then using either P or L (plus R) to corroborate them. The reliability of species hypotheses depends not only on the nature and number of characters but also on the context: the closer the relationship and/or similarity between species, the higher the number of characters and/or specimens that should be analyzed to provide reliable delimitations. Alpha taxonomy should follow scientific evidence and an evolutionary framework but should also offer alternative practical solutions, as long as these are scientifically defendable. Taxa that are delimited phylogenetically but not readily identifiable in the field, or are genuinely cryptic, should not be rejected due to the inaccessibility of proper tools. Instead, they can be provisionally treated as undifferentiated complexes for purposes that do not require precise determinations. The application of infraspecific (gamma) taxonomy should be restricted to cases where there is a biological rationale, i.e., lineages of a species complex that show limited phylogenetic divergence but no evidence of reproductive isolation. Gamma taxonomy should not be used to denote discrete phenotypical variation or ecotypes not warranting the distinction at species level. We revise the species pair concept in lichen-forming fungi, which recognizes sexually and asexually reproducing morphs with the same underlying phenotype as different species. We conclude that in most cases this concept does not hold, but the actual situation is complex and not necessarily correlated with reproductive strategy. In cases where no molecular data are available or where single or multi-marker approaches do not provide resolution, we recommend maintaining species pairs until molecular or phylogenomic data are available. This recommendation is based on the example of the species pair Usnea aurantiacoatra vs. U. antarctica, which can only be resolved with phylogenomic approaches, such as microsatellites or RADseq. Overall, we consider that species delimitation in lichen-forming fungi has advanced dramatically over the past three decades, resulting in a solid framework, but that empirical evidence is still missing for many taxa. Therefore, while phylogenomic approaches focusing on particular examples will be increasingly employed to resolve difficult species complexes, broad screening using single barcoding markers will aid in placing as many taxa as possible into a molecular matrix. We provide a practical protocol how to assess and formally treat taxonomic novelties. While this paper focuses on lichen fungi, many of the aspects discussed herein apply generally to fungal taxonomy. The new combination Arthonia minor (Lücking) Lücking comb. et stat. nov. (Bas.: Arthonia cyanea f. minor Lücking) is proposed.
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Fahmi, Tibbetts IR, Bennett MB, Dudgeon CL. Delimiting cryptic species within the brown-banded bamboo shark, Chiloscyllium punctatum in the Indo-Australian region with mitochondrial DNA and genome-wide SNP approaches. BMC Ecol Evol 2021; 21:121. [PMID: 34134613 PMCID: PMC8207608 DOI: 10.1186/s12862-021-01852-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 06/04/2021] [Indexed: 11/26/2022] Open
Abstract
Background Delimiting cryptic species in elasmobranchs is a major challenge in modern taxonomy due the lack of available phenotypic features. Employing stand-alone genetics in splitting a cryptic species may prove problematic for further studies and for implementing conservation management. In this study, we examined mitochondrial DNA and genome-wide nuclear single nucleotide polymorphisms (SNPs) in the brown-banded bambooshark, Chiloscyllium punctatum to evaluate potential cryptic species and the species-population boundary in the group. Results Both mtDNA and SNP analyses showed potential delimitation within C. punctatum from the Indo-Australian region and consisted of four operational taxonomic units (OTUs), i.e. those from Indo-Malay region, the west coast of Sumatra, Lesser Sunda region, and the Australian region. Each OTU can be interpreted differently depending on available supporting information, either based on biological, ecological or geographical data. We found that SNP data provided more robust results than mtDNA data in determining the boundary between population and cryptic species. Conclusion To split a cryptic species complex and erect new species based purely on the results of genetic analyses is not recommended. The designation of new species needs supportive diagnostic morphological characters that allow for species recognition, as an inability to recognise individuals in the field creates difficulties for future research, management for conservation and fisheries purposes. Moreover, we recommend that future studies use a comprehensive sampling regime that encompasses the full range of a species complex. This approach would increase the likelihood of identification of operational taxonomic units rather than resulting in an incorrect designation of new species. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01852-3.
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Affiliation(s)
- Fahmi
- School of Biological Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia. .,Research Center for Oceanography, Indonesian Institute of Sciences, Jalan Pasir Putih I No. 1 Ancol, Jakarta, 14430, Indonesia.
| | - Ian R Tibbetts
- School of Biological Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Michael B Bennett
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Christine L Dudgeon
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia
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19
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Morales-Martínez DM, López-Arévalo HF, Vargas-Ramírez M. Beginning the quest: phylogenetic hypothesis and identification of evolutionary lineages in bats of the genus Micronycteris (Chiroptera, Phyllostomidae). Zookeys 2021; 1028:135-159. [PMID: 33889049 PMCID: PMC8044067 DOI: 10.3897/zookeys.1028.60955] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 03/04/2021] [Indexed: 11/12/2022] Open
Abstract
Thirteen species of Neotropical bats of the genus Micronycteris are currently recognized and are allocated to four subgenera Leuconycteris, Micronycteris, Schizonycteris, and Xenonectes. Despite that, the presence of polyphyletic clades in molecular phylogenies suggests that its diversity is underestimated. Additionally, the incorrect identification of some genetic sequences, the incorrect assignation of available valid names, and restricted geographic sampling have biased the identification of independently evolutionary lineages within Micronycteris. In this study, several unknown genealogical lineages in the genus are identified and an updated phylogenetic hypothesis is proposed using mitochondrial and nuclear DNA fragments. The phylogenetic analyses congruently showed all individuals in four well-supported subgenera, but M. schmidtorum was revealed as the sister taxon of M. brosseti in the subgenus Leuconycteris. Twenty-seven different genealogical lineages were identified. These included eight confirmed species: M. brosseti, M. buriri, M. giovanniae, M. matses, M. schmidtorum, M. simmonsae, M. tresamici, and M. yatesi. Nineteen either allopatric or parapatric candidate species were also confirmed, two within the M. hirsuta complex, nine within the M. megalotis complex, seven within the M. minuta complex, and one corresponding to "M. sp.". These results revealed an extensive undescribed diversity within each subgenus of Micronycteris. Nevertheless, the evolutionary processes associated with the specific radiations are poorly understood. This is just the beginning of the assessment of the taxonomy and systematics of Micronycteris, which requires additional integrative taxonomical approaches for its advance.
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Affiliation(s)
- Darwin M Morales-Martínez
- Grupo de Biodiversidad y Conservación Genética, Instituto de Genética, Universidad Nacional de Colombia, Universidad Nacional de Colombia, Carrera 45 No 26-85, Bogotá, Colombia Universidad Nacional de Colombia Bogotá Colombia.,Grupo en Conservación y Manejo de Vida Silvestre, Instituto de Ciencias Naturales, Universidad Nacional de Colombia, Carrera 45 No 26-85, Bogotá, Colombia Universidad Nacional de Colombia Bogotá Colombia
| | - Hugo F López-Arévalo
- Grupo en Conservación y Manejo de Vida Silvestre, Instituto de Ciencias Naturales, Universidad Nacional de Colombia, Carrera 45 No 26-85, Bogotá, Colombia Universidad Nacional de Colombia Bogotá Colombia
| | - Mario Vargas-Ramírez
- Grupo de Biodiversidad y Conservación Genética, Instituto de Genética, Universidad Nacional de Colombia, Universidad Nacional de Colombia, Carrera 45 No 26-85, Bogotá, Colombia Universidad Nacional de Colombia Bogotá Colombia.,Estación de Biología Tropical Roberto Franco, Universidad Nacional de Colombia. Carrera 33 #33-76, Barrio El Porvenir, Villavicencio, Meta, Colombia Universidad Nacional de Colombia Bogotá Colombia
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20
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Abreu EF, Jung DMH, Christoff AU, Valiati VH, Jansa SA, Percequillo AR. Systematics of Brucepattersonius Hershkovitz, 1998 (Rodentia, Sigmodontinae): molecular species delimitation and morphological analyses suggest an overestimation in species diversity. SYST BIODIVERS 2021. [DOI: 10.1080/14772000.2021.1890270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Edson Fiedler Abreu
- Laboratório de Mamíferos, Departamento de Ciências Biológicas, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, Piracicaba, 13418900, SP, Brazil
| | - Diego Marques Henriques Jung
- Laboratório de Genética e Biologia Molecular, Universidade do Vale do Rio dos Sinos, São Leopoldo, 93022750, RS, Brazil
| | - Alexandre Uarth Christoff
- Laboratório de Genética e Biologia Molecular, Universidade do Vale do Rio dos Sinos, São Leopoldo, 93022750, RS, Brazil
| | - Victor Hugo Valiati
- Laboratório de Genética e Biologia Molecular, Universidade do Vale do Rio dos Sinos, São Leopoldo, 93022750, RS, Brazil
| | - Sharon A. Jansa
- Department of Ecology, Evolution, and Behavior and Bell Museum of Natural History, University of Minnesota, St Paul, 55108, MN, USA
| | - Alexandre Reis Percequillo
- Laboratório de Mamíferos, Departamento de Ciências Biológicas, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, Piracicaba, 13418900, SP, Brazil
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21
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Chávez-Cortázar A, Oyama K, Ochoa-Zavala M, Mata-Rosas M, Veltjen E, Samain MS, Quesada M. Conservation genetics of relict tropical species of Magnolia (section Macrophylla). CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01334-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
AbstractSpecial conservation efforts should be made for relict species, as they usually have small population sizes and restricted distributions, placing them in critical extinction risk. To achieve conservation, information about genetic diversity distribution is needed. Here, using nine nuclear microsatellites, we analyzed 23 populations of five recently described species of Magnolia distributed in Mexico, which were previously assigned to Magnolia dealbata. We aimed to determine the level of genetic diversity and the distribution of genetic variation and proposed conservation measures. Compared to other endemic and relict species, we found a moderate level of genetic diversity in most populations; however, we identified two populations with no genetic variation. Additionally, we found evidence of positive values of inbreeding likely due to geitonogamy. We found a strong population structure, low effective population size, and no evidence of bottlenecks. Patterns of genetic differentiation did not support the morphological distinction of five species, so we hypothesized that the gene pools may instead represent well-differentiated populations of a single species. We argue that the pattern of genetic differentiation is explained by the natural fragmentation of the cloud forests after glaciation events, and the effects of genetic drift in small populations poorly connected by gene flow. Despite the moderate levels of genetic diversity, special attention is needed to guarantee conservation, with emphasis on the populations in the central region of the country as well as the valuable populations identified in the southwestern region.
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22
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Caraballo DA, Montani ME, Martínez LM, Antoniazzi LR, Sambrana TC, Fernández C, Cisterna DM, Beltrán FJ, Colombo VC. Heterogeneous taxonomic resolution of cytochrome b gene identification of bats from Argentina: Implications for field studies. PLoS One 2021; 15:e0244750. [PMID: 33382800 PMCID: PMC7775095 DOI: 10.1371/journal.pone.0244750] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 12/15/2020] [Indexed: 11/19/2022] Open
Abstract
Bats are among the most diverse, widespread, and abundant mammals. In Argentina, 67 species of bats have been recorded, belonging to 5 families and 29 genera. These high levels of biodiversity are likely to complicate identification at fieldwork, especially between closely related species, where external morphology-based approaches are the only immediate means for a priori species assignment. The use of molecular markers can enhance species identification, and acquires particular relevance in capture-release studies. In this study, we discuss the extent of the use of the mitochondrial cytochrome b gene for species identification, comparing external morphology identification with a molecular phylogenetic classification based on this marker, under the light of current bat systematics. We analyzed 33 samples collected in an eco-epidemiological survey in the province of Santa Fe (Argentina). We further sequenced 27 museum vouchers to test the accuracy of cytochrome b -based phylogenies in taxonomic identification of bats occurring in the Pampean/Chacoan regions of Argentina. The cytochrome b gene was successfully amplified in all Molossid and Vespertilionid species except for Eptesicus, for which we designed a new reverse primer. The resulting Bayesian phylogeny was congruent with current systematics. Cytochrome b proved useful for species-level delimitation in non-conflicting genera (Eumops, Dasypterus, Molossops) and has infrageneric resolution in more complex lineages (Eptesicus, Myotis, Molossus). We discuss four sources of incongruence that may act separately or in combination: 1) molecular processes, 2) biology, 3) limitations in identification, and 4) errors in the current taxonomy. The present study confirms the general applicability of cytochrome b -based phylogenies in eco-epidemiological studies, but its resolution and reliability depend mainly, but not solely, on the level of genetic differentiation within each bat genus.
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Affiliation(s)
- Diego A. Caraballo
- Instituto de Zoonosis Luis Pasteur, Ciudad Autónoma de Buenos Aires, Argentina
- * E-mail:
| | - María E. Montani
- Museo Provincial de Ciencias Naturales “Dr. Ángel Gallardo”, Rosario, Santa Fe, Argentina
- Programa de Investigaciones de Biodiversidad Argentina (PIDBA), Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán, San Miguel de Tucumán, Tucumán, Argentina
- Programa de Conservación de los Murciélagos de Argentina (PCMA), San Miguel de Tucumán, Tucumán, Argentina
| | - Leila M. Martínez
- Servicio de Neurovirosis, Instituto Nacional de Enfermedades Infecciosas, Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) “Dr. Carlos G. Malbrán”, Ciudad Autónoma de Buenos Aires, Argentina
| | - Leandro R. Antoniazzi
- Laboratorio de Ecología de Enfermedades (LEcEn), Instituto de Ciencias Veterinarias del Litoral (ICiVet-Litoral), Universidad Nacional del Litoral (UNL) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Esperanza, Santa Fe, Argentina
| | - Tomás C. Sambrana
- Departamento de Zoonosis, Laboratorio Central de Referencia, Dirección de Promoción y Prevención, Ministerio de Salud de la provincia de Santa Fe, Ciudad de Santa Fe, Santa Fe, Argentina
| | - Camilo Fernández
- Laboratorio de Ecología de Enfermedades (LEcEn), Instituto de Ciencias Veterinarias del Litoral (ICiVet-Litoral), Universidad Nacional del Litoral (UNL) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Esperanza, Santa Fe, Argentina
| | - Daniel M. Cisterna
- Servicio de Neurovirosis, Instituto Nacional de Enfermedades Infecciosas, Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) “Dr. Carlos G. Malbrán”, Ciudad Autónoma de Buenos Aires, Argentina
| | - Fernando J. Beltrán
- Instituto de Zoonosis Luis Pasteur, Ciudad Autónoma de Buenos Aires, Argentina
| | - Valeria C. Colombo
- Servicio de Neurovirosis, Instituto Nacional de Enfermedades Infecciosas, Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) “Dr. Carlos G. Malbrán”, Ciudad Autónoma de Buenos Aires, Argentina
- Laboratorio de Ecología de Enfermedades (LEcEn), Instituto de Ciencias Veterinarias del Litoral (ICiVet-Litoral), Universidad Nacional del Litoral (UNL) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Esperanza, Santa Fe, Argentina
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23
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Rodrigues BL, Baton LA, Shimabukuro PHF. Single-locus DNA barcoding and species delimitation of the sandfly subgenus Evandromyia (Aldamyia). MEDICAL AND VETERINARY ENTOMOLOGY 2020; 34:420-431. [PMID: 32590879 DOI: 10.1111/mve.12458] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 05/05/2020] [Accepted: 05/27/2020] [Indexed: 06/11/2023]
Abstract
Sandfly specimens from the subgenus Evandromyia (Aldamyia) Galati, 2003 (Diptera: Psychodidae: Phlebotominae) were collected between 2012 and 2019 from nine localities in seven Brazilian states, morphologically-identified, and then DNA barcoded by sequencing the mitochondrial cytochrome c oxidase subunit I (coi) gene. Forty-four new barcode sequences generated from 10 morphospecies were combined with 49 previously published sequences from the same subgenus and analysed using sequence-similarity methods (best-match criteria) to assess their ability at specimen identification, while four different species delimitation methods (ABGD, GMYC, PTP and TCS) were used to infer molecular operational taxonomic units (MOTUs). Overall, seven of the 11 morphospecies analysed were congruent with both the well-supported clades identified by phylogenetic analysis and the MOTUs inferred by species delimitation, while the remaining four morphospecies - E. carmelinoi, E. evandroi, E. lenti and E. piperiformis - were merged into a single well-supported clade/MOTU. Although E. carmelinoi, E. evandroi and E. lenti were indistinguishable using coi DNA barcodes, E. piperiformis did form a distinct phylogenetic cluster and could be correctly identified using best-match criteria. Despite their apparent morphological differences, we propose on the basis of the molecular similarity of their DNA barcodes that these latter four morphospecies should be considered members of a recently-diverged species complex.
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Affiliation(s)
- B L Rodrigues
- Grupo de Estudos em Leishmanioses, Instituto René Rachou-Fiocruz Minas, Belo Horizonte, Minas Gerais, Brazil
| | - L A Baton
- 50 Rowntree Way Saffron Walden, Essex, CB11 4DL, U.K
| | - P H F Shimabukuro
- Grupo de Estudos em Leishmanioses, Instituto René Rachou-Fiocruz Minas, Belo Horizonte, Minas Gerais, Brazil
- Coleção de Flebotomíneos (FIOCRUZ/COLFLEB), Instituto René Rachou-Fiocruz Minas, Belo Horizonte, Minas Gerais, Brazil
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24
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Variability and variation in Rhyncholestes raphanurus Osgood (Paucituberculata, Caenolestidae). REVISTA CHILENA DE HISTORIA NATURAL 2020. [DOI: 10.1186/s40693-020-00089-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Abstract
Background
Caenolestids are a group of poorly known South American marsupials with a restricted distribution in Páramo and Subpáramo environments of the Andes from Colombia and western Venezuela to Bolivia (represented by the genera Caenolestes and Lestoros), and Valdivian rainforest in southern Chile (including a separate population in Chiloé Island) and Argentina, where a single species lives: the Long-nosed shrew opossum (Rhyncholestes raphanurus). The objectives of this work were to analyze the intraspecific variability of R. raphanurus, which includes an anatomical description of the skull and dentition, describe its geographic variation, test for sexual dimorphism, and assess potential differences between continental and Island populations.
Methods
Linear Mossimann-transformed variables were used to assess sexual differences within a large population (La Picada), compare sexes within other continental populations, and in a separate analysis, compare continental from Island samples. A full model Principal Components Analysis was performed to assess differences between males and females of the continental and Island populations. A thorough description of the skull and teeth of the species and comparisons with other living Caenolestidae is presented.
Results
Rhyncholestes raphanurus presents little geographic variation, even between Island and continental populations. Similarly, we found no significant difference between sexes of this species in cranial and dental measurements. We provide a detailed description of cranial morphology and its variation, and also, the first description of the occipital bones, which haven’t been previously described for any Paucituberculata.
Conclusions
Comparative studies of continental and Chiloé Island specimens support the treatment of R. raphanurus as a single valid species, especially since morphologic and morphometric differences fall within the extremes of continental populations. The morphology of R. raphanurus clearly separates this genus from other extant Caenolestidae, and in a much greater degree than the differences found between Lestoros and Caenolestes.
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25
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Hosegood J, Humble E, Ogden R, de Bruyn M, Creer S, Stevens GMW, Abudaya M, Bassos-Hull K, Bonfil R, Fernando D, Foote AD, Hipperson H, Jabado RW, Kaden J, Moazzam M, Peel LR, Pollett S, Ponzo A, Poortvliet M, Salah J, Senn H, Stewart JD, Wintner S, Carvalho G. Phylogenomics and species delimitation for effective conservation of manta and devil rays. Mol Ecol 2020; 29:4783-4796. [PMID: 33164287 DOI: 10.1111/mec.15683] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 09/25/2020] [Accepted: 09/30/2020] [Indexed: 02/06/2023]
Abstract
Practical biodiversity conservation relies on delineation of biologically meaningful units. Manta and devil rays (Mobulidae) are threatened worldwide, yet morphological similarities and a succession of recent taxonomic changes impede the development of an effective conservation strategy. Here, we generate genome-wide single nucleotide polymorphism (SNP) data from a geographically and taxonomically representative set of manta and devil ray samples to reconstruct phylogenetic relationships and evaluate species boundaries under the general lineage concept. We show that nominal species units supported by alternative data sources constitute independently evolving lineages, and find robust evidence for a putative new species of manta ray in the Gulf of Mexico. Additionally, we uncover substantial incomplete lineage sorting indicating that rapid speciation together with standing variation in ancestral populations has driven phylogenetic uncertainty within Mobulidae. Finally, we detect cryptic diversity in geographically distinct populations, demonstrating that management below the species level may be warranted in certain species. Overall, our study provides a framework for molecular genetic species delimitation that is relevant to wide-ranging taxa of conservation concern, and highlights the potential for genomic data to support effective management, conservation and law enforcement strategies.
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Affiliation(s)
- Jane Hosegood
- Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, UK.,The Manta Trust, Catemwood House, Norwood Lane, Corscombe, Dorset, DT2 0NT, UK.,NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Emily Humble
- The Manta Trust, Catemwood House, Norwood Lane, Corscombe, Dorset, DT2 0NT, UK.,Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Rob Ogden
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Edinburgh, UK.,TRACE Wildlife Forensics Network, Edinburgh, UK
| | - Mark de Bruyn
- Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, UK.,School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Simon Creer
- Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, UK
| | - Guy M W Stevens
- The Manta Trust, Catemwood House, Norwood Lane, Corscombe, Dorset, DT2 0NT, UK
| | | | - Kim Bassos-Hull
- Mote Marine Laboratory, The Center for Shark Research, Sarasota, FL, USA
| | | | - Daniel Fernando
- The Manta Trust, Catemwood House, Norwood Lane, Corscombe, Dorset, DT2 0NT, UK.,Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden.,Blue Resources Trust, Colombo, Sri Lanka
| | - Andrew D Foote
- Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, UK.,Department of Natural History, Norwegian University of Science and Technology (NTNU), University Museum, Trondheim, Norway
| | - Helen Hipperson
- NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | | | - Jennifer Kaden
- RZSS WildGenes Lab, Royal Zoological Society of Scotland, Edinburgh, UK
| | | | - Lauren R Peel
- The Manta Trust, Catemwood House, Norwood Lane, Corscombe, Dorset, DT2 0NT, UK.,School of Biological Sciences, University of Western Australia, Crawley, WA, Australia.,The Australian Institute of Marine Science, Crawley, WA, Australia.,Save Our Seas Foundation - D'Arros Research Centre, Geneva, Switzerland
| | - Stephen Pollett
- The Manta Trust, Catemwood House, Norwood Lane, Corscombe, Dorset, DT2 0NT, UK
| | - Alessandro Ponzo
- Large Marine Vertebrates Research Institute Philippines, Jagna, Philippines
| | | | - Jehad Salah
- Ministry of Agriculture Directorate General of Fisheries, Gaza City, Palestine
| | - Helen Senn
- RZSS WildGenes Lab, Royal Zoological Society of Scotland, Edinburgh, UK
| | - Joshua D Stewart
- The Manta Trust, Catemwood House, Norwood Lane, Corscombe, Dorset, DT2 0NT, UK
| | - Sabine Wintner
- KwaZulu-Natal Sharks Board, Umhlanga Rocks, South Africa.,School of Life Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Gary Carvalho
- Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, UK
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26
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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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27
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Fordham G, Shanee S, Peck M. Effect of river size on Amazonian primate community structure: A biogeographic analysis using updated taxonomic assessments. Am J Primatol 2020; 82:e23136. [PMID: 32323350 DOI: 10.1002/ajp.23136] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 04/07/2020] [Accepted: 04/08/2020] [Indexed: 11/05/2022]
Abstract
The mechanisms that underlie the diversification of Neotropical primates remain contested. One mechanism that has found support is the riverine barrier hypothesis (RBH), which postulates that large rivers impede gene flow between populations on opposite riverbanks and promote allopatric speciation. Ayres and Clutton-Brock (1992) demonstrated that larger Amazonian rivers acted as barriers, delineating the distribution limits of primate species. However, profound changes in taxonomy and species concepts have led to the proliferation of Neotropical primate taxa, which may have reduced support for their results. Using the most recent taxonomic assessments and distribution maps, we tested the effect of increasing river size on the similarity of opposite riverbank primate communities in the Amazon. First, we conducted a literature review of primate taxonomy and developed a comprehensive spatial database, then applied geographical information system to query mapped primate ranges against the riverine geography of the Amazon watershed to produce a similarity index for opposite riverbank communities. Finally, we ran models to test how measures of river size predicted levels of similarity. We found that, almost without exception, similarity scores were lower than scores from Ayres and Clutton-Brock (1992) for the same rivers. Our model showed a significant negative relationship between streamflow and similarity in all tests, and found river width significant for the segmented Amazon, but not for multiple Amazon watershed rivers. Our results support the RBH insofar as they provide evidence for the prediction that rivers with higher streamflow act as more substantial barriers to dispersal, and accordingly exhibit greater variation in community composition between riverbanks.
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Affiliation(s)
- Gail Fordham
- School of Life Sciences, University of Sussex, Brighton, UK
| | - Sam Shanee
- Neotropical Primate Conservation, Torpoint, Cornwall, UK
| | - Mika Peck
- School of Life Sciences, University of Sussex, Brighton, UK.,Neotropical Primate Conservation, Torpoint, Cornwall, UK
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28
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Tatarenkov A, Earley RL, Taylor DS, Davis WP, Avise JC. Extensive hybridization and past introgression between divergent lineages in a quasi-clonal hermaphroditic fish: Ramifications for species concepts and taxonomy. J Evol Biol 2020; 34:49-59. [PMID: 32242998 DOI: 10.1111/jeb.13624] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 02/23/2020] [Accepted: 03/15/2020] [Indexed: 01/31/2023]
Abstract
Extreme inbreeding is expected to reduce the incidence of hybridization, serving as a prezygotic barrier. Mangrove rivulus is a small killifish that reproduces predominantly by self-fertilization, producing highly homozygous lines throughout its geographic range. The Bahamas and Caribbean are inhabited by two highly diverged phylogeographic lineages of mangrove rivulus, Kryptolebias marmoratus and a 'Central clade' closely related to K. hermaphroditus from Brazil. The two lineages are largely allopatric, but recently were found in syntopy on San Salvador, Bahamas, where a single hybrid was reported. To better characterize the degree of hybridization and the possibility of secondary introgression, here we conducted a detailed genetic analysis of the contact zone on San Salvador. Two mixed populations were identified, one of which contained sexually mature hybrids. The distribution of heterozygosity at diagnostic microsatellite loci in hybrids showed that one of these hybrids was an immediate offspring from the K. marmoratus x Central clade cross, whereas the remaining five hybrids were products of reproduction by self-fertilization for 1-3 generations following the initial cross. Two hybrids had mitochondrial haplotypes of K. marmoratus and the remaining four hybrids had a haplotype of the Central clade, indicating that crosses go in both directions. In hybrids, alleles of parental lineages were represented in equal proportions suggesting lack of recent backcrossing to either of the parental lineages. However, sympatric populations of two lineages were less diverged than allopatric populations, consistent with introgression. Results are discussed in terms of applicability of the biological species concept for isogenic, effectively clonal, organisms.
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Affiliation(s)
- Andrey Tatarenkov
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
| | - Ryan L Earley
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, USA
| | | | | | - John C Avise
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
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29
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Schrago CG, Mello B. Employing statistical learning to derive species‐level genetic diversity for mammalian species. Mamm Rev 2020. [DOI: 10.1111/mam.12192] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Carlos G. Schrago
- Department of Genetics Federal University of Rio de Janeiro Rio de Janeiro RJ21941-617Brazil
| | - Beatriz Mello
- Department of Genetics Federal University of Rio de Janeiro Rio de Janeiro RJ21941-617Brazil
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30
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Hasiniaina AF, Radespiel U, Kessler SE, Rina Evasoa M, Rasoloharijaona S, Randrianambinina B, Zimmermann E, Schmidt S, Scheumann M. Evolutionary significance of the variation in acoustic communication of a cryptic nocturnal primate radiation ( Microcebus spp.). Ecol Evol 2020; 10:3784-3797. [PMID: 32313636 PMCID: PMC7160168 DOI: 10.1002/ece3.6177] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 02/07/2020] [Accepted: 02/18/2020] [Indexed: 11/06/2022] Open
Abstract
Acoustic phenotypic variation is of major importance for speciation and the evolution of species diversity. Whereas selective and stochastic forces shaping the acoustic divergence of signaling systems are well studied in insects, frogs, and birds, knowledge on the processes driving acoustic phenotypic evolution in mammals is limited. We quantified the acoustic variation of a call type exchanged during agonistic encounters across eight distinct species of the smallest-bodied nocturnal primate radiation, the Malagasy mouse lemurs. The species live in two different habitats (dry forest vs. humid forest), differ in geographic distance to each other, and belong to four distinct phylogenetic clades within the genus. Genetically defined species were discriminated reliably on the phenotypic level based on their acoustic distinctiveness in a discriminant function analysis. Acoustic variation was explained by genetic distance, whereas differences in morphology, forest type, or geographic distance had no effect. The strong impact of genetics was supported by a correlation between acoustic and genetic distance and the high agreement in branching pattern between the acoustic and molecular phylogenetic trees. In sum, stochastic factors such as genetic drift best explained acoustic diversification in a social communication call of mouse lemurs.
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Affiliation(s)
| | - Ute Radespiel
- Institute of ZoologyUniversity of Veterinary Medicine HannoverHannoverGermany
| | - Sharon E. Kessler
- Department of PsychologyFaculty of Natural SciencesUniversity of StirlingStirlingScotland
- Department of AnthropologyDurham UniversityDurhamUK
| | - Mamy Rina Evasoa
- Faculty of Science, Technology and EnvironmentUniversity of MahajangaMahajangaMadagascar
| | | | | | - Elke Zimmermann
- Institute of ZoologyUniversity of Veterinary Medicine HannoverHannoverGermany
| | - Sabine Schmidt
- Institute of ZoologyUniversity of Veterinary Medicine HannoverHannoverGermany
| | - Marina Scheumann
- Institute of ZoologyUniversity of Veterinary Medicine HannoverHannoverGermany
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31
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Fernandez-Duque E, Huck M, Van Belle S, Di Fiore A. The evolution of pair-living, sexual monogamy, and cooperative infant care: Insights from research on wild owl monkeys, titis, sakis, and tamarins. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2020; 171 Suppl 70:118-173. [PMID: 32191356 DOI: 10.1002/ajpa.24017] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 12/18/2019] [Accepted: 12/20/2019] [Indexed: 12/28/2022]
Abstract
"Monogamy" and pair bonding have long been of interest to anthropologists and primatologists. Their study contributes to our knowledge of human evolutionary biology and social evolution without the cultural trappings associated with studying human societies directly. Here, we first provide an overview of theoretical considerations, followed by an evaluation of recent comparative studies of the evolution of "social monogamy"; we are left with serious doubts about the conclusions of these studies that stem from the often poor quality of the data used and an overreliance on secondary sources without vetting the data therein. We then describe our field research program on four "monogamous" platyrrhines (owl monkeys, titis, sakis, and tamarins), evaluate how well our data support various hypotheses proposed to explain "monogamy," and compare our data to those reported on the same genera in comparative studies. Overall, we found a distressing lack of agreement between the data used in comparative studies and data from the literature for the taxa that we work with. In the final section, we propose areas of research that deserve more attention. We stress the need for more high-quality natural history data, and we urge researchers to be cautious about the uncritical use of variables of uncertain internal validity. Overall, it is imperative that biological anthropologists establish and follow clear criteria for comparing and combining results from published studies and that researchers, reviewers, and editors alike comply with these standards to improve the transparency, reproducibility, and interpretability of causal inferences made in comparative studies.
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Affiliation(s)
- Eduardo Fernandez-Duque
- Department of Anthropology, Yale University, New Haven, Connecticut.,Owl Monkey Project, Fundación ECO, Formosa, Argentina.,Facultad de Recursos Naturales, Universidad Nacional de Formosa, Formosa, Argentina.,College of Biological and Environmental Sciences, Universidad San Francisco de Quito, Quito, Ecuador
| | - Maren Huck
- School of Environmental Sciences, University of Derby, Derby, UK
| | - Sarie Van Belle
- Department of Anthropology, University of Texas, Austin, Texas.,Primate Molecular Ecology and Evolution Laboratory, University of Texas, Austin, Texas
| | - Anthony Di Fiore
- College of Biological and Environmental Sciences, Universidad San Francisco de Quito, Quito, Ecuador.,Department of Anthropology, University of Texas, Austin, Texas.,Primate Molecular Ecology and Evolution Laboratory, University of Texas, Austin, Texas
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32
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Montgelard C, Behrooz R, Arnal V, Asadi A, Geniez P, Kaboli M. Diversification and cryptic diversity of
Ophisops elegans
(Sauria, Lacertidae). J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12369] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Claudine Montgelard
- CEFE PSL‐EPHE (Biogéographie et Ecologie des Vertébrés) CNRS Université de Montpellier Univ Paul Valéry Montpellier 3 IRD Montpellier France
- Department of Zoology Centre for Ecological Genomics and Wildlife Conservation University of Johannesburg Johannesburg South Africa
| | - Roozbeh Behrooz
- CEFE PSL‐EPHE (Biogéographie et Ecologie des Vertébrés) CNRS Université de Montpellier Univ Paul Valéry Montpellier 3 IRD Montpellier France
| | - Véronique Arnal
- CEFE PSL‐EPHE (Biogéographie et Ecologie des Vertébrés) CNRS Université de Montpellier Univ Paul Valéry Montpellier 3 IRD Montpellier France
| | - Atefeh Asadi
- CEFE PSL‐EPHE (Biogéographie et Ecologie des Vertébrés) CNRS Université de Montpellier Univ Paul Valéry Montpellier 3 IRD Montpellier France
| | - Philippe Geniez
- CEFE PSL‐EPHE (Biogéographie et Ecologie des Vertébrés) CNRS Université de Montpellier Univ Paul Valéry Montpellier 3 IRD Montpellier France
| | - Mohammad Kaboli
- Department of Environmental Science Faculty of Natural Resources University of Tehran Karaj Iran
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33
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Caspers LM, Ferrie GM, Wolfe K, Hoffman EA. Subspecific identity and a comparison of genetic diversity between wild and ex situ wildebeest. Zoo Biol 2020; 39:129-140. [PMID: 31904139 DOI: 10.1002/zoo.21530] [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: 02/01/2019] [Revised: 08/01/2019] [Accepted: 12/18/2019] [Indexed: 11/11/2022]
Abstract
The original North American ex situ wildebeest population was believed to originate from the white-bearded wildebeest (Connochaetes taurinus albojubatus), which is both morphologically distinct and geographically separated from the brindled wildebeest (C. t. taurinus). However, after an import of wildebeest into North America in 2001, managers have suspected that white-bearded and brindled wildebeest were mixed in herds at multiple institutions. We sequenced the mitochondrial control region (d-loop) from a portion of the managed North American population and compared our sequences with previously published sequences from wild individuals to determine the subspecific identity and genetic diversity of our ex situ population. We were able to confidently identify C. t. albojubatus as the subspecies identity of the sampled portion of our population. Within our population, haplotype and nucleotide diversity were low (0.169 and 0.001, respectively) with a single common haplotype (H1) containing 41 of the 45 individuals sequenced, while two rare haplotypes (H2 and H3) were derived from three individuals and a single individual, respectively. Nucleotide and haplotype diversity were greater overall in the wild populations compared with our managed population. However, C. t. albojubatus was found to exhibit lower nucleotide diversity in both wild and ex situ populations when compared to other wild subspecies. Though the overall goal of the North American wildebeest population is for public education and not reintroduction, maintaining genetic diversity is vital for the long-term viability of this managed population, which may benefit from periodic supplementation of wild animals.
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Affiliation(s)
- Lauren M Caspers
- Department of Biology, University of Central Florida, Orlando, Florida
| | - Gina M Ferrie
- Disney's Animals, Science, and Environment, Disney's Animal Kingdom, Lake Buena Vista, Florida
| | - Kristen Wolfe
- Disney's Animals, Science, and Environment, Disney's Animal Kingdom, Lake Buena Vista, Florida
| | - Eric A Hoffman
- Department of Biology, University of Central Florida, Orlando, Florida
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34
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Upham NS, Esselstyn JA, Jetz W. Inferring the mammal tree: Species-level sets of phylogenies for questions in ecology, evolution, and conservation. PLoS Biol 2019; 17:e3000494. [PMID: 31800571 PMCID: PMC6892540 DOI: 10.1371/journal.pbio.3000494] [Citation(s) in RCA: 489] [Impact Index Per Article: 97.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 10/24/2019] [Indexed: 12/18/2022] Open
Abstract
Big, time-scaled phylogenies are fundamental to connecting evolutionary processes to modern biodiversity patterns. Yet inferring reliable phylogenetic trees for thousands of species involves numerous trade-offs that have limited their utility to comparative biologists. To establish a robust evolutionary timescale for all approximately 6,000 living species of mammals, we developed credible sets of trees that capture root-to-tip uncertainty in topology and divergence times. Our "backbone-and-patch" approach to tree building applies a newly assembled 31-gene supermatrix to two levels of Bayesian inference: (1) backbone relationships and ages among major lineages, using fossil node or tip dating, and (2) species-level "patch" phylogenies with nonoverlapping in-groups that each correspond to one representative lineage in the backbone. Species unsampled for DNA are either excluded ("DNA-only" trees) or imputed within taxonomic constraints using branch lengths drawn from local birth-death models ("completed" trees). Joining time-scaled patches to backbones results in species-level trees of extant Mammalia with all branches estimated under the same modeling framework, thereby facilitating rate comparisons among lineages as disparate as marsupials and placentals. We compare our phylogenetic trees to previous estimates of mammal-wide phylogeny and divergence times, finding that (1) node ages are broadly concordant among studies, and (2) recent (tip-level) rates of speciation are estimated more accurately in our study than in previous "supertree" approaches, in which unresolved nodes led to branch-length artifacts. Credible sets of mammalian phylogenetic history are now available for download at http://vertlife.org/phylosubsets, enabling investigations of long-standing questions in comparative biology.
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Affiliation(s)
- Nathan S. Upham
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
- Center for Biodiversity & Global Change, Yale University, New Haven, Connecticut, United States of America
| | - Jacob A. Esselstyn
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Walter Jetz
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
- Center for Biodiversity & Global Change, Yale University, New Haven, Connecticut, United States of America
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35
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Zachos FE, Christidis L, Garnett ST. Mammalian species and the twofold nature of taxonomy: a comment on Taylor et al. 2019. MAMMALIA 2019. [DOI: 10.1515/mammalia-2019-0009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Abstract
In a recently published paper, Taylor and colleagues discussed different approaches and interpretations of mammalian taxonomy and their bearing on more general issues such as conservation and evolutionary biology. We fully endorse the fundamental importance of taxonomy and its being grounded on scientific principles. However, we also deplore a lack of awareness in the literature of the fact that taxonomy is a twofold enterprise that encompasses not only (i) the scientific description and quantitative analysis of biodiversity but also (ii) an executive decision as to how the results of (i) are translated into names. This has serious ramifications for the conservation of our planet’s dwindling biodiversity and when taxonomic names are used as raw data for ecological and evolutionary analyses.
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Affiliation(s)
- Frank E. Zachos
- Natural History Museum Vienna , Mammal Collection , Burgring 7 , 1010 Vienna , Austria
- Department of Genetics , University of the Free State , PO Box 339 , Bloemfontein , South Africa
- Department of Integrative Zoology , University of Vienna , Althanstraße 14 , 1090 Vienna , Austria
| | - Les Christidis
- School of Environment, Science and Engineering , Southern Cross University , Coffs Harbour , NSW 2450 , Australia
| | - Stephen T. Garnett
- Research Institute for the Environment and Livelihoods , Charles Darwin University , Darwin , NT 0909 , Australia
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36
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Minelli A. The galaxy of the non-Linnaean nomenclature. HISTORY AND PHILOSOPHY OF THE LIFE SCIENCES 2019; 41:31. [PMID: 31435827 DOI: 10.1007/s40656-019-0271-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 08/08/2019] [Indexed: 06/10/2023]
Abstract
Contrary to the traditional claim that needs for unambiguous communication about animal and plant species are best served by a single set of names (Linnaean nomenclature) ruled by international Codes, I suggest that a more diversified system is required, especially to cope with problems emerging from aggregation of biodiversity data in large databases. Departures from Linnaean nomenclature are sometimes intentional, but there are also other, less obvious but widespread forms of not Code-compliant grey nomenclature. A first problem is due to the circumstance that the Codes are intended to rule over the way names are applied to species and other taxonomic units, whereas users of taxonomy need names to be applied to specimens. For different reasons, it is often impossible to refer a specimen with certainty to a named species, and in those cases an open nomenclature is employed. Second, molecular taxonomy leads to the discovery of clusters of gene sequence diversity not necessarily equivalent to the species recognized and named by taxonomists. Those clusters are mostly indicated with informal names or formulas that challenge comparison between different publications or databases. In several instances, it is not even clear if a formula refers to an individual voucher specimen, or is a provisional species name. The use of non-Linnaean names and formulas must be revised and strengthened by fixing standard formats for the different kinds of objects or hypotheses and providing permanent association of 'grey names' with standardized source information such as author and year. In the context of a broad-scope revisitation of aims and scope of scientific nomenclature, it may be worth rethinking if natural objects like plant galls and lichens, although other than the 'single-entity' objects traditionally covered by biological classifications, may nevertheless deserve taxonomic names.
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Affiliation(s)
- Alessandro Minelli
- Department of Biology, University of Padova, Via Ugo Bassi 58 B, 35131, Padua, Italy.
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37
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Taxonomic anarchy or an inconvenient truth for conservation? Accelerated species discovery reveals evolutionary patterns and heightened extinction threat in Afro-Malagasy small mammals. MAMMALIA 2019. [DOI: 10.1515/mammalia-2018-0031] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
AbstractWe respond to recent criticisms of supposed “taxonomic anarchy” which is said to hamper conservation efforts. Using examples from African small mammals, we document recent increases of 13% (rodents) and 18% (bats) over the past three decades in the number of recognized species of Afro-Malagasy rodents and bats. By reference to a number of case studies involving Afro-Malagasy taxa (predominantly from montane habitats), and a suggested four-criterion approach to delimiting species accurately, we show that these increases are a genuine reflection of speciation in cryptic species complexes. Moreover, we show that some of these cryptic species are subject to increased extinction risks due to small population size and anthropogenic changes (habitat degradation and climate change). These changes were captured accurately in a recent Mammal Red List of South Africa, Lesotho and Swaziland, indicating that taxonomists and conservationists can work together to assess the Red List status of cryptic species based on robust taxonomic revisions.
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38
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Zhang W, Li F, Whiting-Wagner N, Li Y. Alternative treatments of genetic distances for species delimitation in Callosciurinae and Sciurinae (Rodentia: Sciuridae). Gene 2019; 702:56-65. [PMID: 30926308 DOI: 10.1016/j.gene.2019.03.048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Revised: 03/16/2019] [Accepted: 03/21/2019] [Indexed: 11/17/2022]
Abstract
There are many DNA taxonomy methods available, but single-locus data coupled with distance-based analyses still dominate species identification in practice. Genetic distance thresholds are often used for assigning genetic diversity into entities corresponding to species but are criticized for non-universality or arbitrary. This study investigated an alternative approach for determining genetic thresholds that used iteratively sister-clade clustering for sister species boundary detection within a phylogenetic framework. This method was separately applied to two close subfamilies of Callosciurinae and Sciurinae in Rodentia using the cyt b gene. Our results showed that genetic thresholds for Callosciurinae and Sciurinae were 4.0% and 6.0%, respectively, indicating that the optimized thresholds could be lineage-specific. The use of these thresholds for taxa partitioning yielded a very similar putative species number as the prevailing ABGD method, and increased species diversity by 74.2% and 20.7% in Callosciurinae and Sciurinae, respectively. This suggested that additional cryptic species were present that warrant further investigation. We further tested the performance limitation of our method by simulating the impacts of tree construction and sampling limitation. The results showed that it preformed equally well for different trees but failed to work when inter- or intraspecific sampling is insufficient. These findings support the feasibility of this approach as an alternative tool for species delineation when only single-locus information is available for large datasets.
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Affiliation(s)
- Wei Zhang
- Marine College, Shandong University (Weihai), 180 Wenhua Xilu, Weihai 264209, China
| | - Fangle Li
- Marine College, Shandong University (Weihai), 180 Wenhua Xilu, Weihai 264209, China
| | - Nathan Whiting-Wagner
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523-1878, USA
| | - Yuchun Li
- Marine College, Shandong University (Weihai), 180 Wenhua Xilu, Weihai 264209, China.
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39
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Mori E, Nerva L, Lovari S. Reclassification of the serows and gorals: the end of a neverending story? Mamm Rev 2019. [DOI: 10.1111/mam.12154] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Emiliano Mori
- Dipartimento di Scienze della VitaUniversità degli Studi di Siena Via P.A. Mattioli 4 53100 Siena Italy
| | - Luca Nerva
- Research Centre for Viticulture and EnologyCREA Via XXVIII Aprile 26 31015 Conegliano (Treviso) Italy
- Institute for Sustainable Plant Protection Strada delle Cacce 73 10135 Torino Italy
| | - Sandro Lovari
- Dipartimento di Scienze della VitaUniversità degli Studi di Siena Via P.A. Mattioli 4 53100 Siena Italy
- Museo di Storia Naturale della Maremma Strada Corsini 5 58100 Grosseto Italy
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40
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Stanton DWG, Frandsen P, Waples RK, Heller R, Russo IRM, Orozco-terWengel PA, Pedersen CET, Siegismund HR, Bruford MW. More grist for the mill? Species delimitation in the genomic era and its implications for conservation. CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01149-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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41
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Fin whale (Balaenoptera physalus) mitogenomics: A cautionary tale of defining sub-species from mitochondrial sequence monophyly. Mol Phylogenet Evol 2019; 135:86-97. [PMID: 30771513 DOI: 10.1016/j.ympev.2019.02.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 01/30/2019] [Accepted: 02/04/2019] [Indexed: 11/22/2022]
Abstract
The advent of massive parallel sequencing technologies has resulted in an increase of studies based upon complete mitochondrial genome DNA sequences that revisit the taxonomic status within and among species. Spatially distinct monophyly in such mitogenomic genealogies, i.e., the sharing of a recent common ancestor among con-specific samples collected in the same region has been viewed as evidence for subspecies. Several recent studies in cetaceans have employed this criterion to suggest subsequent intraspecific taxonomic revisions. We reason that employing intra-specific, spatially distinct monophyly at non-recombining, clonally inherited genomes is an unsatisfactory criterion for defining subspecies based upon theoretical (genetic drift) and practical (sampling effort) arguments. This point was illustrated by a re-analysis of a global mitogenomic assessment of fin whales, Balaenoptera physalus spp., published by Archer et al. (2013), which proposed to further subdivide the Northern Hemisphere fin whale subspecies, B. p. physalus. The proposed revision was based upon the detection of spatially distinct monophyly among North Atlantic and North Pacific fin whales in a genealogy based upon complete mitochondrial genome DNA sequences. The extended analysis conducted in this study (1676 mitochondrial control region, 162 complete mitochondrial genome DNA sequences and 20 microsatellite loci genotyped in 380 samples) revealed that the apparent monophyly among North Atlantic fin whales reported by Archer et al. (2013) to be due to low sample sizes. In conclusion, defining sub-species from monophyly (i.e., the absence of para- or polyphyly) can lead to erroneous conclusions due to relatively "trivial" aspects, such as sampling. Basic population genetic processes (i.e., genetic drift and migration) also affect the time to the most recent common ancestor and hence the probability that individuals in a sample are monophyletic.
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42
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Yusefi GH, Faizolahi K, Darvish J, Safi K, Brito JC. The species diversity, distribution, and conservation status of the terrestrial mammals of Iran. J Mammal 2019. [DOI: 10.1093/jmammal/gyz002] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Affiliation(s)
- Gholam Hosein Yusefi
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da, Universidade do Porto, R. Padre Armando Quintas, Vairão, Portugal
- Departamento de Biologia da Faculdade de Ciências da, Universidade do Porto, R. Campo Alegre, Porto, Portugal
- Mohitban Society, Tehran, Iran
| | - Kaveh Faizolahi
- Paazan, Iranian Mammal Quarterly, Tavana Building, Khanbabaee Aly., Ashrafi Esfahani str., Tehran, Iran
| | - Jamshid Darvish
- Department of Biology, Faculty of Sciences, Ferdowsi University of Mashhad, Mashhad, Iran
- Rodentology Research Department, Institute of Applied Zoology, Faculty of Sciences, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Kamran Safi
- Max Planck Institute for Ornithology, Vogelwarte Radolfzell, Radolfzell, Germany
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - José Carlos Brito
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da, Universidade do Porto, R. Padre Armando Quintas, Vairão, Portugal
- Departamento de Biologia da Faculdade de Ciências da, Universidade do Porto, R. Campo Alegre, Porto, Portugal
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Krásová J, Mikula O, Mazoch V, Bryja J, Říčan O, Šumbera R. Evolution of the Grey-bellied pygmy mouse group: Highly structured molecular diversity with predictable geographic ranges but morphological crypsis. Mol Phylogenet Evol 2019; 130:143-155. [DOI: 10.1016/j.ympev.2018.10.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 10/03/2018] [Accepted: 10/11/2018] [Indexed: 02/06/2023]
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46
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Norman AJ, Putnam AS, Ivy JA. Use of molecular data in zoo and aquarium collection management: Benefits, challenges, and best practices. Zoo Biol 2018; 38:106-118. [PMID: 30465726 DOI: 10.1002/zoo.21451] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 10/05/2018] [Accepted: 10/12/2018] [Indexed: 01/06/2023]
Abstract
The global zoo and aquarium community widely recognizes that its animal collections and cooperative breeding programs are facing a sustainability crisis. It has become commonly accepted that numerous priority species cannot be maintained unless new management strategies are adopted. While molecular data have the potential to greatly improve management across a range of scenarios, they have been generally underutilized by the zoo and aquarium community. This failure to effectively apply molecular data to collection management has been due, in part, to a paucity of resources within the community on which to base informed decisions about when the use of such data is appropriate and what steps are necessary to successfully integrate data into management. Here, we identify three broad areas of inquiry where molecular data can inform management: 1) taxonomic identification; 2) incomplete or unknown pedigrees; and 3) hereditary disease. Across these topics, we offer a discussion of the advantages, limitations, and considerations for applying molecular data to ex situ animal populations in a style accessible to zoo and aquarium professionals. Ultimately, we intend for this compiled information to serve as a resource for the community to help ensure that molecular projects directly and effectively benefit the long-term persistence of ex situ populations.
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Affiliation(s)
- Anita J Norman
- Department of Life Sciences, San Diego Zoo Global, San Diego, California
| | - Andrea S Putnam
- Department of Life Sciences, San Diego Zoo Global, San Diego, California
| | - Jamie A Ivy
- Department of Life Sciences, San Diego Zoo Global, San Diego, California
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47
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Differentiation underground: Range-wide multilocus genetic structure of the silvery mole-rat does not support current taxonomy based on mitochondrial sequences. Mamm Biol 2018. [DOI: 10.1016/j.mambio.2018.08.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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48
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Taylor PJ, Neef G, Keith M, Weier S, Monadjem A, Parker DM. Tapping into technology and the biodiversity informatics revolution: updated terrestrial mammal list of Angola, with new records from the Okavango Basin. Zookeys 2018. [DOI: 10.3897/zookeys.778.25964] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Using various sources, including the Global Biodiversity Information Facility (GBIF), published literature, recent (2015–2017) collections, as well as bat detector and camera trap surveys with opportunistic sightings and live capture in the upper Okavango catchment in central Angola, we present an updated mammal checklist of 275 species from 15 different orders for Angola (including the Cabinda region). Recent surveys (captures and bat detectors) of small mammals from the upper Okavango catchment yielded 46 species (33 species of bats, ten species of rodents and three species of shrews). One bat (Pipistrellusrusticus, rusty pipistrelle); two rodents (Mussetzeri, Setzer’s mouse and Zelotomyswoosnami, Woosnam’s broad-faced mouse) and one shrew (Suncusvarilla, lesser dwarf shrew) were captured for the first time, in Angola. While our species lists of bats conformed to predicted totals, terrestrial small mammals were under sampled, with only 13 species recorded by our trapping survey compared to a total of 42 shrew and rodent species expected based on GBIF records for the central Angolan highlands. Seven terrestrial small mammal species (one shrew and six rodents) are endemic to the central and western Angolan highlands but none of these were captured in our survey. The bat detector surveys added three further bat species to the country list: Pipistrellushesperidus, Kerivoulaargentata, and Mopsmidas. Camera trap surveys and opportunistic sightings in the upper Okavango catchment in 2016 yielded a total of 35 species of medium-large mammals, from 17 families, although all of these had been reported previously in Angola. GBIF proved to be an excellent source of biodiversity data for Angolan mammals, most importantly for documenting dramatic historical range changes of larger mammals such as the sable (Hippotragusnigerniger), Kirk’s sable (H.nigerkirkii) and the giant sable (H.nigervariani).
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Taylor PJ, Neef G, Keith M, Weier S, Monadjem A, Parker DM. Tapping into technology and the biodiversity informatics revolution: updated terrestrial mammal list of Angola, with new records from the Okavango Basin. Zookeys 2018:51-88. [PMID: 30108429 PMCID: PMC6085403 DOI: 10.3897/zookeys.779.25964] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 06/18/2018] [Indexed: 11/12/2022] Open
Abstract
Using various sources, including the Global Biodiversity Information Facility (GBIF), published literature, recent (2015-2017) collections, as well as bat detector and camera trap surveys with opportunistic sightings and live capture in the upper Okavango catchment in central Angola, we present an updated mammal checklist of 275 species from 15 different orders for Angola (including the Cabinda region). Recent surveys (captures and bat detectors) of small mammals from the upper Okavango catchment yielded 46 species (33 species of bats, ten species of rodents and three species of shrews). One bat (Pipistrellusrusticus, rusty pipistrelle); two rodents (Mussetzeri, Setzer's mouse and Zelotomyswoosnami, Woosnam's broad-faced mouse) and one shrew (Suncusvarilla, lesser dwarf shrew) were captured for the first time, in Angola. While our species lists of bats conformed to predicted totals, terrestrial small mammals were under sampled, with only 13 species recorded by our trapping survey compared to a total of 42 shrew and rodent species expected based on GBIF records for the central Angolan highlands. Seven terrestrial small mammal species (one shrew and six rodents) are endemic to the central and western Angolan highlands but none of these were captured in our survey. The bat detector surveys added three further bat species to the country list: Pipistrellushesperidus, Kerivoulaargentata, and Mopsmidas. Camera trap surveys and opportunistic sightings in the upper Okavango catchment in 2016 yielded a total of 35 species of medium-large mammals, from 17 families, although all of these had been reported previously in Angola. GBIF proved to be an excellent source of biodiversity data for Angolan mammals, most importantly for documenting dramatic historical range changes of larger mammals such as the sable (Hippotragusnigerniger), Kirk's sable (H.nigerkirkii) and the giant sable (H.nigervariani).
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Affiliation(s)
- Peter J Taylor
- South African Research Chair on Biodiversity Value & Change and Core Team Member of the Centre for Invasion Biology, University of Venda, Thohoyandou 0950, South Africa University of VendaThohoyandouSouth Africa.,School of Life Sciences, University of KwaZulu-Natal Private Bag X54001, Durban 4000, South Africa University of KwaZulu-NatalDurbanSouth Africa.,National Geographic Okavango Wilderness Project, Wild Bird Trust, South Africa National Geographic Okavango Wilderness ProjectJohannesburgSouth Africa
| | - Götz Neef
- National Geographic Okavango Wilderness Project, Wild Bird Trust, South Africa National Geographic Okavango Wilderness ProjectJohannesburgSouth Africa
| | - Mark Keith
- National Geographic Okavango Wilderness Project, Wild Bird Trust, South Africa National Geographic Okavango Wilderness ProjectJohannesburgSouth Africa.,Eugène Marais Chair of Wildlife Management, Mammal Research Institute, University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028, South Africa University of PretoriaPretoriaSouth Africa
| | - Sina Weier
- South African Research Chair on Biodiversity Value & Change and Core Team Member of the Centre for Invasion Biology, University of Venda, Thohoyandou 0950, South Africa University of VendaThohoyandouSouth Africa.,National Geographic Okavango Wilderness Project, Wild Bird Trust, South Africa National Geographic Okavango Wilderness ProjectJohannesburgSouth Africa
| | - Ara Monadjem
- Department of Biological Sciences, University of Swaziland, Private Bag 4, Kwaluseni, Swaziland University of SwazilandKwaluseniSwaziland.,Mammal Research Institute, Department of Zoology & Entomology, University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028, South Africa University of PretoriaPretoriaSouth Africa
| | - Daniel M Parker
- National Geographic Okavango Wilderness Project, Wild Bird Trust, South Africa National Geographic Okavango Wilderness ProjectJohannesburgSouth Africa.,School of Biology and Environmental Sciences, University of Mpumalanga, Private Bag X11283, Nelspruit, 1200, South Africa University of MpumalangaNelspruitSouth Africa.,Wildlife and Reserve Management Research Group, Department of Zoology and Entomology, Rhodes University, Grahamstown, 6140, South Africa Rhodes UniversityGrahamstownSouth Africa
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50
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Tougard C, Justy F, Guinand B, Douzery EJP, Berrebi P. Salmo macrostigma (Teleostei, Salmonidae): Nothing more than a brown trout (S. trutta) lineage? JOURNAL OF FISH BIOLOGY 2018; 93:302-310. [PMID: 29992566 DOI: 10.1111/jfb.13751] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 03/07/2018] [Indexed: 06/08/2023]
Abstract
We examined specimens of the macrostigma trout Salmo macrostigma, which refers to big black spots on the flanks, to assess whether it is an example of taxonomic inflation within the brown trout Salmo trutta complex. Using new specimens, publicly available data and a mitogenomic protocol to amplify the control and cytochrome b regions of the mitochondrial genome from degraded museum samples, including one syntype specimen, the present study shows that the macrostigma trout is not a valid species. Our results suggest the occurrence of a distinct evolutionary lineage of S. trutta in North Africa and Sicily. The name of the North African lineage is proposed for this lineage, which was found to be sister to the Atlantic lineage of brown trout, S. trutta.
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Affiliation(s)
| | - Fabienne Justy
- ISEM, CNRS, Université de Montpellier, IRD, EPHE, Montpellier, France
| | - Bruno Guinand
- ISEM, CNRS, Université de Montpellier, IRD, EPHE, Montpellier, France
| | | | - Patrick Berrebi
- ISEM, CNRS, Université de Montpellier, IRD, EPHE, Montpellier, France
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