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Josić D, Çoraman E, Waurick I, Franzenburg S, Ancillotto L, Bajić B, Budinski I, Dietz C, Görföl T, Hayden Bofill SI, Presetnik P, Russo D, Spada M, Zrnčić V, Blom MPK, Mayer F. Cryptic hybridization between the ancient lineages of Natterer's bat (Myotis nattereri). Mol Ecol 2024; 33:e17411. [PMID: 38785347 DOI: 10.1111/mec.17411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 04/16/2024] [Accepted: 05/08/2024] [Indexed: 05/25/2024]
Abstract
Studying hybrid zones that form between morphologically cryptic taxa offers valuable insights into the mechanisms of cryptic speciation and the evolution of reproductive barriers. Although hybrid zones have long been the focus of evolutionary studies, the awareness of cryptic hybrid zones increased recently due to rapidly growing evidence of biological diversity lacking obvious phenotypic differentiation. The characterization of cryptic hybrid zones with genome-wide analysis is in its early stages and offers new perspectives for studying population admixture and thus the impact of gene flow. In this study, we investigate the population genomics of the Myotis nattereri complex in one of its secondary contact zones, where a putative hybrid zone is formed between two of its cryptic lineages. By utilizing a whole-genome shotgun sequencing approach, we aim to characterize this cryptic hybrid zone in detail. Demographic analysis suggests that the cryptic lineages diverged during the Pliocene, c. 3.6 million years ago. Despite this ancient separation, the populations in the contact zone exhibit mitochondrial introgression and a considerable amount of mixing in nuclear genomes. The genomic structure of the populations corresponds to geographic locations and the genomic admixture changes along a geographic gradient. These findings suggest that there is no effective hybridization barrier between both lineages, nevertheless, their population structure is shaped by dispersal barriers. Our findings highlight how such deeply diverged cryptic lineages can still readily hybridize in secondary contact.
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Affiliation(s)
- Darija Josić
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Emrah Çoraman
- Department of Ecology and Evolution, Eurasia Institute of Earth Sciences, Istanbul Technical University, İstanbul, Türkiye
| | - Isabelle Waurick
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Sören Franzenburg
- IKMB, Institute of Clinical Molecular Biology, University of Kiel, Kiel, Germany
| | - Leonardo Ancillotto
- Laboratory of Animal Ecology and Evolution (AnEcoEvo), Dipartimento di Agraria, Universita degli Studi di Napoli Federico II, Portici, Italy
| | - Branka Bajić
- Department of Genetic Research, Institute for Biological Research 'Siniša Stanković' - National Institute of Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Ivana Budinski
- Department of Genetic Research, Institute for Biological Research 'Siniša Stanković' - National Institute of Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | | | - Tamás Görföl
- Department of Zoology, Hungarian Natural History Museum, Budapest, Hungary
- National Laboratory of Virology, University of Pécs, Pécs, Hungary
| | - Sofia I Hayden Bofill
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Primož Presetnik
- Centre for Cartography of Fauna and Flora, Miklavž na Dravskem Polju, Slovenia
| | - Danilo Russo
- Laboratory of Animal Ecology and Evolution (AnEcoEvo), Dipartimento di Agraria, Universita degli Studi di Napoli Federico II, Portici, Italy
| | - Martina Spada
- Dipartimento Ambiente-Salute-Sicurezza, Universita degli Studi dell'Insubria, Varese, Italy
| | - Vida Zrnčić
- Croatian Biospeleogical Society Zagreb, Zagreb, Croatia
| | - Mozes P K Blom
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Frieder Mayer
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
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Kruskop SV, Zhukova SS. Are Abnormally Large Eastern Bent-Wing Bats, Miniopterus fuliginosus, the Result of a Feature Shift or the Result of Hybridization? DOKLADY BIOLOGICAL SCIENCES : PROCEEDINGS OF THE ACADEMY OF SCIENCES OF THE USSR, BIOLOGICAL SCIENCES SECTIONS 2023; 513:S65-S71. [PMID: 38430299 DOI: 10.1134/s0012496624700911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 01/11/2024] [Accepted: 01/12/2024] [Indexed: 03/03/2024]
Abstract
During a study of morphological variations in bent-wing bats (Miniopterus), we found that specimens originating from the Cao Bang province of Vietnam, identified as M. fuliginosus, were closer in size to the larger species, M. magnater. Mitochondrial gene analysis clearly places these specimens in the former species. At the same time, morphometric analysis of 21 cranial measurements definitely puts these specimens closer to M. magnater and shows their differences from M. fuliginosus samples from different parts of the species range. We assume that, in the low mountains of northern Vietnam and southern China, M. fuliginosus, due to as yet unknown circumstances, occupies the niche of a larger species. However insufficient data on nuclear markers also assume a hybrid origin of this population, with mtDNA introgression from another species.
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Affiliation(s)
- S V Kruskop
- Zoological Museum, Moscow State University, Moscow, Russia.
- Joint Russian-Vietnamese Tropical Scientific Research and Technology Center, Hanoi, Vietnam.
| | - S S Zhukova
- Biological Faculty, Moscow State University, Moscow, Russia
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Kusuminda T, Mannakkara A, Ukuwela KDB, Kruskop SV, Amarasinghe CJ, Saikia U, Venugopal P, Karunarathna M, Gamage R, Ruedi M, Csorba G, Yapa WB, Patterson BD. DNA Barcoding and Morphological Analyses Reveal a Cryptic Species of Miniopterus from India and Sri Lanka. ACTA CHIROPTEROLOGICA 2022. [DOI: 10.3161/15081109acc2022.24.1.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Tharaka Kusuminda
- Department of Agricultural Biology, Faculty of Agriculture, University of Ruhuna, Kamburupitiya, Sri Lanka
| | - Amani Mannakkara
- Department of Agricultural Biology, Faculty of Agriculture, University of Ruhuna, Kamburupitiya, Sri Lanka
| | - Kanishka D. B. Ukuwela
- Department of Biological Sciences, Faculty of Applied Sciences, Rajarata University of Sri Lanka, Mihintale, Sri Lanka
| | - Sergei V. Kruskop
- Zoological Museum of M.V. Lomonosov Moscow State University, Ul. Bol'shata Nikitskaya, 2, Moscow 125009, Russia
| | | | - Uttam Saikia
- Zoological Survey of India, North Eastern Regional Centre, Risa Colony, Shillong 793003, Meghalaya, India
| | - Parvathy Venugopal
- Bat Conservation Trust, London, 8 Battersea Park Road, London SW8 4BG, UK
| | | | | | - Manuel Ruedi
- Department of Vertebrates, Natural History Museum of Geneva, Route de Malagnou 1, 1208 Geneva, Switzerland
| | - Gábor Csorba
- Department of Zoology, Hungarian Natural History Museum, Baross utca 13, Budapest, H-1088, Hungary
| | - Wipula B. Yapa
- Department of Zoology and Environment Sciences, Faculty of Science, University of Colombo, Sri Lanka
| | - Bruce D. Patterson
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, Illinois, USA
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Adavoudi R, Pilot M. Consequences of Hybridization in Mammals: A Systematic Review. Genes (Basel) 2021; 13:50. [PMID: 35052393 PMCID: PMC8774782 DOI: 10.3390/genes13010050] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 12/14/2021] [Accepted: 12/20/2021] [Indexed: 12/18/2022] Open
Abstract
Hybridization, defined as breeding between two distinct taxonomic units, can have an important effect on the evolutionary patterns in cross-breeding taxa. Although interspecific hybridization has frequently been considered as a maladaptive process, which threatens species genetic integrity and survival via genetic swamping and outbreeding depression, in some cases hybridization can introduce novel adaptive variation and increase fitness. Most studies to date focused on documenting hybridization events and analyzing their causes, while relatively little is known about the consequences of hybridization and its impact on the parental species. To address this knowledge gap, we conducted a systematic review of studies on hybridization in mammals published in 2010-2021, and identified 115 relevant studies. Of 13 categories of hybridization consequences described in these studies, the most common negative consequence (21% of studies) was genetic swamping and the most common positive consequence (8%) was the gain of novel adaptive variation. The total frequency of negative consequences (49%) was higher than positive (13%) and neutral (38%) consequences. These frequencies are biased by the detection possibilities of microsatellite loci, the most common genetic markers used in the papers assessed. As negative outcomes are typically easier to demonstrate than positive ones (e.g., extinction vs hybrid speciation), they may be over-represented in publications. Transition towards genomic studies involving both neutral and adaptive variation will provide a better insight into the real impacts of hybridization.
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Affiliation(s)
| | - Małgorzata Pilot
- Museum and Institute of Zoology, Polish Academy of Sciences, ul. Nadwiślańska 108, 80-680 Gdańsk, Poland;
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Uhrová M, Mikula O, Bennett NC, Van Daele P, Piálek L, Bryja J, Visser JH, Jansen van Vuuren B, Šumbera R. Species limits and phylogeographic structure in two genera of solitary African mole-rats Georychus and Heliophobius. Mol Phylogenet Evol 2021; 167:107337. [PMID: 34757170 DOI: 10.1016/j.ympev.2021.107337] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 10/19/2021] [Accepted: 10/27/2021] [Indexed: 11/28/2022]
Abstract
African mole-rats (Bathyergidae) are an intensively studied family of subterranean rodents including three highly social and three solitary genera. Although their phylogenetic interrelations are clear, genetic diversity and the number of species within each genus is much less certain. Among the solitary genera, Heliophobius and Georychus were for a long time considered as monotypic, but molecular studies demonstrated strong phylogeographic structure within each genus and proposed that they represent complexes of cryptic species. The present study re-evaluates their internal genetic/phylogenetic structure using a combination of methodological approaches. We generated datasets of one mitochondrial and six specifically selected nuclear markers as well as of a large number of double digest restriction site associated (ddRAD) loci and then applied species delimitation analyses based on the multispecies coalescent model or clustering on co-ancestry matrices. The population structure was largely congruent across all analyses, but the methods differed in their resolution scale when determining distinct gene pools. While the multispecies coalescent model distinguished five Georychus and between eleven to thirteen Heliophobius gene pools in both Sanger sequenced and ddRAD loci, two clustering algorithms revealed significantly finer or coarser structure in ddRAD based co-ancestry matrices. Tens of clusters were distinguished by fineRADstructure and one (in Georychus) or two clusters (in Heliophobius) by Infomap. The divergence dating of the bathyergid phylogeny estimated that diversification within both genera coincided with the onset of the Pleistocene and was likely driven by repeated large-scale climatic changes. Based on this updated genetic evidence, we suggest recognizing one species of Georychus and two species of Heliophobius, corresponding to a northern and southern major lineage, separated by the Eastern Arc Mountains. Yet, the final taxonomic revision should await integrated evidence stemming from e.g.. morphological, ecological, or behavioral datasets.
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Affiliation(s)
- M Uhrová
- Department of Zoology, Faculty of Sciences, University of South Bohemia
| | - O Mikula
- Department of Zoology, Faculty of Sciences, University of South Bohemia; Institute of Vertebrate Biology, Czech Academy of Sciences
| | - N C Bennett
- Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, 0002, South Africa
| | - P Van Daele
- Department of Zoology, Faculty of Sciences, University of South Bohemia
| | - L Piálek
- Department of Zoology, Faculty of Sciences, University of South Bohemia
| | - J Bryja
- Institute of Vertebrate Biology, Czech Academy of Sciences
| | - J H Visser
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park, Johannesburg, South Africa; Department of Conservation and Marine Sciences, Cape Peninsula University of Technology, P.O. Box 652, Cape Town 8000, South Africa
| | - B Jansen van Vuuren
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park, Johannesburg, South Africa
| | - R Šumbera
- Department of Zoology, Faculty of Sciences, University of South Bohemia
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Kruskop SV, Artyushin IV, Yuzefovich AP, Undrakhbayar E, Speranskya AS, Lisenkova AA, Bannikova AA, Lebedev VS. Genetic Diversity of Mongolian Long-Eared Bats (Plecotus; Vespertilionidae; Chiroptera). ACTA CHIROPTEROLOGICA 2020. [DOI: 10.3161/15081109acc2020.22.2.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Sergei V. Kruskop
- Zoological Museum, Moscow State University, Bolshaya Nikitskaya, 6, 125009 Moscow, Russia
| | - Iliya V. Artyushin
- Lomonosov Moscow State University, Vorobievy Gory, 119991 Moscow, Russia
| | | | - Enkhbat Undrakhbayar
- Institute of General and Experimental Biology of Mongolian Academy of Science, 13330 Ulaanbaatar, Mongolia
| | - Anna S. Speranskya
- Central Research Institute of Epidemiology, Novogireevskaya, 3a, 111123 Moscow, Russia
| | | | - Anna A. Bannikova
- Lomonosov Moscow State University, Vorobievy Gory, 119991 Moscow, Russia
| | - Vladimir S. Lebedev
- Zoological Museum, Moscow State University, Bolshaya Nikitskaya, 6, 125009 Moscow, Russia
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Kafaei S, Sharifi M, Akmali V. Population Genetic Structure and Phylogeography of the Small Mouse-Tailed Bat, Rhinopoma muscatellum Thomas, 1903 (Chiroptera: Rhinopomatidae) in Iran Inferred from Mitochondrial DNA. ACTA CHIROPTEROLOGICA 2020. [DOI: 10.3161/15081109acc2020.22.1.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Sasan Kafaei
- Department of Biology, Faculty of Science, Razi University, Kermanshah, Iran
| | - Mozafar Sharifi
- Department of Biology, Faculty of Science, Razi University, Kermanshah, Iran
| | - Vahid Akmali
- Department of Biology, Faculty of Science, Razi University, Kermanshah, Iran
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8
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Furman A, Çelik YE, Çoraman E, Bilgin R. Reproductive Isolation and Morphological Discrimination of Myotis myotis Macrocephalicus and M. Blythii s.l. (Chiroptera: Vespertilionidae) in Turkey. ACTA CHIROPTEROLOGICA 2020. [DOI: 10.3161/15081109acc2020.22.1.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Andrzej Furman
- Institute of Environmental Sciences, Bo—aziçi University, Hisar Campus, Bebek 34342, Istanbul, Turkey
| | - Yalin Emek Çelik
- Institute of Environmental Sciences, Bo—aziçi University, Hisar Campus, Bebek 34342, Istanbul, Turkey
| | - Emrah Çoraman
- Department of Ecology and Evolution, Eurasia Institute of Earth Sciences, Istanbul Technical University, Maslak, Istanbul, 34469, Turkey
| | - Raşit Bilgin
- Institute of Environmental Sciences, Bo—aziçi University, Hisar Campus, Bebek 34342, Istanbul, Turkey
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Çoraman E, Dundarova H, Dietz C, Mayer F. Patterns of mtDNA introgression suggest population replacement in Palaearctic whiskered bat species. ROYAL SOCIETY OPEN SCIENCE 2020; 7:191805. [PMID: 32742679 PMCID: PMC7353987 DOI: 10.1098/rsos.191805] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 04/23/2020] [Indexed: 06/11/2023]
Abstract
Secondary contacts can play a major role in the evolutionary histories of species. Various taxa diverge in allopatry and later on come into secondary contact during range expansions. When they meet, their interactions and the extent of gene flow depend on the level of their ecological differentiation and the strength of their reproductive isolation. In this study, we present the multilocus phylogeography of two cryptic whiskered bat species, Myotis mystacinus and M. davidii, with a particular focus on their putative sympatric zone. Our findings suggest that M. mystacinus and M. davidii evolved in allopatry and came into secondary contact during range expansions. Individuals in the area of secondary contact, in Anatolia and the Balkans, have discordant population assignments based on the mitochondrial and the nuclear datasets. These observed patterns suggest that the local M. mystacinus populations hybridized with expanding M. davidii populations, which resulted in mitochondrial introgression from the former. In the introgression area, M. mystacinus individuals with concordant nuclear and mitochondrial genotypes were identified in relatively few locations, suggesting that the indigenous populations might have been largely replaced by invading M. davidii. Changing environmental conditions coupled with ecological competition is the likely reason for this replacement. Our study presents one possible example of a historical population replacement that was captured in phylogeographic patterns.
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Affiliation(s)
- Emrah Çoraman
- Eurasia Institute of Earth Sciences, Department of Ecology and Evolution, Istanbul Technical University, Maslak, Istanbul 34469, Turkey
- Museum für Naturkunde, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, Berlin 10115, Germany
- Natural Science Collection, Martin-Luther-University Halle-Wittenberg, Domplatz 4, Halle (Saale) D-06108, Germany
| | - Heliana Dundarova
- Bulgarian Academy of Sciences, Institute of Biodiversity and Ecosystem Research, 1 Tsar Osvoboditel, Sofia 1000, Bulgaria
| | - Christian Dietz
- Biologische Gutachten Dietz, Balinger Str. 15, 72401 Haigerloch, Germany
| | - Frieder Mayer
- Museum für Naturkunde, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, Berlin 10115, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstraße 6, 14195 Berlin, Germany
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10
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Patterson BD, Webala PW, Lavery TH, Agwanda BR, Goodman SM, Peterhans JCK, Demos TC. Evolutionary relationships and population genetics of the Afrotropical leaf-nosed bats (Chiroptera, Hipposideridae). Zookeys 2020; 929:117-161. [PMID: 32390744 PMCID: PMC7197329 DOI: 10.3897/zookeys.929.50240] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 03/16/2020] [Indexed: 11/29/2022] Open
Abstract
The Old World leaf-nosed bats (Hipposideridae) are aerial and gleaning insectivores that occur throughout the Paleotropics. Both their taxonomic and phylogenetic histories are confused. Until recently, the family included genera now allocated to the Rhinonycteridae and was recognized as a subfamily of Rhinolophidae. Evidence that Hipposideridae diverged from both Rhinolophidae and Rhinonycteridae in the Eocene confirmed their family rank, but their intrafamilial relationships remain poorly resolved. We examined genetic variation in the Afrotropical hipposiderids Doryrhina, Hipposideros, and Macronycteris using relatively dense taxon-sampling throughout East Africa and neighboring regions. Variation in both mitochondrial (cyt-b) and four nuclear intron sequences (ACOX2, COPS, ROGDI, STAT5) were analyzed using both maximum likelihood and Bayesian inference methods. We used intron sequences and the lineage delimitation method BPP—a multilocus, multi-species coalescent approach—on supported mitochondrial clades to identify those acting as independent evolutionary lineages. The program StarBEAST was used on the intron sequences to produce a species tree of the sampled Afrotropical hipposiderids. All genetic analyses strongly support generic monophyly, with Doryrhina and Macronycteris as Afrotropical sister genera distinct from a Paleotropical Hipposideros; mitochondrial analyses interpose the genera Aselliscus, Coelops, and Asellia between these clades. Mitochondrial analyses also suggest at least two separate colonizations of Africa by Asian groups of Hipposideros, but the actual number and direction of faunal interchanges will hinge on placement of the unsampled African-Arabian species H.megalotis. Mitochondrial sequences further identify a large number of geographically structured clades within species of all three genera. However, in sharp contrast to this pattern, the four nuclear introns fail to distinguish many of these groups and their geographic structuring disappears. Various distinctive mitochondrial clades are consolidated in the intron-based gene trees and delimitation analyses, calling into question their evolutionary independence or else indicating their very recent divergence. At the same time, there is now compelling genetic evidence in both mitochondrial and nuclear sequences for several additional unnamed species among the Afrotropical Hipposideros. Conflicting appraisals of differentiation among the Afrotropical hipposiderids based on mitochondrial and nuclear loci must be adjudicated by large-scale integrative analyses of echolocation calls, quantitative morphology, and geometric morphometrics. Integrative analyses will also help to resolve the challenging taxonomic issues posed by the diversification of the many lineages associated with H.caffer and H.ruber.
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Affiliation(s)
- Bruce D Patterson
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago IL 60605, USA Field Museum of Natural History Chicago United States of America
| | - Paul W Webala
- Department of Forestry and Wildlife Management, Maasai Mara University, Narok, Kenya Maasai Mara University Narok Kenya
| | - Tyrone H Lavery
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago IL 60605, USA Field Museum of Natural History Chicago United States of America.,Threatened Species Recovery Hub, Fenner School of Environment and Society, The Australian National University, Canberra, ACT, Australia The Australian National University Canberra Australia
| | - Bernard R Agwanda
- Mammalogy Section, National Museums of Kenya, Nairobi, Kenya National Museums of Kenya Nairobi Kenya
| | - Steven M Goodman
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago IL 60605, USA Field Museum of Natural History Chicago United States of America.,Association Vahatra, BP 3972, Antananarivo 101, Madagascar National Museums of Kenya Antananarivo Madagascar
| | - Julian C Kerbis Peterhans
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago IL 60605, USA Field Museum of Natural History Chicago United States of America.,College of Arts and Sciences, Roosevelt University, Chicago, IL, 60605, USA Roosevelt University Chicago United States of America
| | - Terrence C Demos
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago IL 60605, USA Field Museum of Natural History Chicago United States of America
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Schlottau K, Eggerbauer E, Freuling CM, Beer M, Müller T, Hoffmann B. Rapid molecular species identification of indigenous bats from Germany for surveillance purposes. INFECTION GENETICS AND EVOLUTION 2019; 78:104140. [PMID: 31837485 DOI: 10.1016/j.meegid.2019.104140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 11/25/2019] [Accepted: 12/10/2019] [Indexed: 10/25/2022]
Abstract
Chiroptera form the second largest order of mammals and compromise >1200 species, of which only 51 species are abundant in Europe. As bats are important hosts involved in the emergence and spread of zoonotic infections, it is becoming more important to discriminate the different species of bats involved in the maintenance of causative agents. However, traditional taxonomic methods rely on morphological features and are challenging as they require long-lasting experience of an investigator and sometimes fail if the specimen is of poor condition. On the other hand, barcoding requires sequencing and is time consuming. Therefore, a versatile genetic approach for rapid species identification would be valuable. In this study, two mitochondrial loci, cytochrome b (cyt b) and cytochrome c oxidase subunit I (COI) were selected for the development of two multiplex qPCRs for differentiating four very abundant bat species in Germany using DNA extracted from the patagium or organ pools. Verification of the developed assays using a set of 1000 individual bat samples belonging to 20 different European species clearly showed that the multiplex qPCRs were able to determine the four most abundant species in this collection by a COI based qPCR. All other bat species which could not be covered by this approach could be easily identified by sequencing of the amplicon generated by broad-range qPCRs for cyt B and COI, respectively. Moreover, the double-check approach with cyt B and COI makes the identification of bats into species more reliable. The new multiplex PCRs allow a fast and easy genotyping of German bats and could be useful for screening approaches.
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Affiliation(s)
- Kore Schlottau
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Südufer 10, 17493 Greifswald-Insel Riems, Germany.
| | - Elisa Eggerbauer
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Südufer 10, 17493 Greifswald-Insel Riems, Germany
| | - Conrad M Freuling
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Südufer 10, 17493 Greifswald-Insel Riems, Germany
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Südufer 10, 17493 Greifswald-Insel Riems, Germany
| | - Thomas Müller
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Südufer 10, 17493 Greifswald-Insel Riems, Germany
| | - Bernd Hoffmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Südufer 10, 17493 Greifswald-Insel Riems, Germany
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12
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The Skull Integration Pattern and Internal Constraints in Myotis myotis–Myotis blythii Species Group (Vespertilionidae, Chiroptera) Might be Shaped by Natural Selection During Evolution Along the Genetic Line of Least Resistance. Evol Biol 2019. [DOI: 10.1007/s11692-019-09488-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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13
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Gürün K, Furman A, Juste J, Ramos Pereira MJ, Palmeirim JM, Puechmaille SJ, Hulva P, Presetnik P, Hamidovic D, Ibáñez C, Karataş A, Allegrini B, Georgiakakis P, Scaravelli D, Uhrin M, Nicolaou H, Abi-Said MR, Nagy ZL, Gazaryan S, Bilgin R. A continent-scale study of the social structure and phylogeography of the bent-wing bat, Miniopterus schreibersii (Mammalia: Chiroptera), using new microsatellite data. J Mammal 2019. [DOI: 10.1093/jmammal/gyz153] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
AbstractMiniopterus schreibersii is a cave-dwelling bat species with a wide distribution in the western Palearctic spanning southern and central Europe, North Africa, Anatolia, the Middle East, and the Caucasus. We investigated the social structure and its effects on the genetic makeup of this species, using 10 nuclear microsatellite markers and a partial fragment of the mitochondrial cytochrome b gene. Samples were examined from the species' entire circum-Mediterranean range. Local structuring that was previously detected among populations of M. schreibersii using mitochondrial markers was not observed for microsatellite markers, indicating male-biased dispersal for the species. Some support was found for postglacial expansions in Europe, with Anatolia potentially acting as the primary refugium during the Last Glacial Maximum (LGM). However, support for this hypothesis is not as strong as that previously detected using mitochondrial DNA markers. This is likely due to the diminishing effect of male-mediated dispersal, replenishing the nuclear diversity faster than the mitochondrial diversity in regions that are relatively far from the glacial refugia.
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Affiliation(s)
- Kanat Gürün
- Institute of Environmental Sciences, Boğaziçi University, Bebek, Istanbul 34342, Turkey
| | - Andrzej Furman
- Institute of Environmental Sciences, Boğaziçi University, Bebek, Istanbul 34342, Turkey
| | - Javier Juste
- Estación Biológica de Doñana (CSIC), Avda. Américo Vespucio s/n, Seville 41092, Spain
| | - Maria J Ramos Pereira
- CIBER of Epidemiology and Public Health (CIBERESP), Madrid 28029, Spain
- Department of Zoology, Institute of Biosciences, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves 9500, Porto Alegre, RS 91540-000, Brazil
- Centre for Environmental and Marine Studies, Wildlife Research Unit, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Jorge M Palmeirim
- Center for Ecology, Evolution and Environmental Change, Dept. Biologia Animal, Faculdade de Ciencias, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Sebastien J Puechmaille
- University College Dublin, School of Biological and Environmental Sciences, Belfield, Dublin 4, Ireland
- Zoology Institute, University of Greifswald, 17489 Greifswald, Germany
- Chauves-souris Aveyron (CSA), 12310, Vimenet, France
| | - Pavel Hulva
- Department of Zoology, Faculty of Science, Charles University in Prague, Viničná 7, CZ-128 44 Praha 2, Czech Republic
- Department of Biology and Ecology, University of Ostrava, Chittussiho 10, 710 00 Ostrava, Czech Republic
| | - Primoz Presetnik
- Centre for Cartography of Fauna and Flora, Ljubljana Office, Klunova 3, SI-1000, Ljubljana, Slovenia
| | - Daniela Hamidovic
- Croatian Biospeleological Society, Zagreb, Demetrova 1, 10000 Zagreb, Croatia
| | - Carlos Ibáñez
- Estación Biológica de Doñana (CSIC), Avda. Américo Vespucio s/n, Seville 41092, Spain
| | - Ahmet Karataş
- Department of Biology, Niğde University, Niğde 51100, Turkey
| | | | - Panagiotis Georgiakakis
- Natural History Museum of Crete, University of Crete, Knossos Ave., P.O. Box: 2208, GR71 409 Irakleion, Crete, Greece
| | - Dino Scaravelli
- Department Veterinary Medical Sciences, University of Bologna, via Tolara di Sopra 50, 40064 Ozzano dell'Emilia (BO), Italy
| | - Marcel Uhrin
- Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Moyzesova 11, SK-040 01 Košice, Slovakia
- Department of Forest Protection and Wildlife Management, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Kamycká 1176, 165 21 Praha 6, Czech Republic
| | - Haris Nicolaou
- Parks and Environment Sector, Forestry Department, Ministry of Agriculture, Natural Resources and Environment, 1414 Nicosia, Cyprus
| | - Mounir R Abi-Said
- Animal Encounter, Aley, Lebanon
- Faculty of Sciences II, Lebanese University, Al Fanar, 90656 Jdeidet, Lebanon
| | | | - Suren Gazaryan
- Institute of Ecology of Mountain Territories RAS, Armand 37A360000, Nalchik, Russia
| | - Raşit Bilgin
- Institute of Environmental Sciences, Boğaziçi University, Bebek, Istanbul 34342, Turkey
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14
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Mehdizadeh R, Akmali V, Sharifi M. Mitochondrial DNA marker (D-loop) reveals high genetic diversity but low population structure in the pale bent-wing bat (Miniopterus pallidus) in Iran. Mitochondrial DNA A DNA Mapp Seq Anal 2018; 30:424-433. [DOI: 10.1080/24701394.2018.1538365] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Robab Mehdizadeh
- Department of Biology, Faculty of Science, Razi University, Kermanshah, Iran
| | - Vahid Akmali
- Department of Biology, Faculty of Science, Razi University, Kermanshah, Iran
| | - Mozafar Sharifi
- Department of Biology, Faculty of Science, Razi University, Kermanshah, Iran
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15
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Cranial Biometrics of the Iberian Myotis myotis/Myotis blythii Complex: New Data for Studying the Fossil Record. J MAMM EVOL 2018. [DOI: 10.1007/s10914-018-9427-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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16
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Furman A, Çelik YE, Çoraman E. Myotis myotis (Chiroptera: Vespertilionidae) diverges into two distinct, Anatolian and European, populations. Zool J Linn Soc 2017. [DOI: 10.1093/zoolinnean/zlx068] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Andrzej Furman
- Institute of Environmental Sciences, Boğazici University, Hisar Campus, Istanbul, Turkey
| | - Yalin Emek Çelik
- Institute of Environmental Sciences, Boğazici University, Hisar Campus, Istanbul, Turkey
| | - Emrah Çoraman
- Institute of Environmental Sciences, Boğazici University, Hisar Campus, Istanbul, Turkey
- Museum für Naturkunde, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, Invalidenstrasse, Berlin, Germany
- Natural Science Collection, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
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17
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Ammerman LK, Lee DN, Pfau RS. Patterns of Genetic Divergence amongMyotis californicus,M. ciliolabrum, andM. leibiiBased on Amplified Fragment Length Polymorphism. ACTA CHIROPTEROLOGICA 2016. [DOI: 10.3161/15081109acc2016.18.2.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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18
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Postawa T, Nagy Z. Variation of parasitism patterns in bats during hibernation: the effect of host species, resources, health status, and hibernation period. Parasitol Res 2016; 115:3767-78. [PMID: 27240839 PMCID: PMC5040749 DOI: 10.1007/s00436-016-5138-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 05/17/2016] [Indexed: 02/01/2023]
Abstract
During critical periods of food shortage or variable climatic conditions, the choice of an appropriate host can increase the survival and reproductive performance of parasites. In turn, one of the unique adaptations to periodical food shortages is hibernation, which is often found among insectivorous bat species in the temperate zone. While hibernating, bats are completely defenseless against both predators and ectoparasites, their immune and endocrine systems are diminished, and survival is dependent on the accumulated fat reserves. Differences in the health status or in the rate of consumption of the resources might also explain species-specific differences in ectoparasite abundance, especially between closely related host species, such as the greater mouse-eared bat (Myotis myotis) and the lesser mouse-eared bat (M. blythii) during hibernation. In the present study, the abundance of two ecologically distinct (summer and winter) types of ectoparasites was examined in terms of its influence on the body condition and hemoglobin content of the two host species. The effects of demographic factors, such as host sex and age, were also investigated. Despite a similar pattern of deteriorating body condition and hemoglobin concentration, M. myotis was more parasitized than was M. blythii. The marked decrease in hemoglobin content in first-year females of both host species correlated with the highest parasite load and indicated a risk of anemia. At the intraspecific level, ectoparasite abundance was not correlated with body condition (resources), but it negatively affected hemoglobin content; however, this mostly concerned M. blythii, which had a lower parasite load. Therefore, it can be concluded that interspecific differences in ectoparasite abundance may result from parasites selecting the host species that is less sensitive to their activity. In turn, in summer ectoparasites, the preference for female hosts is probably attributable to the likelihood of reinfection rather than to an effect of host resources or health status. The absence of sex-based preferences in winter ectoparasites could be explained by equal host availability.
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Affiliation(s)
- Tomasz Postawa
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Sławkowska 17, 31-016, Kraków, Poland.
| | - Zoltan Nagy
- Foundation for School, Densusianu Str. 6/A, 400428, Cluj-Napoca, Romania
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19
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Jebb D, Foley NM, Puechmaille SJ, Teeling EC. The complete mitochondrial genome of the Greater Mouse-Eared bat, Myotis myotis (Chiroptera: Vespertilionidae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 28:347-349. [PMID: 26713722 DOI: 10.3109/19401736.2015.1122775] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
In this study, we report the complete mitochondrial genome of the Greater Mouse-Eared Bat, Myotis myotis. The mitogenome is 17 213 bp with base composition A (34.2%), G (13%), C (22.4%), and T (30.5%). The genome shows conserved synteny with other mammalian mitogenomes, containing 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and 1 control region (D-Loop). The majority of the genes are encoded on the H-Strand, except for ND6 and eight tRNAs. All protein-coding genes start with the ATG start codon, except for ND2, ND3, and ND5 which begin with ATT or ATA. Seven protein-coding genes terminated in a canonical stop codon, TAA or TAG, five contain incomplete stop codons, T or TA. Cytochrome b terminates in the mitochondria specific stop codon AGA. This mitogenome provides a valuable resource for future studies of M. myotis and other bat and mammal species.
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Affiliation(s)
- David Jebb
- a University College Dublin , Belfield , Dublin , Ireland
| | - Nicole M Foley
- a University College Dublin , Belfield , Dublin , Ireland
| | - Sébastien J Puechmaille
- a University College Dublin , Belfield , Dublin , Ireland.,b Greifswald University , Greifswald , Germany
| | - Emma C Teeling
- a University College Dublin , Belfield , Dublin , Ireland
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20
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Ermakov OA, Simonov E, Surin VL, Titov SV, Brandler OV, Ivanova NV, Borisenko AV. Implications of hybridization, NUMTs, and overlooked diversity for DNA Barcoding of Eurasian ground squirrels. PLoS One 2015; 10:e0117201. [PMID: 25617768 PMCID: PMC4305304 DOI: 10.1371/journal.pone.0117201] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 12/19/2014] [Indexed: 11/30/2022] Open
Abstract
The utility of DNA Barcoding for species identification and discovery has catalyzed a concerted effort to build the global reference library; however, many animal groups of economical or conservational importance remain poorly represented. This study aims to contribute DNA barcode records for all ground squirrel species (Xerinae, Sciuridae, Rodentia) inhabiting Eurasia and to test efficiency of this approach for species discrimination. Cytochrome c oxidase subunit 1 (COI) gene sequences were obtained for 97 individuals representing 16 ground squirrel species of which 12 were correctly identified. Taxonomic allocation of some specimens within four species was complicated by geographically restricted mtDNA introgression. Exclusion of individuals with introgressed mtDNA allowed reaching a 91.6% identification success rate. Significant COI divergence (3.5-4.4%) was observed within the most widespread ground squirrel species (Spermophilus erythrogenys, S. pygmaeus, S. suslicus, Urocitellus undulatus), suggesting the presence of cryptic species. A single putative NUMT (nuclear mitochondrial pseudogene) sequence was recovered during molecular analysis; mitochondrial COI from this sample was amplified following re-extraction of DNA. Our data show high discrimination ability of 100 bp COI fragments for Eurasian ground squirrels (84.3%) with no incorrect assessments, underscoring the potential utility of the existing reference librariy for the development of diagnostic 'mini-barcodes'.
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Affiliation(s)
- Oleg A. Ermakov
- Department of Zoology and Ecology, Penza State University, Penza, Russia
| | - Evgeniy Simonov
- Institute of Systematics and Ecology of Animals, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- Tomsk State University, Tomsk, Russia
| | - Vadim L. Surin
- Hematological Research Center, Russian Academy of Medical Sciences, Moscow, Russia
| | - Sergey V. Titov
- Department of Zoology and Ecology, Penza State University, Penza, Russia
| | - Oleg V. Brandler
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, Russia
| | | | - Alex V. Borisenko
- Biodiversity Institute of Ontario, University of Guelph, Guelph, Canada
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