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Taylor PJ, Kearney TC, Clark VR, Howard A, Mdluli MV, Markotter W, Geldenhuys M, Richards LR, Rakotoarivelo AR, Watson J, Balona J, Monadjem A. Southern Africa's Great Escarpment as an amphitheater of climate-driven diversification and a buffer against future climate change in bats. GLOBAL CHANGE BIOLOGY 2024; 30:e17344. [PMID: 38837566 DOI: 10.1111/gcb.17344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 04/20/2024] [Accepted: 04/29/2024] [Indexed: 06/07/2024]
Abstract
Hosting 1460 plant and 126 vertebrate endemic species, the Great Escarpment (hereafter, Escarpment) forms a semi-circular "amphitheater" of mountains girdling southern Africa from arid west to temperate east. Since arid and temperate biota are usually studied separately, earlier studies overlooked the biogeographical importance of the Escarpment as a whole. Bats disperse more widely than other mammalian taxa, with related species and intraspecific lineages occupying both arid and temperate highlands of the Escarpment, providing an excellent model to address this knowledge gap. We investigated patterns of speciation and micro-endemism from modeled past, present, and future distributions in six clades of southern African bats from three families (Rhinolophidae, Cistugidae, and Vespertilionidae) having different crown ages (Pleistocene to Miocene) and biome affiliations (temperate to arid). We estimated mtDNA relaxed clock dates of key divergence events across the six clades in relation both to biogeographical features and patterns of phenotypic variation in crania, bacula and echolocation calls. In horseshoe bats (Rhinolophidae), both the western and eastern "arms" of the Escarpment have facilitated dispersals from the Afrotropics into southern Africa. Pleistocene and pre-Pleistocene "species pumps" and temperate refugia explained observed patterns of speciation, intraspecific divergence and, in two cases, mtDNA introgression. The Maloti-Drakensberg is a center of micro-endemism for bats, housing three newly described or undescribed species. Vicariance across biogeographic barriers gave rise to 29 micro-endemic species and intraspecific lineages whose distributions were congruent with those identified in other phytogeographic and zoogeographic studies. Although Köppen-Geiger climate models predict a widespread replacement of current temperate ecosystems in southern Africa by tropical or arid ecosystems by 2070-2100, future climate Maxent models for 13 bat species (all but one of those analyzed above) showed minimal range changes in temperate species from the eastern Escarpment by 2070, possibly due to the buffering effect of mountains to climate change.
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Affiliation(s)
- Peter J Taylor
- Afromontane Research Unit & Department of Zoology & Entomology, University of the Free State Qwaqwa Campus, Phuthaditjhaba, South Africa
| | - Teresa C Kearney
- Ditsong National Museum of Natural History, Pretoria, South Africa
- School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Vincent Ralph Clark
- Afromontane Research Unit & Department of Geography, University of the Free State: Qwaqwa Campus, Phuthaditjhaba, South Africa
| | - Alexandra Howard
- Afromontane Research Unit & Department of Zoology & Entomology, University of the Free State Qwaqwa Campus, Phuthaditjhaba, South Africa
| | - Monday V Mdluli
- Afromontane Research Unit & Department of Zoology & Entomology, University of the Free State Qwaqwa Campus, Phuthaditjhaba, South Africa
| | - Wanda Markotter
- Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa
| | - Marike Geldenhuys
- Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa
| | | | - Andrinajoro R Rakotoarivelo
- Afromontane Research Unit & Department of Zoology & Entomology, University of the Free State Qwaqwa Campus, Phuthaditjhaba, South Africa
| | - Johan Watson
- Department of Economic Development, Tourism and Environmental Affairs, Biodiversity Research, Bloemfontein, South Africa
| | - Julio Balona
- Gauteng and Northern Regions Bat Interest Group, Johannesburg, South Africa
| | - Ara Monadjem
- Department of Biological Sciences, University of Eswatini, Kwaluseni, Eswatini
- Mammal Research Institute, Department of Zoology & Entomology, University of Pretoria, Hatfield, South Africa
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Alboasud M, Jeong H, Lee T. Complete Mitochondrial Genomes and Phylogenetic Analysis of Genus Henricia (Asteroidea: Spinulosida: Echinasteridae). Int J Mol Sci 2024; 25:5575. [PMID: 38891763 PMCID: PMC11171911 DOI: 10.3390/ijms25115575] [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: 04/08/2024] [Revised: 05/16/2024] [Accepted: 05/17/2024] [Indexed: 06/21/2024] Open
Abstract
The genus Henricia is known to have intraspecific morphological variations, making species identification difficult. Therefore, molecular phylogeny analysis based on genetic characteristics is valuable for species identification. We present complete mitochondrial genomic sequences of Henricia longispina aleutica, H. reniossa, and H. sanguinolenta for the first time in this study. This study will make a significant contribution to our understanding of Henricia species and its relationships within the class Asteroidea. Lengths of mitochondrial genomes of the three species are 16,217, 16,223, and 16,194 bp, respectively, with a circular form. These genomes contained 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and a D-loop. The gene order and direction aligned with other asteroid species. Phylogenetic relationship analysis showed that our Henricia species were in a monophyletic clade with other Henricia species and in a large clade with species (Echinaster brasiliensis) from the same family. These findings provide valuable insight into understanding the phylogenetic relationships of species in the genus Henricia.
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Affiliation(s)
- Maria Alboasud
- Marine Biological Resource Institute, Sahmyook University, Seoul 01795, Republic of Korea;
- Department of Convergence Science, Sahmyook University, Seoul 01795, Republic of Korea
| | - Hoon Jeong
- Department of Animal Resources Science, Sahmyook University, Seoul 01795, Republic of Korea
| | - Taekjun Lee
- Marine Biological Resource Institute, Sahmyook University, Seoul 01795, Republic of Korea;
- Department of Animal Resources Science, Sahmyook University, Seoul 01795, Republic of Korea
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Weber N, Nagy M, Markotter W, Schaer J, Puechmaille SJ, Sutton J, Dávalos LM, Dusabe MC, Ejotre I, Fenton MB, Knörnschild M, López-Baucells A, Medellin RA, Metz M, Mubareka S, Nsengimana O, O'Mara MT, Racey PA, Tuttle M, Twizeyimana I, Vicente-Santos A, Tschapka M, Voigt CC, Wikelski M, Dechmann DK, Reeder DM. Robust evidence for bats as reservoir hosts is lacking in most African virus studies: a review and call to optimize sampling and conserve bats. Biol Lett 2023; 19:20230358. [PMID: 37964576 PMCID: PMC10646460 DOI: 10.1098/rsbl.2023.0358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 10/25/2023] [Indexed: 11/16/2023] Open
Abstract
Africa experiences frequent emerging disease outbreaks among humans, with bats often proposed as zoonotic pathogen hosts. We comprehensively reviewed virus-bat findings from papers published between 1978 and 2020 to evaluate the evidence that African bats are reservoir and/or bridging hosts for viruses that cause human disease. We present data from 162 papers (of 1322) with original findings on (1) numbers and species of bats sampled across bat families and the continent, (2) how bats were selected for study inclusion, (3) if bats were terminally sampled, (4) what types of ecological data, if any, were recorded and (5) which viruses were detected and with what methodology. We propose a scheme for evaluating presumed virus-host relationships by evidence type and quality, using the contrasting available evidence for Orthoebolavirus versus Orthomarburgvirus as an example. We review the wording in abstracts and discussions of all 162 papers, identifying key framing terms, how these refer to findings, and how they might contribute to people's beliefs about bats. We discuss the impact of scientific research communication on public perception and emphasize the need for strategies that minimize human-bat conflict and support bat conservation. Finally, we make recommendations for best practices that will improve virological study metadata.
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Affiliation(s)
- Natalie Weber
- Department of Migration, Max Planck Institute of Animal Behavior, Radolfzell, Germany
- University of Ulm, Institute of Evolutionary Ecology and Conservation Genomics, Ulm, Germany
| | - Martina Nagy
- Museum für Naturkunde, Leibniz-Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Wanda Markotter
- Centre for Viral Zoonoses, Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Juliane Schaer
- Museum für Naturkunde, Leibniz-Institute for Evolution and Biodiversity Science, Berlin, Germany
- Institute of Biology, Humboldt University, Berlin, Germany
| | - Sébastien J. Puechmaille
- ISEM, University of Montpellier, Montpellier, France
- Institut Universitaire de France, Paris, France
- Zoological Institute and Museum, University of Greifswald, Greifswald, Germany
| | | | - Liliana M. Dávalos
- Department of Ecology and Evolution and Consortium for Inter-Disciplinary Environmental Research, Stony Brook University, Stony Brook, USA
| | | | - Imran Ejotre
- Institute of Biology, Humboldt University, Berlin, Germany
- Muni University, Arua, Uganda
| | - M. Brock Fenton
- Department of Biology, University of Western Ontario, London, Ontario, Canada
| | - Mirjam Knörnschild
- Museum für Naturkunde, Leibniz-Institute for Evolution and Biodiversity Science, Berlin, Germany
- Evolutionary Ethology, Institute for Biology, Humboldt-Universität zu Berlin, Berlin, Germany
- Smithsonian Tropical Research Institute, Balboa, Ancón, Panama
| | | | - Rodrigo A. Medellin
- Institute of Ecology, National Autonomous University of Mexico, Mexico City, Mexico
| | | | - Samira Mubareka
- Sunnybrook Research Institute and Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | | | - M. Teague O'Mara
- Department of Migration, Max Planck Institute of Animal Behavior, Radolfzell, Germany
- Smithsonian Tropical Research Institute, Balboa, Ancón, Panama
- Bat Conservation International Austin, TX, USA
- Department of Biological Sciences, Southeastern Louisiana University, Hammond, LA, USA
| | - Paul A. Racey
- Centre for Ecology and Conservation, University of Exeter, Exeter, UK
| | - Merlin Tuttle
- Merlin Tuttle's Bat Conservation, Austin, TX USA
- Department of Integrative Biology, University of Texas, Austin, USA
| | | | - Amanda Vicente-Santos
- Graduate Program in Population Biology, Ecology and Emory University, Atlanta, GA, USA
- Department of Biology, University of Oklahoma, Norman, OK, USA
| | - Marco Tschapka
- University of Ulm, Institute of Evolutionary Ecology and Conservation Genomics, Ulm, Germany
- Smithsonian Tropical Research Institute, Balboa, Ancón, Panama
| | | | - Martin Wikelski
- Department of Migration, Max Planck Institute of Animal Behavior, Radolfzell, Germany
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Dina K.N. Dechmann
- Department of Migration, Max Planck Institute of Animal Behavior, Radolfzell, Germany
- Smithsonian Tropical Research Institute, Balboa, Ancón, Panama
- Department of Biology, University of Konstanz, Konstanz, Germany
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Benda P, Uvizl M, Vallo P, Reiter A, Uhrin M. A Revision of the Rhinolophus hipposideros group (Chiroptera: Rhinolophidae) with Definition of an Additional Species from the Middle East. ACTA CHIROPTEROLOGICA 2023. [DOI: 10.3161/15081109acc2022.24.2.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Petr Benda
- Department of Zoology, Department of Zoology, National Museum (Natural History), Václavské nám. 68, CZ-115 79 Praha 1, Czech Republic
| | - Marek Uvizl
- Department of Zoology, Department of Zoology, National Museum (Natural History), Václavské nám. 68, CZ-115 79 Praha 1, Czech Republic
| | - Peter Vallo
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Květná 8, CZ-603 65 Brno, Czech Republic
| | - Antonín Reiter
- South Moravian Museum in Znojmo, Přemyslovců 129/8, CZ-669 02 Znojmo, Czech Republic
| | - Marcel Uhrin
- Department of Zoology, Institute of Biology and Ecology, Faculty of Science, P. J. Šafárik University, Šrobárova 2, SK-041 80 Košice, Slovakia
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Howard A, Monadjem A, MacFadyen D, Chimimba CT. Testing the efficacy of bat monitoring methods for identification and species surveys in KwaZulu-Natal province, South Africa. AFRICAN ZOOLOGY 2022. [DOI: 10.1080/15627020.2022.2138722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Affiliation(s)
- Alexandra Howard
- Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
- Department of Zoology and Entomology, University of the Free State, Phuthaditjhaba, South Africa
| | - Ara Monadjem
- Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
- Department of Biological Sciences, University of Eswatini, Kwaluseni, Eswatini
| | - Duncan MacFadyen
- Department of Research and Conservation, Oppenheimer Generations, Johannesburg, South Africa
| | - Christian T Chimimba
- Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
- DSI-NRF Centre of Excellence for Invasion Biology (CIB), Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
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Chornelia A, Hughes AC. The evolutionary history and ancestral biogeographic range estimation of old-world Rhinolophidae and Hipposideridae (Chiroptera). BMC Ecol Evol 2022; 22:112. [PMID: 36192699 PMCID: PMC9528145 DOI: 10.1186/s12862-022-02066-x] [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: 04/13/2022] [Accepted: 09/15/2022] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Family Rhinolophidae (horseshoe bats), Hipposideridae (leaf-nosed bats) and Rhinonycteridae (trident bats) are exclusively distributed in the Old-World, and their biogeography reflects the complex historic geological events throughout the Cenozoic. Here we investigated the origin of these families and unravel the conflicting family origin theories using a high resolution tree covering taxa from each zoogeographic realm from Africa to Australia. Ancestral range estimations were performed using a probabilistic approach implemented in BioGeoBEARS with subset analysis per biogeographic range [Old-World as whole, Australia-Oriental-Oceania (AOO) and Afrotropical-Madagascar-Palearctic (AMP)]. RESULT Our result supports an Oriental origin for Rhinolophidae, whereas Hipposideridae originated from the Oriental and African regions in concordance with fossil evidence of both families. The fossil evidence indicates that Hipposideridae has diversified across Eurasia and the Afro-Arabian region since the Middle Eocene. Meanwhile, Rhinonycteridae (the sister family of Hipposideridae) appears to have originated from the Africa region splitting from the common ancestor with Hipposideridae in Africa. Indomalaya is the center of origin of Rhinolophidae AOO lineages, and Indomalayan + Philippines appears to be center of origin of Hipposideridae AOO lineage indicating allopatric speciation and may have involved jump-dispersal (founder-event) speciation within AOO lineage. Wallacea and the Philippines may have been used as stepping stones for dispersal towards Oceania and Australia from the Oriental region. Multiple colonization events via different routes may have occurred in the Philippines (i.e., Palawan and Wallacea) since the Late Miocene. The colonization of Rhinolophidae towards Africa from Asia coincided with the estimated time of Tethys Ocean closure around the Oligocene to Miocene (around 27 Ma), allowing species to disperse via the Arabian Peninsula. Additionally, the number of potential cryptic species in Rhinolophidae in Southeast Asia may have increased since Plio-Pleistocene and late Miocene. CONCLUSION Overall, we conclude an Oriental origin for Rhinolophidae, and Oriental + African for Hipposideridae. The result demonstrates that complex historical events, in addition to species specific ecomorphology and specialization of ecological niches may shape current distributions.
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Affiliation(s)
- Ada Chornelia
- grid.9227.e0000000119573309Landscape Ecology Group, Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden (XTBG), Chinese Academy of Sciences, Yunnan, People’s Republic of China ,grid.410726.60000 0004 1797 8419International College, University of Chinese Academy of Sciences (UCAS), Huairou, Beijing, People’s Republic of China ,grid.194645.b0000000121742757School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong SAR People’s Republic of China
| | - Alice Catherine Hughes
- grid.194645.b0000000121742757School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong SAR People’s Republic of China
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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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Finger NM, Holderied M, Jacobs DS. Detection distances in desert dwelling, high duty cycle echolocators: A test of the foraging habitat hypothesis. PLoS One 2022; 17:e0268138. [PMID: 35588425 PMCID: PMC9119505 DOI: 10.1371/journal.pone.0268138] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 04/24/2022] [Indexed: 11/18/2022] Open
Abstract
High Duty Cycle (HDC) echolocating bats use high frequency echolocation pulses that are clutter resistant, but their high frequencies give them limited range. Despite their unique ability to reject background clutter while simultaneously detecting fluttering prey, the frequency of their echolocation pulses has a strong correlation with level of environmental clutter, lower frequency pulses of HDC bats being associated with more open environments. The Foraging Habitat Hypothesis (FHH) proposes that the ecological significance of these lower frequency pulses in HDC bats in open environments is that they allow longer prey detection distances. To test the FHH, we compared the frequencies, Source Levels (SLs) and detection distances of Rhinolophus capensis, a HDC bat that has been shown to vary its call frequency in relation to habitat structure. As a further test of the FHH we investigated the SLs and detection distances of Rhinolophus damarensis (a heterospecific species that occurs in the same open desert environment as R. capensis but echolocates at a higher dominant pulse frequency). In the open desert, R. capensis emitted both lower frequency and higher SL pulses giving them longer detection distances than R. capensis in the cluttered fynbos. SL contributed more to differences in detection distances in both R. capensis and R. damarensis than frequency. In a few instances, R. damarensis achieved similar detection distances to desert–inhabiting R. capensis by emitting much higher SLs despite their average SLs being lower. These results suggest that lower frequency echolocation pulses are not a prerequisite for open desert living but may increase detection distance while avoiding energetic costs required for high SLs.
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Affiliation(s)
- Nikita M. Finger
- Department of Biological Sciences, University of Cape Town, Cape Town, South Africa
| | - Marc Holderied
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - David S. Jacobs
- Department of Biological Sciences, University of Cape Town, Cape Town, South Africa
- * E-mail:
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Hutter CR, Cobb KA, Portik DM, Travers SL, Wood PL, Brown RM. FrogCap: A modular sequence capture probe-set for phylogenomics and population genetics for all frogs, assessed across multiple phylogenetic scales. Mol Ecol Resour 2022; 22:1100-1119. [PMID: 34569723 DOI: 10.1111/1755-0998.13517] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 09/08/2021] [Accepted: 09/14/2021] [Indexed: 12/01/2022]
Abstract
Despite the prevalence of high-throughput sequencing in phylogenetics, many relationships remain difficult to resolve because of conflicting signal among genomic regions. Selection of different types of molecular markers from different genomic regions is required to overcome these challenges. For evolutionary studies in frogs, we introduce the publicly available FrogCap suite of genomic resources, which is a large collection of ~15,000 markers that unifies previous genetic sequencing efforts. FrogCap is designed to be modular, such that subsets of markers and SNPs can be selected based on the desired phylogenetic scale. FrogCap uses a variety of marker types that include exons and introns, ultraconserved elements, and previously sequenced Sanger markers, which span up to 10,000 bp in alignment lengths; in addition, we demonstrate potential for SNP-based analyses. We tested FrogCap using 121 samples distributed across five phylogenetic scales, comparing probes designed using a consensus- or exemplar genome-based approach. Using the consensus design is more resilient to issues with sensitivity, specificity, and missing data than picking an exemplar genome sequence. We also tested the impact of different bait kit sizes (20,020 vs. 40,040) on depth of coverage and found triple the depth for the 20,020 bait kit. We observed sequence capture success (i.e., missing data, sequenced markers/bases, marker length, and informative sites) across phylogenetic scales. The incorporation of different marker types is effective for deep phylogenetic relationships and shallow population genetics studies. Having demonstrated FrogCap's utility and modularity, we conclude that these new resources are efficacious for high-throughput sequencing projects across variable timescales.
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Affiliation(s)
- Carl R Hutter
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
| | - Kerry A Cobb
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
| | - Daniel M Portik
- California Academy of Sciences, San Francisco, California, USA
| | - Scott L Travers
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
- Department of Biological Sciences, Rutgers University-Newark, Newark, New Jersey, USA
| | - Perry L Wood
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
| | - Rafe M Brown
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
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Chornelia A, Lu J, Hughes AC. How to Accurately Delineate Morphologically Conserved Taxa and Diagnose Their Phenotypic Disparities: Species Delimitation in Cryptic Rhinolophidae (Chiroptera). Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.854509] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Systematics and taxonomy are the backbone of all components of biology and ecology, yet cryptic species present a major challenge for accurate species identification. This is especially problematic as they represent a substantial portion of undiscovered biodiversity, and have implications for not only species conservation, but even assaying potential risk of zoonotic spillover. Here, we use integrative approaches to delineate potential cryptic species in horseshoe bats (Rhinolophidae), evaluate the phenotypic disparities between cryptic species, and identify key traits for their identification. We tested the use of multispecies coalescent models (MSC) using Bayesian Phylogenetic and Phylogeography (BPP) and found that BPP was useful in delineating potential cryptic species, and consistent with acoustic traits. Our results show that around 40% of Asian rhinolophid species are potentially cryptic and have not been formally described. In order to avoid potential misidentification and allow species to be accurately identified, we identified quantitative noseleaf sella and acoustic characters as the most informative traits in delineating between potential cryptic species in Rhinolophidae. This highlights the physical differences between cryptic species that are apparent in noseleaf traits which often only qualitatively described but rarely measured. Each part of the noseleaf including the sella, lateral lappets, and lancet furrows, play roles in focusing acoustic beams and thus, provide useful characteristics to identify cryptic Rhinolophus species. Finally, species delimitation for cryptic species cannot rely on genetic data alone, but such data should be complemented by other evidence, including phenotypic, acoustic data, and geographic distributions to ensure accurate species identification and delineation.
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Idnan M, Mansoor S, Khawar MB, Javid A, Hussain A, Imran M, Ullah A. Range extension and species confirmation of Rhyneptesicus nasutus (Sind Serotine Bat) (Mammalia:Chiroptera) from Bajaur Agency, FATA, Pakistan. Mol Biol Rep 2022; 49:1791-1797. [PMID: 34981337 DOI: 10.1007/s11033-021-06989-4] [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: 08/27/2021] [Accepted: 11/18/2021] [Indexed: 10/19/2022]
Abstract
BACKGROUND The lack of morphological differentiation among chiropteran species and cryptic speciation impedes species identification. DNA-based approaches help species identification and contribute to the discovery of additional species. Rhyneptesicus nasutus (Sind Serotine Bat) is a rare and poorly studied species in Pakistan. METHODS This study explores the range extension of Sind Bat within the territorial limits of Pakistan from Sind and Baluchistan to Federally Administered Areas of Pakistan. No molecular record exists for the species in Pakistan. In the present study, we for the first time confirm species identification of Rhyneptesicus nasutus from Pakistan using a genetic marker (cytochrome b) along with morphometric analysis. A neighbor-joining tree based on Kimura-2 parameters was created to infer phylogenetic relationships. We sequenced the cytochrome b gene segment and conducted a phylogenetic analysis with previously published data from other countries. RESULTS Sequences from Pakistan formed a clade with Iranian Rhyneptesicus nasutus specimens suggesting a common ancestry. Various morphometric parameters (mean values) were measured, including Head and Body length (44.3 mm), Tail length (43.4 mm), Hindfoot length (8.3 mm), Forearm length (35.7 mm), and Ear length 36 mm while 5th Metacarpal Length, 4th Metacarpal Length, and 3rd Metacarpal Lengths were 33.2 mm, 34.7 mm, and 35.3 mm. Approaches based on DNA barcoding reveal a high diversity of bat species in the study area. CONCLUSION The data will enable researchers to build an improved evolutionary framework of the Serotine Bats from this region and subsequently reconstruct a detailed evolutionary history of the genus. Further research is required to test other molecular markers to support the findings of the current study in Pakistan.
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Affiliation(s)
- Muhammad Idnan
- Department of Wildlife and Ecology, University of Veterinary and Animal Sciences, Lahore, Pakistan. .,Department of Zoology, Faculty of Sciences, University of Central Punjab, Lahore, Pakistan.
| | - Sajid Mansoor
- Department of Microbiology, Faculty of Life Science, University of Central Punjab, Lahore, Pakistan
| | - Muhammad Babar Khawar
- Department of Zoology, Faculty of Sciences, University of Central Punjab, Lahore, Pakistan
| | - Arshad Javid
- Department of Wildlife and Ecology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Ali Hussain
- Department of Wildlife and Ecology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Muhammad Imran
- Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Arif Ullah
- Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, Pakistan
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12
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Uvizl M, Benda P. Intraspecific Variation of Myotis emarginatus (Chiroptera: Vespertilionidae) Inferred from Mitochondrial and Nuclear Genetic Markers. ACTA CHIROPTEROLOGICA 2022. [DOI: 10.3161/15081109acc2021.23.2.002] [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)
- Marek Uvizl
- Department of Zoology, Faculty of Science, Charles University in Prague, Viničná 7, 128 44 Praha 2, Czech Republic
| | - Petr Benda
- Department of Zoology, Faculty of Science, Charles University in Prague, Viničná 7, 128 44 Praha 2, Czech Republic
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13
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Peres PHF, Luduvério DJ, Bernegossi AM, Galindo DJ, Nascimento GB, Oliveira ML, Sandoval EDP, Vozdova M, Kubickova S, Cernohorska H, Duarte JMB. Revalidation of Mazama rufa (Illiger 1815) (Artiodactyla: Cervidae) as a Distinct Species out of the Complex Mazama americana (Erxleben 1777). Front Genet 2022; 12:742870. [PMID: 34970296 PMCID: PMC8712859 DOI: 10.3389/fgene.2021.742870] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 11/09/2021] [Indexed: 11/13/2022] Open
Abstract
The red brocket deer Mazama americana Erxleben, 1777 is considered a polyphyletic complex of cryptic species with wide chromosomal divergence. Evidence indicates that the observed chromosomal divergences result in reproductive isolation. The description of a neotype for M. americana allowed its genetic characterization and represented a comparative basis to resolve the taxonomic uncertainties of the group. Thus, we designated a neotype for the synonym Mazama rufa Illiger, 1815 and tested its recognition as a distinct species from the M. americana complex with the analysis of morphological, cytogenetic and molecular data. We also evaluated its distribution by sampling fecal DNA in the wild. Morphological data from craniometry and body biometry indicated an overlap of quantitative measurements between M. rufa and the entire M. americana complex. The phylogenetic hypothesis obtained through mtDNA confirmed the reciprocal monophyly relationship between M. americana and M. rufa, and both were identified as distinct molecular operational taxonomic units by the General Mixed Yule Coalescent species delimitation analysis. Finally, classic cytogenetic data and fluorescence in situ hybridization with whole chromosome painting probes showed M. rufa with a karyotype of 2n = 52, FN = 56. Comparative analysis indicate that at least fifteen rearrangements separate M. rufa and M. americana (sensu stricto) karyotypes, which confirmed their substantial chromosomal divergence. This divergence should represent an important reproductive barrier and allow its characterization as a distinct and valid species. Genetic analysis of fecal samples demonstrated a wide distribution of M. rufa in the South American continent through the Atlantic Forest, Cerrado and south region of Amazon. Thus, we conclude for the revalidation of M. rufa as a distinct species under the concept of biological isolation, with its karyotype as the main diagnostic character. The present work serves as a basis for the taxonomic review of the M. americana complex, which should be mainly based on cytogenetic characterization and directed towards a better sampling of the Amazon region, the evaluation of available names in the species synonymy and a multi-locus phylogenetic analysis.
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Affiliation(s)
- Pedro H F Peres
- Deer Research and Conservation Center (NUPECCE), São Paulo State University (UNESP), Jaboticabal, Brazil
| | - Douglas J Luduvério
- Deer Research and Conservation Center (NUPECCE), São Paulo State University (UNESP), Jaboticabal, Brazil
| | - Agda Maria Bernegossi
- Deer Research and Conservation Center (NUPECCE), São Paulo State University (UNESP), Jaboticabal, Brazil
| | - David J Galindo
- Faculty of Veterinary Medicine, National University of San Marcos (UNMSM), Lima, Peru
| | | | - Márcio L Oliveira
- Deer Research and Conservation Center (NUPECCE), São Paulo State University (UNESP), Jaboticabal, Brazil
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14
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Mutumi GL, Jacobs DS, Bam L. Geographic variation in the skulls of the horseshoe bats, Rhinolophus simulator and R. cf. simulator: Determining the relative contributions of adaptation and drift using geometric morphometrics. Ecol Evol 2021; 11:15916-15935. [PMID: 34824800 PMCID: PMC8601903 DOI: 10.1002/ece3.8262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 09/21/2021] [Accepted: 09/21/2021] [Indexed: 11/07/2022] Open
Abstract
The relative contributions of adaptation and genetic drift to morphological diversification of the skulls of echolocating mammals were investigated using two horseshoe bat species, Rhinolophus simulator and R. cf. simulator, as test cases. We used 3D geometric morphometrics to compare the shapes of skulls of the two lineages collected at various localities in southern Africa. Size and shape variation was predominantly attributed to selective forces; the between-population variance (B) was not proportional to the within-population variance (W). Modularity was evident in the crania of R. simulator but absent in the crania of R. cf. simulator and the mandibles of both species. The skulls of the two lineages thus appeared to be under different selection pressures, despite the overlap in their distributions. Difference in the crania of R. cf. simulator was centered largely on the nasal dome region of R. cf. simulator but on the cranium and mandibles of R. simulator. It is likely that the size and shape of the nasal dome, which acts as a frequency-dependent acoustic horn, is more crucial in R. cf. simulator than in R. simulator because of the higher echolocation frequencies used by R. cf. simulator. A larger nasal dome in R. cf. simulator would allow the emission of higher intensity pulses, resulting in comparable detection distances to that of R. simulator. In contrast, selection pressure is probably more pronounced on the mandibles and cranium of R. simulator to compensate for the loss in bite force because of its elongated rostrum. The predominance of selection probably reflects the stringent association between environment and the optimal functioning of phenotypic characters associated with echolocation and feeding in bats.
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Affiliation(s)
- Gregory L. Mutumi
- Animal Evolution and Systematics Group (AES)Department of Biological SciencesUniversity of Cape TownCape TownSouth Africa
- Life and Environmental Sciences DepartmentUniversity of California–MercedMercedCaliforniaUSA
| | - David S. Jacobs
- Animal Evolution and Systematics Group (AES)Department of Biological SciencesUniversity of Cape TownCape TownSouth Africa
| | - Lunga Bam
- Radiation Science DepartmentSouth Africa Nuclear Energy CorporationPretoriaSouth Africa
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15
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Doniol‐Valcroze P, Ursenbacher S, Mebert K, Ghielmi S, Laddaga L, Sourrouille P, Kariş M, Crochet P. Conflicting relationships of
Vipera walser
inferred from nuclear genes sequences and mitochondrial DNA. J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12543] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Sylvain Ursenbacher
- Department of Environmental Sciences Section of Conservation Biology University of Basel Basel Switzerland
- Info fauna ‐ karch University of Neuchâtel Neuchâtel Switzerland
| | - Konrad Mebert
- IDECCInstitute of Development, Ecology, Conservation and Cooperation Rome Italy
| | - Samuele Ghielmi
- Tropical Biodiversity Section MUSE ‐ Museo delle Scienze Trento Italy
| | - Lorenzo Laddaga
- Società di Scienze Naturali del Verbano Cusio Ossola Museo di Scienze Naturali Collegio Mellerio Rosmini Domodossola Italy
| | | | - Mert Kariş
- Program of Laboratory Technology Department of Chemistry and Chemical Process Technologies Acıgöl Vocational School of Technical Sciences Nevşehir Hacı Bektaş Veli University Nevşehir Turkey
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16
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Idnan M, Javid A, Tayyab M, Hussain A, Mansoor S, Bukhari SM, Irfan, Shahbaz M, Rehman KU, Andleeb S, Azam SM, Ali W. Molecular identification of genus Pipistrellus (Mammalia: Chiroptera) from Fata region, Pakistan. BRAZ J BIOL 2021; 83:e246322. [PMID: 34431908 DOI: 10.1590/1519-6984.246322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 02/02/2021] [Indexed: 11/22/2022] Open
Abstract
A total of 10 specimens were captured from selected sites of Bajaur Agency FATA, Pakistan using mist nets. The captured specimens were morphologically identified and various morphometric measurements were taken. The head and Body length (HB) of Pipistrellus coromondra and Pipistrellus kuhlii lepidus (n=10) was 43±0.11 mm and 45±1.1 respectively. Morphologically identified Pipistrellus kuhlii confirmed as Pipistrellus kuhlii lepidus based on 16S rRNA sequences. The DNA sequences were submitted to GenBank and accession numbers were obtained (MN 719478 and MT430902). The available 16S rRNA gene sequences of Pipistrellus coromondra and Pipistrellus kuhlii lepidus were retrieved from NCBI and incorporated in N-J tree analysis. Overall, the interspecific genetic variations among Pipistrellus coromondra and Pipistrellus kuhlii lepidus were 8% and 1% respectively. In our recommendation, a comprehensive molecular identification of bats is need of hour to report more cryptic and new species from Pakistan.
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Affiliation(s)
- M Idnan
- University of Veterinary and Animal Sciences, Department of Wildlife and Ecology, Lahore, Pakistan
| | - A Javid
- University of Veterinary and Animal Sciences, Department of Wildlife and Ecology, Lahore, Pakistan
| | - M Tayyab
- University of Veterinary and Animal Sciences, Institute of Biochemistry and Biotechnology, Lahore, Pakistan
| | - A Hussain
- University of Veterinary and Animal Sciences, Department of Wildlife and Ecology, Lahore, Pakistan
| | - S Mansoor
- University of Central Punjab, Faculty of Life Sciences, Department of Microbiology, Lahore, Pakistan
| | - S M Bukhari
- University of Veterinary and Animal Sciences, Department of Wildlife and Ecology, Lahore, Pakistan
| | - Irfan
- Cholistan University of Veterinary and Animal Sciences, Department of Zoology, Lahore, Pakistan
| | - M Shahbaz
- Women University Azad Jamu and Kashmir, Department of Zoology, Bagh, Pakistan
| | - K Ur Rehman
- Govt. College Women University, Department of environmental Sciences, Sailkot, Pakistan
| | - S Andleeb
- Govt. College Women University, Department of environmental Sciences, Sailkot, Pakistan
| | - S M Azam
- University of Education, Department of Zoology, Lahore, Pakistan
| | - W Ali
- University of Veterinary and Animal Sciences, Department of Wildlife and Ecology, Lahore, Pakistan
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17
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Tu VT, Görföl T, Csorba G, Arai S, Kikuchi F, Fukui D, Koyabu D, Furey NM, Bawm S, Lin KS, Alviola P, Hang CT, Son NT, Tuan TA, Hassanin A. Integrative taxonomy and biogeography of Asian yellow house bats (Vespertilionidae:
Scotophilus
) in the Indomalayan Region. J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Vuong Tan Tu
- Institute of Ecology and Biological Resources Vietnam Academy of Science and Technology Hanoi Vietnam
- Graduate University of Science and TechnologyVietnam Academy of Science and Technology Hanoi Vietnam
- Institut de Systématique, Évolution, Biodiversité (ISYEB) Sorbonne UniversitéMNHNCNRSEPHE, UA ‐ Muséum National d’Histoire Naturelle Paris France
- Service de Systématique Moléculaire UMS 2700 Muséum national d’Histoire naturelle Paris France
| | - Tamás Görföl
- Department of Zoology Hungarian Natural History Museum Budapest Hungary
- National Laboratory of Virology Szentágothai Research Centre University of Pécs Pécs Hungary
| | - Gábor Csorba
- Department of Zoology Hungarian Natural History Museum Budapest Hungary
| | - Satoru Arai
- Infectious Disease Surveillance Center National Institute of Infectious Diseases Shinjuku, Tokyo Japan
| | - Fuka Kikuchi
- Infectious Disease Surveillance Center National Institute of Infectious Diseases Shinjuku, Tokyo Japan
- Tokyo University of Science Shinjuku, Tokyo Japan
- Research and Education Center for Prevention of Global Infectious Diseases of Animals Tokyo University of Agriculture and Technology Fuchu, Tokyo Japan
| | - Dai Fukui
- The University of Tokyo Hokkaido Forest Graduate School of Agricultural and Life Sciences The University of Tokyo Hokkaido Japan
| | - Daisuke Koyabu
- Jockey Club College of Veterinary Medicine and Life Sciences City University of Hong Kong Kowloon Hong Kong
- Department of Molecular Craniofacial Embryology Graduate School of Medical and Dental Sciences Tokyo Medical and Dental University Bunkyo‐ku, Tokyo Japan
| | - Neil M. Furey
- Fauna & Flora International, Cambodia Programme Chamkarmorn, Phnom Penh Cambodia
- Harrison InstituteBowerwood House Sevenoaks Kent UK
| | - Saw Bawm
- University of Veterinary Science Yezin, Nay Pyi Taw Myanmar
| | - Kyaw San Lin
- University of Veterinary Science Yezin, Nay Pyi Taw Myanmar
| | - Phillip Alviola
- Institute of Biological Sciences and Museum of Natural History University of the Philippines Los Banos Laguna Philippines
| | - Chu Thi Hang
- Institute of Ecology and Biological Resources Vietnam Academy of Science and Technology Hanoi Vietnam
- Graduate University of Science and TechnologyVietnam Academy of Science and Technology Hanoi Vietnam
| | - Nguyen Truong Son
- Institute of Ecology and Biological Resources Vietnam Academy of Science and Technology Hanoi Vietnam
- Graduate University of Science and TechnologyVietnam Academy of Science and Technology Hanoi Vietnam
| | - Tran Anh Tuan
- Institute of Ecology and Biological Resources Vietnam Academy of Science and Technology Hanoi Vietnam
- Graduate University of Science and TechnologyVietnam Academy of Science and Technology Hanoi Vietnam
| | - Alexandre Hassanin
- Institut de Systématique, Évolution, Biodiversité (ISYEB) Sorbonne UniversitéMNHNCNRSEPHE, UA ‐ Muséum National d’Histoire Naturelle Paris France
- Service de Systématique Moléculaire UMS 2700 Muséum national d’Histoire naturelle Paris France
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18
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Gaudino M, Aurine N, Dumont C, Fouret J, Ferren M, Mathieu C, Reynard O, Volchkov VE, Legras-Lachuer C, Georges-Courbot MC, Horvat B. High Pathogenicity of Nipah Virus from Pteropus lylei Fruit Bats, Cambodia. Emerg Infect Dis 2021; 26:104-113. [PMID: 31855143 PMCID: PMC6924896 DOI: 10.3201/eid2601.191284] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We conducted an in-depth characterization of the Nipah virus (NiV) isolate previously obtained from a Pteropus lylei bat in Cambodia in 2003 (CSUR381). We performed full-genome sequencing and phylogenetic analyses and confirmed CSUR381 is part of the NiV-Malaysia genotype. In vitro studies revealed similar cell permissiveness and replication of CSUR381 (compared with 2 other NiV isolates) in both bat and human cell lines. Sequence alignments indicated conservation of the ephrin-B2 and ephrin-B3 receptor binding sites, the glycosylation site on the G attachment protein, as well as the editing site in phosphoprotein, suggesting production of nonstructural proteins V and W, known to counteract the host innate immunity. In the hamster animal model, CSUR381 induced lethal infections. Altogether, these data suggest that the Cambodia bat-derived NiV isolate has high pathogenic potential and, thus, provide insight for further studies and better risk assessment for future NiV outbreaks in Southeast Asia.
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19
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Wells HL, Letko M, Lasso G, Ssebide B, Nziza J, Byarugaba DK, Navarrete-Macias I, Liang E, Cranfield M, Han BA, Tingley MW, Diuk-Wasser M, Goldstein T, Johnson CK, Mazet JAK, Chandran K, Munster VJ, Gilardi K, Anthony SJ. The evolutionary history of ACE2 usage within the coronavirus subgenus Sarbecovirus. Virus Evol 2021; 7:veab007. [PMID: 33754082 PMCID: PMC7928622 DOI: 10.1093/ve/veab007] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 1 (SARS-CoV-1) and SARS-CoV-2 are not phylogenetically closely related; however, both use the angiotensin-converting enzyme 2 (ACE2) receptor in humans for cell entry. This is not a universal sarbecovirus trait; for example, many known sarbecoviruses related to SARS-CoV-1 have two deletions in the receptor binding domain of the spike protein that render them incapable of using human ACE2. Here, we report three sequences of a novel sarbecovirus from Rwanda and Uganda that are phylogenetically intermediate to SARS-CoV-1 and SARS-CoV-2 and demonstrate via in vitro studies that they are also unable to utilize human ACE2. Furthermore, we show that the observed pattern of ACE2 usage among sarbecoviruses is best explained by recombination not of SARS-CoV-2, but of SARS-CoV-1 and its relatives. We show that the lineage that includes SARS-CoV-2 is most likely the ancestral ACE2-using lineage, and that recombination with at least one virus from this group conferred ACE2 usage to the lineage including SARS-CoV-1 at some time in the past. We argue that alternative scenarios such as convergent evolution are much less parsimonious; we show that biogeography and patterns of host tropism support the plausibility of a recombination scenario, and we propose a competitive release hypothesis to explain how this recombination event could have occurred and why it is evolutionarily advantageous. The findings provide important insights into the natural history of ACE2 usage for both SARS-CoV-1 and SARS-CoV-2 and a greater understanding of the evolutionary mechanisms that shape zoonotic potential of coronaviruses. This study also underscores the need for increased surveillance for sarbecoviruses in southwestern China, where most ACE2-using viruses have been found to date, as well as other regions such as Africa, where these viruses have only recently been discovered.
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Affiliation(s)
- H L Wells
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, 1200 Amsterdam Ave, New York, NY 10027, USA
| | - M Letko
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 903 S. 4th St, Hamilton, MT 59840, USA.,Paul G. Allen School for Global Animal Health, Washington State University, 1155 College Ave, Pullman, WA 99164, USA
| | - G Lasso
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY 10462, USA
| | - B Ssebide
- Gorilla Doctors, c/o MGVP, Inc., 1089 Veterinary Medicine Drive, Davis, CA 95616, USA
| | - J Nziza
- Gorilla Doctors, c/o MGVP, Inc., 1089 Veterinary Medicine Drive, Davis, CA 95616, USA
| | - D K Byarugaba
- Makerere University Walter Reed Project, Plot 42, Nakasero Road, Kampala, Uganda.,Makerere University, College of Veterinary Medicine, Living Stone Road, Kampala, Uganda
| | - I Navarrete-Macias
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, 722 W 168th St, New York, NY 10032, USA
| | - E Liang
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, 722 W 168th St, New York, NY 10032, USA
| | - M Cranfield
- One Health Institute and Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California Davis, 1089 Veterinary Medicine Drive, Davis, CA 95616, USA.,Department of Microbiology and Immunology, University of North Carolina School of Medicine, 125 Mason Farm Road, Chapel Hill, NC 27599, USA
| | - B A Han
- Cary Institute of Ecosystem Studies, 2801 Sharon Turnpike, Millbrook, NY 12545, USA
| | - M W Tingley
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, 612 Charles E. Young Drive South, Los Angeles, CA 90095, USA
| | - M Diuk-Wasser
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, 1200 Amsterdam Ave, New York, NY 10027, USA
| | - T Goldstein
- One Health Institute and Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California Davis, 1089 Veterinary Medicine Drive, Davis, CA 95616, USA
| | - C K Johnson
- One Health Institute and Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California Davis, 1089 Veterinary Medicine Drive, Davis, CA 95616, USA
| | - J A K Mazet
- One Health Institute and Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California Davis, 1089 Veterinary Medicine Drive, Davis, CA 95616, USA
| | - K Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY 10462, USA
| | - V J Munster
- Paul G. Allen School for Global Animal Health, Washington State University, 1155 College Ave, Pullman, WA 99164, USA
| | - K Gilardi
- Makerere University Walter Reed Project, Plot 42, Nakasero Road, Kampala, Uganda.,One Health Institute and Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California Davis, 1089 Veterinary Medicine Drive, Davis, CA 95616, USA
| | - S J Anthony
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California Davis, One Shields Avenue, Davis, CA 95616, USA
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20
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Wells H, Letko M, Lasso G, Ssebide B, Nziza J, Byarugaba D, Navarrete-Macias I, Liang E, Cranfield M, Han B, Tingley M, Diuk-Wasser M, Goldstein T, Johnson C, Mazet J, Chandran K, Munster V, Gilardi K, Anthony S. The evolutionary history of ACE2 usage within the coronavirus subgenus Sarbecovirus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2020.07.07.190546. [PMID: 32676605 PMCID: PMC7359528 DOI: 10.1101/2020.07.07.190546] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
SARS-CoV-1 and SARS-CoV-2 are not phylogenetically closely related; however, both use the ACE2 receptor in humans for cell entry. This is not a universal sarbecovirus trait; for example, many known sarbecoviruses related to SARS-CoV-1 have two deletions in the receptor binding domain of the spike protein that render them incapable of using human ACE2. Here, we report three sequences of a novel sarbecovirus from Rwanda and Uganda which are phylogenetically intermediate to SARS-CoV-1 and SARS-CoV-2 and demonstrate via in vitro studies that they are also unable to utilize human ACE2. Furthermore, we show that the observed pattern of ACE2 usage among sarbecoviruses is best explained by recombination not of SARS-CoV-2, but of SARS-CoV-1 and its relatives. We show that the lineage that includes SARS-CoV-2 is most likely the ancestral ACE2-using lineage, and that recombination with at least one virus from this group conferred ACE2 usage to the lineage including SARS-CoV-1 at some time in the past. We argue that alternative scenarios such as convergent evolution are much less parsimonious; we show that biogeography and patterns of host tropism support the plausibility of a recombination scenario; and we propose a competitive release hypothesis to explain how this recombination event could have occurred and why it is evolutionarily advantageous. The findings provide important insights into the natural history of ACE2 usage for both SARS-CoV-1 and SARS-CoV-2, and a greater understanding of the evolutionary mechanisms that shape zoonotic potential of coronaviruses. This study also underscores the need for increased surveillance for sarbecoviruses in southwestern China, where most ACE2-using viruses have been found to date, as well as other regions such as Africa, where these viruses have only recently been discovered.
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Affiliation(s)
- H.L Wells
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY, USA
| | - M Letko
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, USA
| | - G Lasso
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY 10461, USA
| | - B Ssebide
- Gorilla Doctors, c/o MGVP, Inc., Davis, California, USA
| | - J Nziza
- Gorilla Doctors, c/o MGVP, Inc., Davis, California, USA
| | - D.K Byarugaba
- Makerere University Walter Reed Project, Kampala, Uganda
- Makerere University, College of Veterinary Medicine, Kampala, Uganda
| | - I Navarrete-Macias
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - E Liang
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - M Cranfield
- One Health Institute and Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California Davis, California, USA
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - B.A Han
- Cary Institute of Ecosystem Studies, Millbrook, New York, USA
| | - M.W Tingley
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA, USA
| | - M Diuk-Wasser
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - T Goldstein
- One Health Institute and Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California Davis, California, USA
| | - C.K Johnson
- One Health Institute and Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California Davis, California, USA
| | - J Mazet
- One Health Institute and Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California Davis, California, USA
| | - K Chandran
- Gorilla Doctors, c/o MGVP, Inc., Davis, California, USA
| | - V.J Munster
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, USA
| | - K Gilardi
- Makerere University Walter Reed Project, Kampala, Uganda
- One Health Institute and Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California Davis, California, USA
| | - S.J Anthony
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY, USA
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California Davis, California, USA
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21
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Fouret J, Brunet FG, Binet M, Aurine N, Enchéry F, Croze S, Guinier M, Goumaidi A, Preininger D, Volff JN, Bailly-Bechet M, Lachuer J, Horvat B, Legras-Lachuer C. Sequencing the Genome of Indian Flying Fox, Natural Reservoir of Nipah Virus, Using Hybrid Assembly and Conservative Secondary Scaffolding. Front Microbiol 2020; 11:1807. [PMID: 32849415 PMCID: PMC7403528 DOI: 10.3389/fmicb.2020.01807] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 07/09/2020] [Indexed: 11/20/2022] Open
Abstract
Indian fruit bats, flying fox Pteropus medius was identified as an asymptomatic natural host of recently emerged Nipah virus, which is known to induce a severe infectious disease in humans. The absence of P. medius genome sequence presents an important obstacle for further studies of virus–host interactions and better understanding of mechanisms of zoonotic viral emergence. Generation of the high-quality genome sequence is often linked to a considerable effort associated to elevated costs. Although secondary scaffolding methods have reduced sequencing expenses, they imply the development of new tools for the integration of different data sources to achieve more reliable sequencing results. We initially sequenced the P. medius genome using the combination of Illumina paired-end and Nanopore sequencing, with a depth of 57.4x and 6.1x, respectively. Then, we introduced the novel scaff2link software to integrate multiple sources of information for secondary scaffolding, allowing to remove the association with discordant information among two sources. Different quality metrics were next produced to validate the benefits from secondary scaffolding. The P. medius genome, assembled by this method, has a length of 1,985 Mb and consists of 33,613 contigs and 16,113 scaffolds with an NG50 of 19 Mb. At least 22.5% of the assembled sequences is covered by interspersed repeats already described in other species and 19,823 coding genes are annotated. Phylogenetic analysis demonstrated the clustering of P. medius genome with two other Pteropus bat species, P. alecto and P. vampyrus, for which genome sequences are currently available. SARS-CoV entry receptor ACE2 sequence of P. medius was 82.7% identical with ACE2 of Rhinolophus sinicus bats, thought to be the natural host of SARS-CoV. Altogether, our results confirm that a lower depth of sequencing is enough to obtain a valuable genome sequence, using secondary scaffolding approaches and demonstrate the benefits of the scaff2link application. The genome sequence is now available to the scientific community to (i) proceed with further genomic analysis of P. medius, (ii) to characterize the underlying mechanism allowing Nipah virus maintenance and perpetuation in its bat host, and (iii) to monitor their evolutionary pathways toward a better understanding of bats’ ability to control viral infections.
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Affiliation(s)
- Julien Fouret
- CIRI, International Center for Infectiology Research, Team Immunobiology of Viral Infections, Univ Lyon, INSERM U1111, CNRS UMR 5308, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, Lyon, France.,Viroscan3D, Trévoux, France
| | - Frédéric G Brunet
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Martin Binet
- CIRI, International Center for Infectiology Research, Team Immunobiology of Viral Infections, Univ Lyon, INSERM U1111, CNRS UMR 5308, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, Lyon, France.,Viroscan3D, Trévoux, France
| | - Noémie Aurine
- CIRI, International Center for Infectiology Research, Team Immunobiology of Viral Infections, Univ Lyon, INSERM U1111, CNRS UMR 5308, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Francois Enchéry
- CIRI, International Center for Infectiology Research, Team Immunobiology of Viral Infections, Univ Lyon, INSERM U1111, CNRS UMR 5308, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Séverine Croze
- Plateforme Profilexpert, Université Claude Bernard Lyon 1, Lyon, France
| | | | | | | | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | | | - Joël Lachuer
- Cancer Research Center of Lyon, INSERM 1052/CNRS 5286, Université de Lyon, Lyon, France.,Plateforme Profilexpert, Université Claude Bernard Lyon 1, Lyon, France
| | - Branka Horvat
- CIRI, International Center for Infectiology Research, Team Immunobiology of Viral Infections, Univ Lyon, INSERM U1111, CNRS UMR 5308, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Catherine Legras-Lachuer
- Viroscan3D, Trévoux, France.,Ecologie Microbienne, CNRS UMR 5557, LEM, INRA, VetAgro Sup, Université Claude Bernard Lyon 1, Villeurbanne, France
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22
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Vidovszky MZ, Tan Z, Carr MJ, Boldogh S, Harrach B, Gonzalez G. Bat-borne polyomaviruses in Europe reveal an evolutionary history of intrahost divergence with horseshoe bats distributed across the African and Eurasian continents. J Gen Virol 2020; 101:1119-1130. [PMID: 32644038 DOI: 10.1099/jgv.0.001467] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Polyomaviruses (PyVs) are small, circular dsDNA viruses carried by diverse vertebrates, including bats. Although previous studies have reported several horseshoe bat PyVs collected in Zambia and China, it is still unclear how PyVs evolved in this group of widely dispersed mammals. Horseshoe bats (genus Rhinolophus) are distributed across the Old World and are natural reservoirs of numerous pathogenic viruses. Herein, non-invasive bat samples from European horseshoe bat species were collected in Hungary for PyV identification and novel PyVs with complete genomes were successfully recovered from two different European horseshoe bat species. Genomic and phylogenetic analysis of the Hungarian horseshoe bat PyVs supported their classification into the genera Alphapolyomavirus and Betapolyomavirus. Notably, despite the significant geographical distances between the corresponding sampling locations, Hungarian PyVs exhibited high genetic relatedness with previously described Zambian and Chinese horseshoe bat PyVs, and phylogenetically clustered with these viruses in each PyV genus. Correlation and virus-host relationship analysis suggested that these PyVs co-diverged with their European, African and Asian horseshoe bat hosts distributed on different continents during their evolutionary history. Additionally, assessment of selective pressures over the major capsid protein (VP1) of horseshoe bat PyVs showed sites under positive selection located in motifs exposed to the exterior of the capsid. In summary, our findings revealed a pattern of stable intrahost divergence of horseshoe bat PyVs with their mammalian hosts on the African and Eurasian continents over evolutionary time.
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Affiliation(s)
- Márton Z Vidovszky
- Institute for Veterinary Medical Research, Centre for Agricultural Research, H-1143 Budapest, Hungary
| | - Zhizhou Tan
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, PR China
| | - Michael J Carr
- Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan
- National Virus Reference Laboratory, School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | | | - Balázs Harrach
- Institute for Veterinary Medical Research, Centre for Agricultural Research, H-1143 Budapest, Hungary
| | - Gabriel Gonzalez
- National Virus Reference Laboratory, School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland
- Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan
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23
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Yao L, Witt K, Li H, Rice J, Salinas NR, Martin RD, Huerta-Sánchez E, Malhi RS. Population genetics of wild Macaca fascicularis with low-coverage shotgun sequencing of museum specimens. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2020; 173:21-33. [PMID: 32643146 DOI: 10.1002/ajpa.24099] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Revised: 05/10/2020] [Accepted: 05/15/2020] [Indexed: 11/12/2022]
Abstract
OBJECTIVES Long-tailed macaques (Macaca fascicularis) are widely distributed throughout the mainland and islands of Southeast Asia, making them a useful model for understanding the complex biogeographical history resulting from drastic changes in sea levels throughout the Pleistocene. Past studies based on mitochondrial genomes (mitogenomes) of long-tailed macaque museum specimens have traced their colonization patterns throughout the archipelago, but mitogenomes trace only the maternal history. Here, our objectives were to trace phylogeographic patterns of long-tailed macaques using low-coverage nuclear DNA (nDNA) data from museum specimens. METHODS We performed population genetic analyses and phylogenetic reconstruction on nuclear single nucleotide polymorphisms (SNPs) from shotgun sequencing of 75 long-tailed macaque museum specimens from localities throughout Southeast Asia. RESULTS We show that shotgun sequencing of museum specimens yields sufficient genome coverage (average ~1.7%) for reconstructing population relationships using SNP data. Contrary to expectations of divergent results between nuclear and mitochondrial genomes for a female philopatric species, phylogeographical patterns based on nuclear SNPs proved to be closely similar to those found using mitogenomes. In particular, population genetic analyses and phylogenetic reconstruction from the nDNA identify two major clades within M. fascicularis: Clade A includes all individuals from the mainland along with individuals from northern Sumatra, while Clade B consists of the remaining island-living individuals, including those from southern Sumatra. CONCLUSIONS Overall, we demonstrate that low-coverage sequencing of nDNA from museum specimens provides enough data for examining broad phylogeographic patterns, although greater genome coverage and sequencing depth would be needed to distinguish between very closely related populations, such as those throughout the Philippines.
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Affiliation(s)
- Lu Yao
- American Museum of Natural History, New York, New York, USA
| | - Kelsey Witt
- Brown University, Providence, Rhode Island, USA.,University of California Merced, Merced, California, USA
| | - Hongjie Li
- University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Jonathan Rice
- University of California Merced, Merced, California, USA
| | - Nelson R Salinas
- American Museum of Natural History, New York, New York, USA.,Instituto de Hidrología, Metereología y Estudios Ambientales IDEAM, Bogotá, Colombia
| | - Robert D Martin
- The Field Museum of Natural History, Chicago, Illinois, USA.,University of Zürich, Zürich, Switzerland
| | | | - Ripan S Malhi
- University of Illinois Urbana-Champaign, Urbana, Illinois, USA
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Extensive Genetic Diversity of Polyomaviruses in Sympatric Bat Communities: Host Switching versus Coevolution. J Virol 2020; 94:JVI.02101-19. [PMID: 32075934 DOI: 10.1128/jvi.02101-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 02/11/2020] [Indexed: 01/17/2023] Open
Abstract
Polyomaviruses (PyVs) are small DNA viruses carried by diverse vertebrates. The evolutionary relationships of viruses and hosts remain largely unclear due to very limited surveillance in sympatric communities. In order to investigate whether PyVs can transmit among different mammalian species and to identify host-switching events in the field, we conducted a systematic study of a large collection of bats (n = 1,083) from 29 sympatric communities across China which contained multiple species with frequent contact. PyVs were detected in 21 bat communities, with 192 PyVs identified in 186 bats from 15 species within 6 families representing at least 28 newly described PyVs. Surveillance results and phylogenetic analyses surprisingly revealed three interfamily PyV host-switching events in these sympatric bat communities: two distinct PyVs were identified in two bat species in restricted geographical locations, while another PyV clustered phylogenetically with PyVs carried by bats from a different host family. Virus-host relationships of all discovered PyVs were also evaluated, and no additional host-switching events were found. PyVs were identified in different horseshoe bat species in sympatric communities without observation of host-switching events, showed high genomic identities, and clustered with each other. This suggested that even for PyVs with high genomic identities in closely related host species, the potential for host switching is low. In summary, our findings revealed that PyV host switching in sympatric bat communities can occur but is limited and that host switching of bat-borne PyVs is relatively rare on the predominantly evolutionary background of codivergence with their hosts.IMPORTANCE Since the discovery of murine polyomavirus in the 1950s, polyomaviruses (PyVs) have been considered highly host restricted in mammals. Sympatric bat communities commonly contain several different bat species in an ecological niche facilitating viral transmission, and they therefore represent a model to identify host-switching events of PyVs. In this study, we screened PyVs in a large number of bats in sympatric communities from diverse habitats across China. We provide evidence that cross-species bat-borne PyV transmission exists, though is limited, and that host-switching events appear relatively rare during the evolutionary history of these viruses. PyVs with close genomic identities were also identified in different bat species without host-switching events. Based on these findings, we propose an evolutionary scheme for bat-borne PyVs in which limited host-switching events occur on the background of codivergence and lineage duplication, generating the viral genetic diversity in bats.
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25
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Demos TC, Webala PW, Kerbis Peterhans JC, Goodman SM, Bartonjo M, Patterson BD. Molecular phylogenetics of slit-faced bats (Chiroptera: Nycteridae) reveal deeply divergent African lineages. J ZOOL SYST EVOL RES 2019; 57:1019-1038. [PMID: 31894177 PMCID: PMC6919933 DOI: 10.1111/jzs.12313] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 05/05/2019] [Accepted: 05/09/2019] [Indexed: 02/04/2023]
Abstract
The bat family Nycteridae contains only the genus Nycteris, which comprises 13 currently recognized species from Africa and the Arabian Peninsula, one species from Madagascar, and two species restricted to Malaysia and Indonesia in South-East Asia. We investigated genetic variation, clade membership, and phylogenetic relationships in Nycteridae with broad sampling across Africa for most clades. We sequenced mitochondrial cytochrome b (cytb) and four independent nuclear introns (2,166 bp) from 253 individuals. Although our samples did not include all recognized species, we recovered at least 16 deeply divergent monophyletic lineages using independent mitochondrial and multilocus nuclear datasets in both gene tree and species tree analyses. Mean pairwise uncorrected genetic distances among species-ranked Nycteris clades (17% for cytb and 4% for concatenated introns) suggest high levels of phylogenetic diversity in Nycteridae. We found a large number of designated clades whose members are distributed wholly or partly in East Africa (10 of 16 clades), indicating that Nycteris diversity has been historically underestimated and raising the possibility that additional unsampled and/or undescribed Nycteris species occur in more poorly sampled Central and West Africa. Well-resolved mitochondrial, concatenated nuclear, and species trees strongly supported African ancestry for SE Asian species. Species tree analyses strongly support two deeply diverged subclades that have not previously been recognized, and these clades may warrant recognition as subgenera. Our analyses also strongly support four traditionally recognized species groups of Nycteris. Mitonuclear discordance regarding geographic population structure in Nycteris thebaica appears to result from male-biased dispersal in this species. Our analyses, almost wholly based on museum voucher specimens, serve to identify species-rank clades that can be tested with independent datasets, such as morphology, vocalizations, distributions, and ectoparasites. Our analyses highlight the need for a comprehensive revision of Nycteridae.
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Affiliation(s)
- Terrence C. Demos
- Integrative Research Center, Field Museum of Natural HistoryChicagoIllinois
| | - Paul W. Webala
- Department of Forestry and Wildlife ManagementMaasai Mara UniversityNarokKenya
| | - Julian C. Kerbis Peterhans
- Integrative Research Center, Field Museum of Natural HistoryChicagoIllinois
- College of Arts and SciencesRoosevelt UniversityChicagoIllinois
| | - Steven M. Goodman
- Integrative Research Center, Field Museum of Natural HistoryChicagoIllinois
- Association VahatraAntananarivoMadagascar
| | | | - Bruce D. Patterson
- Integrative Research Center, Field Museum of Natural HistoryChicagoIllinois
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26
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Najafi N, Sharifi M, Akmali V. First insights into the population genetic structure and the phylogeographic status of the Mehely’s horseshoe bat Rhinolophus mehelyi (Chiroptera: Rhinolophidae) in Iran inferred from mitochondrial genes. Mamm Biol 2019. [DOI: 10.1016/j.mambio.2019.11.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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27
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Dool SE, Künzel S, Haase M, Picker MD, Eberhard MJB. Variable Molecular Markers for the Order Mantophasmatodea (Insecta). J Hered 2019; 109:477-483. [PMID: 29206981 DOI: 10.1093/jhered/esx109] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 11/23/2017] [Indexed: 01/12/2023] Open
Abstract
The recently discovered insect order Mantophasmatodea currently comprises 19 Southern African species. These mainly occur in allopatry, have high levels of color polymorphism and communicate via species- and gender-specific vibratory signals. High levels of interspecific morphological conservatism mean that cryptic species are likely to be uncovered. These aspects of Mantophasmatodean biology make them an ideal group in which to investigate population divergence due to habitat-specific adaptation, sexual selection, and potentially sensory speciation. Lack of appropriate genetic markers has thus far rendered such studies unfeasible. To address this need, the first microsatellite loci for this order were developed. Fifty polymorphic loci were designed specifically for Karoophasma biedouwense (Austrophasmatidae), out of which 23 were labeled and tested for amplification across the order using 2-3 individuals from 10 species, representing all 4 currently known families. A Bayesian mitochondrially encoded cytochrome c oxidase I (COI) topology was reconstructed and divergence dates within the order were estimated for the first time. Amplification success and levels of polymorphism were compared with genetic divergence and time since divergence. In agreement with studies on vertebrate taxa, both amplification and variability were negatively correlated with distance (temporal and genetic). The high number of informative loci will offer sufficient resolution for both broad level population genetic analysis and individual based pedigree or parentage analyses for most species in Austrophasmatidae, with at least some loci available for the other families. This resource will facilitate research into the evolutionary biology of this understudied but fascinating group.
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Affiliation(s)
- Serena E Dool
- From the General and Systematic Zoology, Zoological Institute and Museum, University of Greifswald, Greifswald, Germany
| | - Sven Künzel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Martin Haase
- Vogelwarte, Zoological Institute and Museum, University of Greifswald, Greifswald, Germany
| | - Mike D Picker
- Department of Biological Sciences, University of Cape Town, Rondebosch, Cape Town, South Africa
| | - Monika J B Eberhard
- From the General and Systematic Zoology, Zoological Institute and Museum, University of Greifswald, Greifswald, Germany
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28
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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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Uvizl M, Šmíd J, Aghová T, Varadínová ZK, Benda P. Molecular Phylogeny and Systematics of the Sheath-Tailed Bats from the Middle East (Emballonuridae: Taphozous and Coleura). ACTA CHIROPTEROLOGICA 2019. [DOI: 10.3161/15081109acc2019.21.1.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Marek Uvizl
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44 Praha, Czech Republic
| | - Jiří Šmíd
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44 Praha, Czech Republic
| | - Tatiana Aghová
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44 Praha, Czech Republic
| | | | - Petr Benda
- Department of Zoology, National Museum (Natural History), Václavské náměstí 68, 115 79 Praha, Czech Republic
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30
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Loureiro LO, Engstrom M, Lim B, González CL, Juste J. Not All Molossus are Created Equal: Genetic Variation in the Mastiff Bat Reveals Diversity Masked by Conservative Morphology. ACTA CHIROPTEROLOGICA 2019. [DOI: 10.3161/15081109acc2019.21.1.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Livia O. Loureiro
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2,Canada
| | - Mark Engstrom
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2,Canada
| | - Burton Lim
- Department of Natural History, Royal Ontario Museum, Toronto, ON M5S 2C6, Canada
| | - Celia López González
- Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional (CIIDIR) Unidad Durango, Instituto Politécnico Nacional, Calle Sigma 119, Fraccionamiento 20 de Noviembre II, Durango, 34220 Mexico
| | - Javier Juste
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Cientifica (CSIC), 41092 Seville, Spain
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31
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Taylor PJ, MacDonald A, Goodman SM, Kearney T, Cotterill FPD, Stoffberg S, Monadjem A, Schoeman MC, Guyton J, Naskrecki P, Engelbrecht A, Richards LR. CORRIGENDUM: Integrative taxonomy resolves three new cryptic species of small southern African horseshoe bats (Rhinolophus). Zool J Linn Soc 2019. [DOI: 10.1093/zoolinnean/zlz030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Peter J Taylor
- School of Mathematical & Natural Sciences, University of Venda, Thohoyandou, South Africa
- School of Life Sciences, University of KwaZulu-Natal, Biological Sciences Building, Durban, KwaZulu-Natal, South Africa
| | - Angus MacDonald
- School of Life Sciences, University of KwaZulu-Natal, Biological Sciences Building, Durban, KwaZulu-Natal, South Africa
| | - Steven M Goodman
- Field Museum of Natural History, Chicago, IL, USA
- Association Vahatra, Antananarivo, Madagascar
| | - Teresa Kearney
- Ditsong National Museum of Natural History, Pretoria, South Africa
- School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Wits, South Africa
| | - Fenton P D Cotterill
- Geoecodynamics Research Hub, c/o Department of Botany and Zoology, University of Stellenbosch, Stellenbosch, South Africa
| | - Sam Stoffberg
- Department of Botany and Zoology, University of Stellenbosch, Stellenbosch, South Africa
| | - Ara Monadjem
- Department of Biological Sciences, University of Eswatini, Kwaluseni, Eswatini
- Mammal Research Institute, Department of Zoology & Entomology, University of Pretoria, Hatfield, Pretoria, South Africa
| | - M Corrie Schoeman
- School of Life Sciences, University of KwaZulu-Natal, Biological Sciences Building, Durban, KwaZulu-Natal, South Africa
| | - Jennifer Guyton
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Piotr Naskrecki
- Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
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Demos TC, Webala PW, Goodman SM, Kerbis Peterhans JC, Bartonjo M, Patterson BD. Molecular phylogenetics of the African horseshoe bats (Chiroptera: Rhinolophidae): expanded geographic and taxonomic sampling of the Afrotropics. BMC Evol Biol 2019; 19:166. [PMID: 31434566 PMCID: PMC6704657 DOI: 10.1186/s12862-019-1485-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 07/19/2019] [Indexed: 11/24/2022] Open
Abstract
Background The Old World insectivorous bat genus Rhinolophus is highly speciose. Over the last 15 years, the number of its recognized species has grown from 77 to 106, but knowledge of their interrelationships has not kept pace. Species limits and phylogenetic relationships of this morphologically conservative group remain problematic due both to poor sampling across the Afrotropics and to repeated instances of mitochondrial-nuclear discordance. Recent intensive surveys in East Africa and neighboring regions, coupled with parallel studies by others in West Africa and in Southern Africa, offer a new basis for understanding its evolutionary history. Results We investigated phylogenetic relationships and intraspecific genetic variation in the Afro-Palearctic clade of Rhinolophidae using broad sampling. We sequenced mitochondrial cytochrome-b (1140 bp) and four independent and informative nuclear introns (2611 bp) for 213 individuals and incorporated sequence data from 210 additional individuals on GenBank that together represent 24 of the 33 currently recognized Afrotropical Rhinolophus species. We addressed the widespread occurrence of mito-nuclear discordance in Rhinolophus by inferring concatenated and species tree phylogenies using only the nuclear data. Well resolved mitochondrial, concatenated nuclear, and species trees revealed phylogenetic relationships and population structure of the Afrotropical species and species groups. Conclusions Multiple well-supported and deeply divergent lineages were resolved in each of the six African Rhinolophus species groups analyzed, suggesting as many as 12 undescribed cryptic species; these include several instances of sympatry among close relatives. Coalescent lineage delimitation offered support for new undescribed lineages in four of the six African groups in this study. On the other hand, two to five currently recognized species may be invalid based on combined mitochondrial and/or nuclear phylogenetic analyses. Validation of these cryptic lineages as species and formal relegation of current names to synonymy will require integrative taxonomic assessments involving morphology, ecology, acoustics, distribution, and behavior. The resulting phylogenetic framework offers a powerful basis for addressing questions regarding their ecology and evolution. Electronic supplementary material The online version of this article (10.1186/s12862-019-1485-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Terrence C Demos
- Integrative Research Center, Field Museum of Natural History, Chicago, IL, 60605, USA.
| | - Paul W Webala
- Department of Forestry and Wildlife Management, Maasai Mara University, Narok, Kenya
| | - Steven M Goodman
- Integrative Research Center, Field Museum of Natural History, Chicago, IL, 60605, USA.,Association Vahatra, BP 3972, 101, Antananarivo, Madagascar
| | - Julian C Kerbis Peterhans
- Integrative Research Center, Field Museum of Natural History, Chicago, IL, 60605, USA.,College of Professional Studies, Roosevelt University, Chicago, IL, 60605, USA
| | | | - Bruce D Patterson
- Integrative Research Center, Field Museum of Natural History, Chicago, IL, 60605, USA
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Liu T, Sun K, Csorba G, Zhang K, Zhang L, Zhao H, Jin L, Thong VD, Xiao Y, Feng J. Species delimitation and evolutionary reconstruction within an integrative taxonomic framework: A case study on Rhinolophus macrotis complex (Chiroptera: Rhinolophidae). Mol Phylogenet Evol 2019; 139:106544. [PMID: 31252069 DOI: 10.1016/j.ympev.2019.106544] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 06/21/2019] [Accepted: 06/24/2019] [Indexed: 10/26/2022]
Abstract
Species delimitation and evolutionary reconstruction remain challenging for non-model species that have experienced reticulate evolution and exhibit conflicting patterns of differentiation among multiple lines of evidence, such as mitochondrial and nuclear data and phenotypes. Here, we applied an integrative taxonomic approach to a case study of Rhinolophus macrotis complex, whose taxonomic status remains controversial, to provide insight into the systematics and evolutionary history of these species. By integrating traditional genetic markers with different modes of inheritance, genome-wide SNPs as well as phenotypic characteristics, we clarified the presence of three closely related species, R. episcopus, R. siamensis, and R. osgoodi, within this complex, and proposed a new taxonomic treatment for R. osgoodi. Our results suggested that hybridization and introgression are the main causes of low mtDNA divergence in these species. Combined with the demographic inference, we deduced that glacial-interglacial cycles drove geographic isolation and secondary contacts of these species, then promoted hybridization and lineage fusion among them, finally resulting in a reticulate evolutionary pattern. Overall, our study highlights the importance of combining multiple types of data to delimit species, especially those with conserved morphology, and to reveal the sophisticated processes of speciation.
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Affiliation(s)
- Tong Liu
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Keping Sun
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China; Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun, China.
| | - Gábor Csorba
- Department of Zoology, Hungarian Natural History Museum, Budapest, Hungary
| | - Kangkang Zhang
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Lin Zhang
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Hanbo Zhao
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Longru Jin
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Vu Dinh Thong
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Viet Nam; Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, Hanoi, Viet Nam
| | - Yanhong Xiao
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Jiang Feng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China; College of Life Science, Jilin Agricultural University, Changchun, China.
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Juste J, Ruedi M, Puechmaille SJ, Salicini I, Ibáñez C. Two New Cryptic Bat Species within the Myotis nattereri Species Complex (Vespertilionidae, Chiroptera) from the Western Palaearctic. ACTA CHIROPTEROLOGICA 2019. [DOI: 10.3161/15081109acc2018.20.2.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Javier Juste
- Estación Biológica de Doñana (CSIC), Avda. Américo Vespucio 26, 41092 Sevilla, Spain
| | - Manuel Ruedi
- Natural History Museum of Geneva, P.O. Box, 6334, 1211 Genève 6, Switzerland
| | | | - Irene Salicini
- Estación Biológica de Doñana (CSIC), Avda. Américo Vespucio 26, 41092 Sevilla, Spain
| | - Carlos Ibáñez
- Estación Biológica de Doñana (CSIC), Avda. Américo Vespucio 26, 41092 Sevilla, Spain
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35
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Echolocation call frequency and mitochondrial control region variation in the closely related bat species of the genus Rhinolophus (Chiroptera: Rhinolophidae) occurring in Iran: implications for taxonomy and intraspecific phylogeny. MAMMAL RES 2019. [DOI: 10.1007/s13364-019-00417-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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36
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Sousa-Santos C, Jesus TF, Fernandes C, Robalo JI, Coelho MM. Fish diversification at the pace of geomorphological changes: evolutionary history of western Iberian Leuciscinae (Teleostei: Leuciscidae) inferred from multilocus sequence data. Mol Phylogenet Evol 2018; 133:263-285. [PMID: 30583043 DOI: 10.1016/j.ympev.2018.12.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 12/12/2018] [Accepted: 12/15/2018] [Indexed: 01/05/2023]
Abstract
The evolutionary history of western Iberian Leuciscinae, obligatory freshwater fish, is directly linked to the evolution of the hydrographic network of the Iberian Peninsula after its isolation from the rest of Europe, which involved dramatic rearrangements such as the transition from endorheic lakes to open basins draining to the Atlantic. Previous phylogenetic research on western Iberian leuciscines, using mainly mitochondrial DNA and more recently one or two nuclear genes, has found contradictory results and there remain many unresolved issues regarding species relationships, taxonomy, and evolutionary history. Moreover, there is a lack of integration between phylogenetic and divergence time estimates and information on the timing of geomorphological changes and paleobasin rearrangements in the Iberian Peninsula. This study presents the first comprehensive fossil-calibrated multilocus coalescent species tree of western Iberian Leuciscinae (including 14 species of Achondrostoma, Iberochondrostoma, Pseudochondrostoma and Squalius endemic to the Iberian Peninsula, seven of which endemic to Portugal) based on seven nuclear genes, and from which we infer their biogeographic history by comparing divergence time estimates to known dated geological events. The phylogenetic pattern suggests slow-paced evolution of leuciscines during the Early-Middle Miocene endorheic phase of the main Iberian river basins, with the shift to exorheism in the late Neogene-Quaternary allowing westward dispersals that resulted in many cladogenetic events and a high rate of endemism in western Iberia. The results of this study also: (i) confirm the paraphyly of S. pyrenaicus with respect to S. carolitertii, and thus the possible presence of a new taxon in the Portuguese Tagus currently assigned to S. pyrenaicus; (ii) support the taxonomic separation of the Guadiana and Sado populations of S. pyrenaicus; (iii) show the need for further population sampling and taxonomic research to clarify the phylogenetic status of A. arcasii from the Minho basin and of the I. lusitanicum populations in the Sado and Tagus basins; and (iv) indicate that A. occidentale, I. olisiponensis and P. duriensis are the most ancient lineages within their respective genera.
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Affiliation(s)
- C Sousa-Santos
- MARE - Marine and Environmental Sciences Centre, ISPA-Instituto Universitário, Rua Jardim do Tabaco 34, 1149-041 Lisbon, Portugal.
| | - T F Jesus
- cE3c - Center for Ecology, Evolution and Environmental Changes, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisbon, Portugal; Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Av. Professor Egaz Moniz, 1649-028 Lisbon, Portugal(2).
| | - C Fernandes
- cE3c - Center for Ecology, Evolution and Environmental Changes, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisbon, Portugal.
| | - J I Robalo
- MARE - Marine and Environmental Sciences Centre, ISPA-Instituto Universitário, Rua Jardim do Tabaco 34, 1149-041 Lisbon, Portugal.
| | - M M Coelho
- cE3c - Center for Ecology, Evolution and Environmental Changes, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisbon, Portugal.
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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: 23] [Impact Index Per Article: 3.8] [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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38
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High Duty Cycle Echolocation May Constrain the Evolution of Diversity within Horseshoe Bats (Family: Rhinolophidae). DIVERSITY-BASEL 2018. [DOI: 10.3390/d10030085] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The phenotype of organisms is the net result of various evolutionary forces acting upon their lineages over time. When an innovative trait arises that confers a substantial advantage in terms of survival and reproduction, the evolution of adaptive complexes between such an innovation and other traits may constrain diversification of that lineage. The specialized echolocation system of the Rhinolophidae may represent such an innovation which affects other parts of the phenotype. We investigated a potential constraint on the diversity of phenotypes of several species of horseshoe bats within a phylogenetic framework. If phenotypic convergence stems from stasis as a result of the specialized echolocation system, phenotypes should converge not only among members of the same species and between sexes but also among species. We analyzed the phenotypic diversity of >800 individuals of 13–16 species. The phenotypes in the horseshoe bats did indeed converge. There was no sexual size dimorphism in mass, forearm length and wingspan within species and there was marked interspecific similarity in both wing and echolocation variables but marked variability in body mass. Furthermore, correlations of wing and echolocation variables with mass suggest that variability within horseshoe bats was largely the result of selection on body size with allometric responses in wing and echolocation parameters, a potential consequence of constraints imposed by their specialized echolocation.
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Zhang L, Sun K, Liu T, Zhao H, Csorba G, Jin L, Thong VD, Feng J. Multilocus phylogeny and species delimitation within the philippinensis
group (Chiroptera: Rhinolophidae). ZOOL SCR 2018. [DOI: 10.1111/zsc.12308] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Lin Zhang
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization; Northeast Normal University; Changchun China
| | - Keping Sun
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization; Northeast Normal University; Changchun China
| | - Tong Liu
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization; Northeast Normal University; Changchun China
| | - Hanbo Zhao
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization; Northeast Normal University; Changchun China
| | - Gábor Csorba
- Department of Zoology; Hungarian Natural History Museum; Budapest Hungary
| | - Longru Jin
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization; Northeast Normal University; Changchun China
| | - Vu Dinh Thong
- Graduate University of Science and Technology; Vietnam Academy of Science and Technology; Hanoi Vietnam
- Institute of Ecology and Biological Resources; Vietnam Academy of Science and Technology; Hanoi Vietnam
| | - Jiang Feng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization; Northeast Normal University; Changchun China
- Jilin Agricultural University; Changchun China
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40
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Demos TC, Webala PW, Bartonjo M, Patterson BD. Hidden Diversity of African Yellow House Bats (Vespertilionidae, Scotophilus): Insights From Multilocus Phylogenetics and Lineage Delimitation. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00086] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
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Mota TFM, Fabrin TMC, Gasques LS, Ortêncio Filho H, Prioli AJ, Prioli SMAP. Extraction of DNA from micro-tissue for bat species identification. Mitochondrial DNA B Resour 2018; 3:758-762. [PMID: 33474313 PMCID: PMC7800230 DOI: 10.1080/23802359.2018.1484261] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 05/29/2018] [Indexed: 11/05/2022] Open
Abstract
Bat populations are declining worldwide. Accurate identification is essential to promote species' conservation. However, minimal morphological differences and a high rate of cryptic species make identification difficult, unless voucher specimens are kept, a controversial issue today. The objective of this work was to standardize a method of extracting non-lethal DNA using bats' uropatagium micro-tissue, aiming the molecular identification of species that occur in the region of Maringá PR. The method standardized was efficient, and does not cause serious damage to bats. For future field studies, collection of micro-tissue and morphometry of the specimens will be sufficient for accurate identification.
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Affiliation(s)
| | - Thomaz Mansini Carrenho Fabrin
- Programa de Pós-Graduação em Ecologia de Ambientes Aquáticos Continentais, Universidade Estadual de Maringá, Maringá, Brazil
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Tsang SM, Wiantoro S, Veluz MJ, Simmons NB, Lohman DJ. Low Levels of Population Structure among Geographically Distant Populations of Pteropus vampyrus (Chiroptera: Pteropodidae). ACTA CHIROPTEROLOGICA 2018. [DOI: 10.3161/15081109acc2018.20.1.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Susan M. Tsang
- Department of Biology, City College and the Graduate Center, The City University of New York, 365 Fifth Avenue, New York, NY, 10016, USA
| | - Sigit Wiantoro
- Museum Zoologicum Bogoriense, Indonesian Institute of Sciences, Jl. Raya Jakarta-Bogor, Km. 46, Cibinong, 16911, Indonesia
| | - Maria Josefa Veluz
- Zoology Division, National Museum of the Philippines, Padres Burgos Ave, Ermita, Manila, 1000 Metro Manila, Philippines
| | - Nancy B. Simmons
- Department of Mammalogy, American Museum of Natural History, Central Park West and 79th Street, New York, NY, 10024, USA
| | - David J. Lohman
- Department of Biology, City College and the Graduate Center, The City University of New York, 365 Fifth Avenue, New York, NY, 10016, USA
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Patterson BD, Webala PW, Bartonjo M, Nziza J, Dick CW, Demos TC. On the taxonomic status and distribution of African species of Otomops (Chiroptera: Molossidae). PeerJ 2018; 6:e4864. [PMID: 29844995 PMCID: PMC5971098 DOI: 10.7717/peerj.4864] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 05/08/2018] [Indexed: 11/20/2022] Open
Abstract
Background Free-tailed bats of the genus Otomops are poorly known, and most species are documented from a handful of widely scattered localities. Recently, two allopatric species of Otomops were recognized in continental Africa: Otomops martiensseni (Matschie, 1897) in southern, central and western Africa, and the new species O. harrisoniRalph et al., 2015 in the northeast and in Yemen. Methods We collected additional samples of Otomops in Kenya and Rwanda where the ranges of these taxa approach one another to clarify their geographic ranges and taxonomic status. Mitochondrial and nuclear intron sequences served to identify and delimit species; we also documented their echolocation call variation and ectoparasite complements. Results Otomops martiensseni, the southern African species, was documented in northern Kenya in Marsabit National Park. O. harrisoni, the northeastern African–Arabian species, was documented in southern Kenya and in a cave in Musanze District, Rwanda. Moreover, individuals of both species were found together at the Musanze cave, establishing them in precise spatial and temporal sympatry. Analyses of mitochondrial and nuclear loci identify no evidence of admixture between these forms, although available samples limit the power of this analysis. Echolocation call differences are also apparent among the three localities we analyzed. Three orders of insects and two families of mites are newly reported as ectoparasites of O. harrisoni. Discussion Our results corroborate species rank for O. harrisoni and establish a zone of potential geographic overlap with O. martiensseni spanning at least 800 km of latitude. The new records establish the species in sympatry in northern Rwanda and add an additional species to the bat faunas of both Kenya and Rwanda. Future studies are needed to understand Otomops roosting requirements and movements, thereby explaining the paucity of known colonies and yielding better estimates of their conservation status. The discovery of mixed roosting associations in Rwanda invites further investigation.
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Affiliation(s)
- Bruce D Patterson
- Integrative Research Center, Field Museum of Natural History, Chicago, IL, USA
| | - Paul W Webala
- Department of Forestry and Wildlife Management, Maasai Mara University, Narok, Kenya
| | | | - Julius Nziza
- Regional Headquarters, Mountain Gorilla Veterinary Project, Musanze, Rwanda
| | - Carl W Dick
- Department of Biology, Western Kentucky University, Bowling Green, KY, USA
| | - Terrence C Demos
- Integrative Research Center, Field Museum of Natural History, Chicago, IL, USA
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Chen MY, Liang D, Zhang P. Phylogenomic Resolution of the Phylogeny of Laurasiatherian Mammals: Exploring Phylogenetic Signals within Coding and Noncoding Sequences. Genome Biol Evol 2018; 9:1998-2012. [PMID: 28830116 PMCID: PMC5737624 DOI: 10.1093/gbe/evx147] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/30/2017] [Indexed: 12/12/2022] Open
Abstract
The interordinal relationships of Laurasiatherian mammals are currently one of the most controversial questions in mammalian phylogenetics. Previous studies mainly relied on coding sequences (CDS) and seldom used noncoding sequences. Here, by data mining public genome data, we compiled an intron data set of 3,638 genes (all introns from a protein-coding gene are considered as a gene) (19,055,073 bp) and a CDS data set of 10,259 genes (20,994,285 bp), covering all major lineages of Laurasiatheria (except Pholidota). We found that the intron data contained stronger and more congruent phylogenetic signals than the CDS data. In agreement with this observation, concatenation and species-tree analyses of the intron data set yielded well-resolved and identical phylogenies, whereas the CDS data set produced weakly supported and incongruent results. Further analyses showed that the phylogeny inferred from the intron data is highly robust to data subsampling and change in outgroup, but the CDS data produced unstable results under the same conditions. Interestingly, gene tree statistical results showed that the most frequently observed gene tree topologies for the CDS and intron data are identical, suggesting that the major phylogenetic signal within the CDS data is actually congruent with that within the intron data. Our final result of Laurasiatheria phylogeny is (Eulipotyphla,((Chiroptera, Perissodactyla),(Carnivora, Cetartiodactyla))), favoring a close relationship between Chiroptera and Perissodactyla. Our study 1) provides a well-supported phylogenetic framework for Laurasiatheria, representing a step towards ending the long-standing "hard" polytomy and 2) argues that intron within genome data is a promising data resource for resolving rapid radiation events across the tree of life.
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Affiliation(s)
- Meng-Yun Chen
- State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Dan Liang
- State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Peng Zhang
- State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
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Najafi N, Akmali V, Sharifi M. Historical explanation of genetic variation in the Mediterranean horseshoe bat Rhinolophus euryale (Chiroptera: Rhinolophidae) inferred from mitochondrial cytochrome-b and D-loop genes in Iran. Mitochondrial DNA A DNA Mapp Seq Anal 2018; 30:135-147. [PMID: 29697024 DOI: 10.1080/24701394.2018.1463375] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Molecular phylogeography and species distribution modelling (SDM) suggest that late Quaternary glacial cycles have portrayed a significant role in structuring current population genetic structure and diversity. Based on phylogenetic relationships using Bayesian inference and maximum likelihood of 535 bp mtDNA (D-loop) and 745 bp mtDNA (Cytb) in 62 individuals of the Mediterranean Horseshoe Bat, Rhinolophus euryale, from 13 different localities in Iran we identified two subspecific populations with differing population genetic structure distributed in southern Zagros Mts. and northern Elburz Mts. Analysis of molecular variance (AMOVA) obtained from D-loop sequences indicates that 21.18% of sequence variation is distributed among populations and 10.84% within them. Moreover, a degree of genetic subdivision, mainly attributable to the existence of significant variance among the two regions is shown (θCT = 0.68, p = .005). The positive and significant correlation between geographic and genetic distances (R2 = 0.28, r = 0.529, p = .000) is obtained following controlling for environmental distance. Spatial distribution of haplotypes indicates that marginal population of the species in southern part of the species range have occupied this section as a glacial refugia. However, this genetic variation, in conjunction with results of the SDM shows a massive postglacial range expansion for R. euryale towards higher latitudes in Iran.
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Affiliation(s)
- Nargess Najafi
- a Department of Biology, Faculty of Science , Razi University , Kermanshah , Iran
| | - Vahid Akmali
- a Department of Biology, Faculty of Science , Razi University , Kermanshah , Iran
| | - Mozafar Sharifi
- a Department of Biology, Faculty of Science , Razi University , Kermanshah , Iran
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Taylor PJ, Macdonald A, Goodman SM, Kearney T, Cotterill FPD, Stoffberg S, Monadjem A, Schoeman MC, Guyton J, Naskrecki P, Richards LR. Integrative taxonomy resolves three new cryptic species of small southern African horseshoe bats (Rhinolophus). Zool J Linn Soc 2018. [DOI: 10.1093/zoolinnean/zly024] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Examination of historical and recent collections of small Rhinolophus bats revealed cryptic taxonomic diversity within southern African populations previously referred to as R. swinnyi Gough, 1908 and R. landeri Martin, 1832. Specimens from Mozambique morphologically referable to R. swinnyi were phylogenetically unrelated to topotypic R. swinnyi from the Eastern Cape Province of South Africa based on cytochrome b sequences and showed distinctive echolocation, baculum and noseleaf characters. Due to their genetic similarity to a previously reported molecular operational taxonomic unit (OTU) from north-eastern South Africa, Zimbabwe and Zambia, we recognize the available synonym (R. rhodesiae Roberts, 1946) to denote this distinct evolutionary species. This new taxon is genetically identical to R. simulator K. Andersen, 1904 based on mtDNA and nuclear DNA sequences but can easily be distinguished on morphological and acoustic grounds. We attribute this genetic similarity to historical introgression, a frequently documented phenomenon in bats. An additional genetically distinct and diminutive taxon in the swinnyi s.l. group (named herein, R. gorongosae sp. nov.) is described from Gorongosa National Park, central Mozambique. Specimens from Mozambique referable based on morphology to R. landeri were distinct from topotypic landeri from West Africa based on mtDNA sequences, and acoustic, noseleaf and baculum characters. This Mozambique population is assigned to the available synonym R. lobatus Peters, 1952.
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Affiliation(s)
- Peter J Taylor
- SARChI Chair on Biodiversity Value & Change and Core Team Member of the Centre for Invasion Biology, School of Mathematical & Natural Sciences, University of Venda, Thohoyandou, South Africa
- School of Life Sciences, University of KwaZulu-Natal, Durban, KwaZulu-Natal, South Africa
| | - Angus Macdonald
- School of Life Sciences, University of KwaZulu-Natal, Durban, KwaZulu-Natal, South Africa
| | - Steven M Goodman
- Field Museum of Natural History, Chicago, IL, USA
- Association Vahatra, Antananarivo, Madagascar
| | - Teresa Kearney
- Ditsong National Museum of Natural History, Pretoria, South Africa
- School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Wits, South Africa
| | - Fenton P D Cotterill
- Geoecodynamics Research Hub, c/o Department of Botany and Zoology, University of Stellenbosch, Stellenbosch, South Africa
| | - Sam Stoffberg
- Department of Botany and Zoology, University of Stellenbosch, Stellenbosch, South Africa
| | - Ara Monadjem
- All Out Africa Research Unit, Department of Biological Sciences, University of Swaziland, Kwaluseni, Swaziland
- Mammal Research Institute, Department of Zoology & Entomology, University of Pretoria, Pretoria, South Africa
| | - M Corrie Schoeman
- School of Life Sciences, University of KwaZulu-Natal, Durban, KwaZulu-Natal, South Africa
| | - Jennifer Guyton
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Piotr Naskrecki
- Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
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47
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Hron T, Farkašová H, Gifford RJ, Benda P, Hulva P, Görföl T, Pačes J, Elleder D. Remnants of an Ancient Deltaretrovirus in the Genomes of Horseshoe Bats (Rhinolophidae). Viruses 2018; 10:v10040185. [PMID: 29642581 PMCID: PMC5923479 DOI: 10.3390/v10040185] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 03/31/2018] [Accepted: 04/07/2018] [Indexed: 12/24/2022] Open
Abstract
Endogenous retrovirus (ERV) sequences provide a rich source of information about the long-term interactions between retroviruses and their hosts. However, most ERVs are derived from a subset of retrovirus groups, while ERVs derived from certain other groups remain extremely rare. In particular, only a single ERV sequence has been identified that shows evidence of being related to an ancient Deltaretrovirus, despite the large number of vertebrate genome sequences now available. In this report, we identify a second example of an ERV sequence putatively derived from a past deltaretroviral infection, in the genomes of several species of horseshoe bats (Rhinolophidae). This sequence represents a fragment of viral genome derived from a single integration. The time of the integration was estimated to be 11-19 million years ago. This finding, together with the previously identified endogenous Deltaretrovirus in long-fingered bats (Miniopteridae), suggest a close association of bats with ancient deltaretroviruses.
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Affiliation(s)
- Tomáš Hron
- Institute of Molecular Genetics, The Czech Academy of Sciences, Videnska 1083, 14220 Prague, Czech Republic.
| | - Helena Farkašová
- Institute of Molecular Genetics, The Czech Academy of Sciences, Videnska 1083, 14220 Prague, Czech Republic.
| | - Robert J Gifford
- MRC-University of Glasgow, Centre for Virus Research, 464 Bearsden Road, Glasgow G12 8TA, UK.
| | - Petr Benda
- Department of Zoology, Charles University, Vinicna 7, 12844 Prague, Czech Republic.
- Department of Zoology, National Museum (Natural History), Vaclavske nam. 68, 11579 Prague, Czech Republic.
| | - Pavel Hulva
- Department of Zoology, Charles University, Vinicna 7, 12844 Prague, Czech Republic.
- Department of Biology and Ecology, University of Ostrava, Chitussiho 10, 71000 Ostrava, Czech Republic.
| | - Tamás Görföl
- Department of Zoology, Hungarian Natural History Musem, Baross Utca 13, 1088 Budapest, Hungary.
| | - Jan Pačes
- Institute of Molecular Genetics, The Czech Academy of Sciences, Videnska 1083, 14220 Prague, Czech Republic.
| | - Daniel Elleder
- Institute of Molecular Genetics, The Czech Academy of Sciences, Videnska 1083, 14220 Prague, Czech Republic.
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48
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Wu H, Jiang T, Huang X, Feng J. Patterns of sexual size dimorphism in horseshoe bats: Testing Rensch's rule and potential causes. Sci Rep 2018; 8:2616. [PMID: 29422495 PMCID: PMC5805768 DOI: 10.1038/s41598-018-21077-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 01/29/2018] [Indexed: 11/10/2022] Open
Abstract
Rensch's rule, stating that sexual size dimorphism (SSD) becomes more evident and male-biased with increasing body size, has been well supported for taxa that exhibit male-biased SSD. Bats, primarily having female-biased SSD, have so far been tested for whether SSD allometry conforms to Rensch's rule in only three studies. However, these studies did not consider phylogeny, and thus the mechanisms underlying SSD variations in bats remain unclear. Thus, the present study reviewed published and original data, including body size, baculum size, and habitat types in 45 bats of the family Rhinolophidae to determine whether horseshoe bats follow Rensch's rule using a phylogenetic comparative framework. We also investigated the potential effect of postcopulatory sexual selection and habitat type on SSD. Our findings indicated that Rensch's rule did not apply to Rhinolophidae, suggesting that SSD did not significantly vary with increasing size. This pattern may be attributable interactions between weak sexual selection to male body size and strong fecundity selection for on female body size. The degree of SSD among horseshoe bats may be attributed to a phylogenetic effect rather than to the intersexual competition for food or to baculum length. Interestingly, we observed that species in open habitats exhibited greater SSD than those in dense forests, suggesting that habitat types may be associated with variations in SSD in horseshoe bats.
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Affiliation(s)
- Hui Wu
- College of Animal Science and Technology, Jilin Agricultural University, Xincheng ST 2888, Changchun, 130118, China
- Jilin Provincal Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Jingyue St 2555, Changchun, 130117, China
| | - Tinglei Jiang
- Jilin Provincal Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Jingyue St 2555, Changchun, 130117, China.
- Key Laboratory of Vegetation Ecology of Education Ministry, Institute of Grassland Science, Northeast Normal University, Changchun, 130024, China.
| | - Xiaobin Huang
- Jilin Provincal Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Jingyue St 2555, Changchun, 130117, China
| | - Jiang Feng
- College of Animal Science and Technology, Jilin Agricultural University, Xincheng ST 2888, Changchun, 130118, China.
- Jilin Provincal Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Jingyue St 2555, Changchun, 130117, China.
- Key Laboratory of Vegetation Ecology of Education Ministry, Institute of Grassland Science, Northeast Normal University, Changchun, 130024, China.
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49
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Li J, He C, Guo P, Zhang P, Liang D. A workflow of massive identification and application of intron markers using snakes as a model. Ecol Evol 2017; 7:10042-10055. [PMID: 29238535 PMCID: PMC5723593 DOI: 10.1002/ece3.3525] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 09/27/2017] [Accepted: 10/02/2017] [Indexed: 11/29/2022] Open
Abstract
Relative to the commonly used mitochondrial and nuclear protein-coding genes, the noncoding intron sequences are a promising source of informative markers that have the potential to resolve difficult phylogenetic nodes such as rapid radiations and recent divergences. Yet many issues exist in the use of intron markers, which prevent their extensive application as conventional markers. We used the diverse group of snakes as an example to try paving the way for massive identification and application of intron markers. We performed a series of bioinformatics screenings which identified appropriate introns between single-copy and conserved exons from two snake genomes, adding particular constraints on sequence length variability and sequence variability. A total of 1,273 candidate intron loci were retrieved. Primers for nested polymerase chain reaction (PCR) were designed for over a hundred candidates and tested in 16 snake representatives. 96 intron markers were developed that could be amplified across a broad range of snake taxa with high PCR successful rates. The markers were then applied to 49 snake samples. The large number of amplicons was subjected to next-generation sequencing (NGS). An analytic strategy was developed to accurately recover the amplicon sequences, and approximately, 76% of the marker sequences were recovered. The average p-distances of the intron markers at interfamily, intergenus, interspecies, and intraspecies levels were .168, .052, .015, and .004, respectively, suggesting that they were useful to study snake relationships of different evolutionary depths. A snake phylogeny was constructed with the intron markers, which produced concordant results with robust support at both interfamily and intragenus levels. The intron markers provide a convenient way to explore the signals in the noncoding regions to address the controversies on the snake tree. Our improved strategy of genome screening is effective and can be applied to other animal groups. NGS coupled with appropriate sequence processing can greatly facilitate the extensive application of molecular markers.
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Affiliation(s)
- Jiang‐Ni Li
- State Key Laboratory of BiocontrolCollege of Ecology and EvolutionSchool of Life SciencesSun Yat‐sen UniversityGuangzhouChina
| | - Chong He
- State Key Laboratory of BiocontrolCollege of Ecology and EvolutionSchool of Life SciencesSun Yat‐sen UniversityGuangzhouChina
| | - Peng Guo
- College of Life Sciences and Food EngineeringYibin UniversityYibinChina
| | - Peng Zhang
- State Key Laboratory of BiocontrolCollege of Ecology and EvolutionSchool of Life SciencesSun Yat‐sen UniversityGuangzhouChina
| | - Dan Liang
- State Key Laboratory of BiocontrolCollege of Ecology and EvolutionSchool of Life SciencesSun Yat‐sen UniversityGuangzhouChina
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50
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Jacobs DS, Catto S, Mutumi GL, Finger N, Webala PW. Testing the Sensory Drive Hypothesis: Geographic variation in echolocation frequencies of Geoffroy's horseshoe bat (Rhinolophidae: Rhinolophus clivosus). PLoS One 2017; 12:e0187769. [PMID: 29186147 PMCID: PMC5706677 DOI: 10.1371/journal.pone.0187769] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 10/25/2017] [Indexed: 12/14/2022] Open
Abstract
Geographic variation in sensory traits is usually influenced by adaptive processes because these traits are involved in crucial life-history aspects including orientation, communication, lineage recognition and mate choice. Studying this variation can therefore provide insights into lineage diversification. According to the Sensory Drive Hypothesis, lineage diversification may be driven by adaptation of sensory systems to local environments. It predicts that acoustic signals vary in association with local climatic conditions so that atmospheric attenuation is minimized and transmission of the signals maximized. To test this prediction, we investigated the influence of climatic factors (specifically relative humidity and temperature) on geographic variation in the resting frequencies of the echolocation pulses of Geoffroy's horseshoe bat, Rhinolophus clivosus. If the evolution of phenotypic variation in this lineage tracks climate variation, human induced climate change may lead to decreases in detection volumes and a reduction in foraging efficiency. A complex non-linear interaction between relative humidity and temperature affects atmospheric attenuation of sound and principal components composed of these correlated variables were, therefore, used in a linear mixed effects model to assess their contribution to observed variation in resting frequencies. A principal component composed predominantly of mean annual temperature (factor loading of -0.8455) significantly explained a proportion of the variation in resting frequency across sites (P < 0.05). Specifically, at higher relative humidity (around 60%) prevalent across the distribution of R. clivosus, increasing temperature had a strong negative effect on resting frequency. Climatic factors thus strongly influence acoustic signal divergence in this lineage, supporting the prediction of the Sensory Drive Hypothesis. The predicted future increase in temperature due to climate change is likely to decrease the detection volume in echolocating bats and adversely impact their foraging efficiency.
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Affiliation(s)
- David S. Jacobs
- University of Cape Town, Department of Biological Sciences, Rondebosch, Cape Town, South Africa
| | - Sarah Catto
- University of Cape Town, Department of Biological Sciences, Rondebosch, Cape Town, South Africa
| | - Gregory L. Mutumi
- University of Cape Town, Department of Biological Sciences, Rondebosch, Cape Town, South Africa
| | - Nikita Finger
- University of Cape Town, Department of Biological Sciences, Rondebosch, Cape Town, South Africa
| | - Paul W. Webala
- Maasai Mara University, Department of Forestry and Wildlife Management, Narok, Kenya
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