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Martin AM, Vonhof MJ, Henshaw M, Dreyer JM, Munster SK, Kirby L, Russell AL. Genetic Structure of the Vulnerable Tricolored Bat (Perimyotis subflavus). ACTA CHIROPTEROLOGICA 2023. [DOI: 10.3161/15081109acc2022.24.2.002] [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)
- Alynn M. Martin
- Caesar Kleberg Wildlife Research Institute, Texas A&M University-Kingsville, Kingsville, TX 78363, USA
| | - Maarten J. Vonhof
- Department of Biological Sciences, Western Michigan University, 1903 W Michigan Avenue, Kalamazoo, MI 49008, USA
| | - Michael Henshaw
- Department of Biology, Grand Valley State University, 1 Campus Drive, Allendale, MI 49401, USA
| | - Jessica M. Dreyer
- Department of Ecology and Evolutionary Biology, University of Tennessee, 1502 Cumberland Avenue, Knoxville, TN 37996, USA
| | - Susan K. Munster
- Department of Biology, Grand Valley State University, 1 Campus Drive, Allendale, MI 49401, USA
| | - Laura Kirby
- Department of Human Genetics, University of Michigan, 500 S. State Street, Ann Arbor, MI 48409, USA
| | - Amy L. Russell
- Department of Biology, Grand Valley State University, 1 Campus Drive, Allendale, MI 49401, USA
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Pinzari CA, Bellinger MR, Price D, Bonaccorso FJ. Genetic diversity, structure, and effective population size of an endangered, endemic hoary bat, 'ōpe'ape'a, across the Hawaiian Islands. PeerJ 2023; 11:e14365. [PMID: 36718450 PMCID: PMC9884036 DOI: 10.7717/peerj.14365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 10/19/2022] [Indexed: 01/26/2023] Open
Abstract
Island bat species are disproportionately at risk of extinction, and Hawai'i's only native terrestrial land mammal, the Hawaiian hoary bat (Lasiurus semotus) locally known as 'ōpe'ape'a, is no exception. To effectively manage this bat species with an archipelago-wide distribution, it is important to determine the population size on each island and connectivity between islands. We used 18 nuclear microsatellite loci and one mitochondrial gene from 339 individuals collected from 1988-2020 to evaluate genetic diversity, population structure and estimate effective population size on the Islands of Hawai'i, Maui, O'ahu, and Kaua'i. Genetic differentiation occurred between Hawai'i and Maui, both of which were differentiated from O'ahu and Kaua'i. The population on Maui presents the greatest per-island genetic diversity, consistent with their hypothesized status as the original founding population. A signature of isolation by distance was detected between islands, with contemporary migration analyses indicating limited gene flow in recent generations, and male-biased sex dispersal within Maui. Historical and long-term estimates of genetic effective population sizes were generally larger than contemporary estimates, although estimates of contemporary genetic effective population size lacked upper bounds in confidence intervals for Hawai'i and Kaua'i. Contemporary genetic effective population sizes were smaller on O'ahu and Maui. We also detected evidence of past bottlenecks on all islands with the exception of Hawai'i. Our study provides population-level estimates for the genetic diversity and geographic structure of 'ōpe'ape'a, that could be used by agencies tasked with wildlife conservation in Hawai'i.
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Affiliation(s)
- Corinna A. Pinzari
- Tropical Conservation Biology and Environmental Science Graduate Program, University of Hawaiʻi at Hilo, Hilo, Hawaiʻi, United States of America,Hawaiʻi Cooperative Studies Unit, University of Hawaiʻi at Hilo, Hawaiʻi National Park, Hawaiʻi, United States of America
| | - M. Renee Bellinger
- Tropical Conservation Biology and Environmental Science Graduate Program, University of Hawaiʻi at Hilo, Hilo, Hawaiʻi, United States of America,Hawaiʻi Cooperative Studies Unit, University of Hawaiʻi at Hilo, Hawaiʻi National Park, Hawaiʻi, United States of America,Pacific Island Ecosystems Research Center, U.S. Geological Survey, Hawaiʻi National Park, Hawaiʻi, United States of America
| | - Donald Price
- Tropical Conservation Biology and Environmental Science Graduate Program, University of Hawaiʻi at Hilo, Hilo, Hawaiʻi, United States of America,School of Life Sciences, University of Nevada - Las Vegas, Las Vegas, NV, United States of America
| | - Frank J. Bonaccorso
- Pacific Island Ecosystems Research Center, U.S. Geological Survey, Hawaiʻi National Park, Hawaiʻi, United States of America
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Environmentally driven phenotypic convergence and niche conservatism accompany speciation in hoary bats. Sci Rep 2022; 12:21877. [PMID: 36536003 PMCID: PMC9763480 DOI: 10.1038/s41598-022-26453-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
Species that are geographically widespread may exist across environmentally heterogeneous landscapes that could influence patterns of occupation and phylogeographic structure. Previous studies have suggested that geographic range size should be positively correlated with niche breadth, allowing widespread species to sustain viable populations over diverse environmental gradients. We examined the congruence of phenotypic and phylogenetic divergence with the environmental factors that help maintain species level diversity in the geographically widespread hoary bats (Lasiurus cinereus sensu lato) across their distribution. Genetic sequences were analyzed using multiple phylogenetic and species delimitation methods, and phenotypic data were analyzed using supervised and unsupervised machine learning approaches. Spatial data from environmental, geographic, and topographic features were analyzed in a multiple regression analysis to determine their relative effect on phenotypic diversity. Ecological niches of each hoary bat species were examined in environmental space to quantify niche overlap, equivalency, and the magnitude of niche differentiation. Phylogenetic and species delimitation analyses support existence of three geographically structured species of hoary bat, each of which is phenotypically distinct. However, the Hawaiian hoary bat is morphologically more similar to the South American species than to the North American species despite a closer phylogenetic relationship to the latter. Multiple regression and niche analyses revealed higher environmental similarities between the South American and Hawaiian species. Hoary bats thus exhibit a pattern of phenotypic variation that disagrees with well-supported genetic divergences, instead indicating phenotypic convergence driven by similar environmental features and relatively conserved niches occupied in tropical latitudes.
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Rau D, Attene G, Rodriguez M, Baghino L, Pisanu AB, Sanna D, Acquadro A, Portis E, Comino C. The Population Structure of a Globe Artichoke Worldwide Collection, as Revealed by Molecular and Phenotypic Analyzes. FRONTIERS IN PLANT SCIENCE 2022; 13:898740. [PMID: 35865281 PMCID: PMC9294547 DOI: 10.3389/fpls.2022.898740] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 05/13/2022] [Indexed: 05/27/2023]
Abstract
The knowledge of the organization of the domesticated gene pool of crop species is an essential requirement to understand crop evolution, to rationalize conservation programs, and to support practical decisions in plant breeding. Here, we integrate simple sequence repeat (SSR) analysis and phenotypic characterization to investigate a globe artichoke collection that comprises most of the varieties cultivated worldwide. We show that the cultivated gene pool of globe artichoke includes five distinct genetic groups associated with the major phenotypic typologies: Catanesi (which based on our analysis corresponds to Violetti di Provenza), Spinosi, Violetti di Toscana, Romaneschi, and Macau. We observed that 17 and 11% of the molecular and phenotypic variance, respectively, is between these groups, while within groups, strong linkage disequilibrium and heterozygote excess are evident. The divergence between groups for quantitative traits correlates with the average broad-sense heritability within the groups. The phenotypic divergence between groups for both qualitative and quantitative traits is strongly and positively correlated with SSR divergence (FST) between groups. All this implies a low population size and strong bottleneck effects, and indicates a long history of clonal propagation and selection during the evolution of the domesticated gene pool of globe artichoke. Moreover, the comparison between molecular and phenotypic population structures suggests that harvest time, plant architecture (i.e., plant height, stem length), leaf spininess, head morphology (i.e., head shape, bract shape, spininess) together with the number of heads per plant were the main targets of selection during the evolution of the cultivated germplasm. We emphasize our findings in light of the potential exploitation of this collection for association mapping studies.
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Affiliation(s)
- Domenico Rau
- Dipartimento di Agraria, Sezione di Agronomia, Coltivazioni Erbacee e Genetica (SACEG), Università degli Studi di Sassari, Sassari, Italy
| | - Giovanna Attene
- Dipartimento di Agraria, Sezione di Agronomia, Coltivazioni Erbacee e Genetica (SACEG), Università degli Studi di Sassari, Sassari, Italy
| | - Monica Rodriguez
- Dipartimento di Agraria, Sezione di Agronomia, Coltivazioni Erbacee e Genetica (SACEG), Università degli Studi di Sassari, Sassari, Italy
| | - Limbo Baghino
- Agenzia AGRIS Sardegna (Servizio Ricerca sui Sistemi Colturali Erbacei, Settore Innovazione dei Modelli Gestionali e Studio Della Biodiversità Nelle Colture Intensive), Oristano, Italy
| | - Anna Barbara Pisanu
- Agenzia AGRIS Sardegna (Servizio Ricerca sui Sistemi Colturali Erbacei, Settore Innovazione dei Modelli Gestionali e Studio Della Biodiversità Nelle Colture Intensive), Oristano, Italy
| | - Davide Sanna
- Agenzia AGRIS Sardegna (Servizio Ricerca sui Sistemi Colturali Erbacei, Settore Innovazione dei Modelli Gestionali e Studio Della Biodiversità Nelle Colture Intensive), Oristano, Italy
| | - Alberto Acquadro
- Dipartimento di Scienze Agrarie, Forestali ed Alimentari (DISAFA), Genetica Vegetale (Plant Genetics), Università degli Studi di Torino, Turin, Italy
| | - Ezio Portis
- Dipartimento di Scienze Agrarie, Forestali ed Alimentari (DISAFA), Genetica Vegetale (Plant Genetics), Università degli Studi di Torino, Turin, Italy
| | - Cinzia Comino
- Dipartimento di Scienze Agrarie, Forestali ed Alimentari (DISAFA), Genetica Vegetale (Plant Genetics), Università degli Studi di Torino, Turin, Italy
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Ikeda Y, Motokawa M. Phylogeography of the Japanese greater horseshoe bat Rhinolophus nippon (Mammalia: Chiroptera) in Northeast Asia: New insight into the monophyly of the Japanese populations. Ecol Evol 2021; 11:18181-18195. [PMID: 35003666 PMCID: PMC8717313 DOI: 10.1002/ece3.8414] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 11/11/2021] [Accepted: 11/16/2021] [Indexed: 11/29/2022] Open
Abstract
The Japanese greater horseshoe bat (Rhinolophus nippon) is distributed widely in East Asia. Within the species, R. nippon in Northeast Asia is regarded as the lineage that diverged most recently. However, the monophyly of the Japanese populations is unclear due to insufficient data about phylogenetic relationship of the western Japanese populations. To test the monophyly of the Japanese populations of R. nippon, we sampled R. nippon from western Japan and performed a phylogeographic analysis based on mitochondrial DNA cytochrome b and the D-loop. The Northeast Asian lineage consisted of three main clades in eastern Japan (clade I), western Japan (clade II), and the continent as well as the Kumamoto population in westernmost Japan (clade III). The results of this study do not support the monophyly of the Japanese population. The findings suggest the "reverse colonization" of R. nippon from the Japanese Archipelago to the Eurasian continent, and provide important insight into the role of the island system in creation and supply of diversity to the continent.
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Affiliation(s)
- Yugo Ikeda
- Graduate School of ScienceKyoto UniversitySakyoKyotoJapan
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Lack of intraspecific variations of the mitochondrial cytochrome b gene in the greater mouse-tailed bat Rhinopoma microphyllum (Chiroptera: Rhinopomatidae) in Iran. Genetica 2020; 149:37-45. [PMID: 33247794 DOI: 10.1007/s10709-020-00109-z] [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: 01/15/2020] [Accepted: 11/13/2020] [Indexed: 10/22/2022]
Abstract
Rhinopoma microphyllum is one of the species of bats that lives in arid and semi-arid areas of Iran. The initial suggestion of the presence of two subspecies R. m. microphyllum and R. m. harrisoni based on their morphological characteristics has been questioned on the basis of small differences between the populations. Later, other researchers assigned Iranian populations of this species to one or two subspecies based on their morphological and molecular characteristics. The present study provides a phylogeographical analysis of this species using 687 bp of the mitochondrial cytochrome b in 81 bats in Iran, Jordan, Levant and Ethiopia. Based on mtDNA sequences, we found a low degree of genetic diversity in the Iranian populations of R. microphyllum (π = 0.0025), which shows a close relationship between the haplotypes. The analysis of genetic distance (0.15-1.93%), phylogenetic trees, and statistical parsimony network showed that all Iranian samples were grouped in the same clade, while Levant, Jordan and Ethiopian samples belonged to a different clade. Molecular dating suggested the Iranian R. microphyllum lineage split from the R. microphyllum of the Levant and Jordan clade during the Pliocene 3.18 (2.11-4.32 Ma). Taking these results into consideration, we can conclude that all Iranian specimens belong to the same subspecies as R. m. harrisoni since molecular results indicate that Iranian samples are differ from Levant subspecies (R. m. microphyllum).
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Kafaei S, Sharifi M, Akmali V. Population Genetic Structure and Phylogeography of the Small Mouse-Tailed Bat, Rhinopoma muscatellum Thomas, 1903 (Chiroptera: Rhinopomatidae) in Iran Inferred from Mitochondrial DNA. ACTA CHIROPTEROLOGICA 2020. [DOI: 10.3161/15081109acc2020.22.1.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Sasan Kafaei
- Department of Biology, Faculty of Science, Razi University, Kermanshah, Iran
| | - Mozafar Sharifi
- Department of Biology, Faculty of Science, Razi University, Kermanshah, Iran
| | - Vahid Akmali
- Department of Biology, Faculty of Science, Razi University, Kermanshah, Iran
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8
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Ikeda Y, Jiang T, Oh H, Csorba G, Motokawa M. Geographic variations of skull morphology in the Rhinolophus ferrumequinum species complex (Mammalia: Chiroptera). ZOOL ANZ 2020. [DOI: 10.1016/j.jcz.2020.08.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Mao X, Rossiter SJ. Genome-wide data reveal discordant mitonuclear introgression in the intermediate horseshoe bat (Rhinolophus affinis). Mol Phylogenet Evol 2020; 150:106886. [PMID: 32534185 DOI: 10.1016/j.ympev.2020.106886] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 06/01/2020] [Accepted: 06/03/2020] [Indexed: 10/24/2022]
Abstract
Closely related taxa often exhibit mitonuclear discordance attributed to introgression of mitochondrial DNA (mtDNA), yet few studies have considered the underlying causes of mtDNA introgression. Here we test for demographic versus adaptive processes as explanations for mtDNA introgression in three subspecies of the intermediate horseshoe bat (Rhinolophus affinis). We generated sequences of 1692 nuclear genes and 13 mitochondrial protein-coding genes for 48 individuals. Phylogenetic reconstructions based on 320 exon sequences and 2217 single nucleotide polymorphisms (SNPs) both revealed conflicts between the species tree and mtDNA tree. These results, together with geographic patterns of mitonuclear discordance, and shared identical or near-identical mtDNA sequences, suggest extensive introgression of mtDNA between the two parapatric mainland subspecies. Under demographic hypotheses, we would also expect to uncover traces of ncDNA introgression, however, population structure and gene flow analyses revealed little nuclear admixture. Furthermore, we found inconsistent estimates of the timing of population expansion and that of the most recent common ancestor for the clade containing introgressed haplotypes. Without a clear demographic explanation, we also examined whether introgression likely arises from adaptation. We found that five mtDNA genes contained fixed amino acid differences between introgressed and non-introgressed individuals, including putative positive selection found in one codon, although this did not show introgression. While our evidence for rejecting demographic hypotheses is arguably stronger than that for rejecting adaptation, we find no definitive support for either explanation. Future efforts will focus on larger-scale resequencing to decipher the underlying causes of discordant mitonuclear introgression in this system.
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Affiliation(s)
- Xiuguang Mao
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200062, China; Institute of Eco-Chongming (IEC), East China Normal University, Shanghai 200062, China.
| | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK.
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Mehdizadeh R, Akmali V, Sharifi M. Population genetic structure and phylogeography of the greater horseshoe bat ( Rhinolophus ferrumequinum) along Alborz and Zagros Mts. in Iran. Mitochondrial DNA A DNA Mapp Seq Anal 2020; 31:87-97. [PMID: 32202175 DOI: 10.1080/24701394.2020.1741562] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
In this paper, we investigate the genetic structure and phylogeography of Rhinolophus ferrumequinum, using the mitochondrial cytochrome b gene (1017 bp) in Iran and adjacent regions. The total haplotype and nucleotide diversity are 0.63 ± 0.055 and 0.0021 ± 0.00017, respectively which suggest that R. ferrumequinum exhibits low genetic diversity. AMOVA analysis shows that more variation of genetic differentiation is present among populations of phylogenetic groupings than within populations. Our phylogenetic results support the monophyly of R. ferrumequinum and suggest this taxon comprises three allopatric/parapatric phylogroups that are distributed in Europe-western Turkey, eastern Turkey-northern Iran, and southern Iran. The Europe-western Turkey lineage (clade 2) split from the eastern Turkey-Iran lineage (clade 1) during the middle Pleistocene (0.8534 (ca.I)-0.6454 (ca.II) Ma). The divergence time among subclades A and B occurred during the mid-Pleistocene (0.4849 (ca.I)-0.369 (ca.II) Ma). All phylogenetic analyses also indicate that the Iranian and eastern Turkey R. ferrumequinum diverged from Europe and western Turkey R. ferrumequinum, with the mean percentage sequence differences ranging from 0.92%-0.75% between them. We infer that long-term isolation of R. ferrumequinum in spatially distinct refugia in parts of southwestern and northeastern Iran has promoted distinct phylogeographic lineages during the Pleistocene.
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Affiliation(s)
- Robab Mehdizadeh
- Department of Biology, Faculty of Science, Razi University, Baghabrisham, Kermanshah, Iran
| | - Vahid Akmali
- Department of Biology, Faculty of Science, Razi University, Baghabrisham, Kermanshah, Iran
| | - Mozafar Sharifi
- Department of Biology, Faculty of Science, Razi University, Baghabrisham, Kermanshah, Iran
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Yue X, Hughes AC, Tomlinson KW, Xia S, Li S, Chen J. Body size and diet–related morphological variation of bats over the past 65 years in China. J Mammal 2019. [DOI: 10.1093/jmammal/gyz161] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Abstract
We examined both historical (1960s) and recent (2017) specimens of an insectivorous bat species (Hipposideros armiger) and a phytophagous bat (Rousettus leschenaultii) from the same latitudinal range to explore phenotypic responses to environmental change in China over the past 65 years. Hipposideros armiger exhibited significant increases in forearm length and three diet-related cranial traits, as well as carbon and nitrogen stable isotope composition, suggesting that modern H. armiger must travel farther for food and may now use different food resources. In contrast, R. leschenaultii showed no change in forearm length but displayed significant increases in diet-related cranial traits. This study provides evidence for differential responses to recent environmental changes in bat species with different diets. The changes in diet-related traits of the two species and the forearm length change on the insectivorous bats suggest that recent phenotypic changes may be adaptions to land-use changes rather than to climate change.
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Affiliation(s)
- Xinke Yue
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Alice C Hughes
- Centre for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, China
| | - Kyle W Tomlinson
- Centre for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, China
| | - Shangwen Xia
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, China
| | - Song Li
- Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Jin Chen
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, China
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Lisón F, Jiménez‐Franco MV, Altamirano A, Haz Á, Calvo JF, Jones G. Bat ecology and conservation in semi‐arid and arid landscapes: a global systematic review. Mamm Rev 2019. [DOI: 10.1111/mam.12175] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Fulgencio Lisón
- Laboratorio de Ecología del Paisaje y Conservación Departamento de Ciencias Forestales Universidad de La Frontera Box‐45D Temuco Chile
- Departamento de Zoología Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Casilla 160-C Concepción Chile
| | - María V. Jiménez‐Franco
- Área de Ecología Departamento de Biología Aplicada Universidad Miguel Hernández Avda. Universidad, s/n. Edf. Vinalopó 03202 Elche, Alicante Spain
- Department of Ecological Modelling UFZ‐Helmholtz Centre for Environmental Research D‐04301 Leipzig Germany
| | - Adison Altamirano
- Laboratorio de Ecología del Paisaje y Conservación Departamento de Ciencias Forestales Universidad de La Frontera Box‐45D Temuco Chile
| | - Ángeles Haz
- Paseo Rosales 10 4D, Molina de Segura 30500 Murcia Spain
| | - José F. Calvo
- Departamento de Ecología e Hidrología Universidad de Murcia 30100 Campus de Espinardo Murcia Spain
| | - Gareth Jones
- School of Biological Sciences University of Bristol 24 Tyndall Avenue BS8 1TQ Bristol UK
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Tournayre O, Pons J, Leuchtmann M, Leblois R, Piry S, Filippi‐Codaccioni O, Loiseau A, Duhayer J, Garin I, Mathews F, Puechmaille S, Charbonnel N, Pontier D. Integrating population genetics to define conservation units from the core to the edge of Rhinolophus ferrumequinum western range. Ecol Evol 2019; 9:12272-12290. [PMID: 31832159 PMCID: PMC6854333 DOI: 10.1002/ece3.5714] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 09/11/2019] [Accepted: 09/11/2019] [Indexed: 11/06/2022] Open
Abstract
The greater horseshoe bat (Rhinolophus ferrumequinum) is among the most widespread bat species in Europe but it has experienced severe declines, especially in Northern Europe. This species is listed Near Threatened in the European IUCN Red List of Threatened Animals, and it is considered to be highly sensitive to human activities and particularly to habitat fragmentation. Therefore, understanding the population boundaries and demographic history of populations of this species is of primary importance to assess relevant conservation strategies. In this study, we used 17 microsatellite markers to assess the genetic diversity, the genetic structure, and the demographic history of R. ferrumequinum colonies in the western part of its distribution. We identified one large population showing high levels of genetic diversity and large population size. Lower estimates were found in England and northern France. Analyses of clustering and isolation by distance suggested that the Channel and the Mediterranean seas could impede R. ferrumequinum gene flow. These results provide important information to improve the delineation of R. ferrumequinum management units. We suggest that a large management unit corresponding to the population ranging from Spanish Basque Country to northern France must be considered. Particular attention should be given to mating territories as they seem to play a key role in maintaining high levels of genetic mixing between colonies. Smaller management units corresponding to English and northern France colonies must also be implemented. These insular or peripheral colonies could be at higher risk of extinction in the near future.
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Affiliation(s)
- Orianne Tournayre
- CBGPINRACIRADIRDMontpellier SupAgroUniversité de MontpellierMontferrier‐sur‐Lez CedexFrance
| | - Jean‐Baptiste Pons
- LabEx ECOFECT «Ecoevolutionary Dynamics of Infectious Diseases»Université de LyonLyonFrance
| | | | - Raphael Leblois
- CBGPINRACIRADIRDMontpellier SupAgroUniversité de MontpellierMontferrier‐sur‐Lez CedexFrance
| | - Sylvain Piry
- CBGPINRACIRADIRDMontpellier SupAgroUniversité de MontpellierMontferrier‐sur‐Lez CedexFrance
| | | | - Anne Loiseau
- CBGPINRACIRADIRDMontpellier SupAgroUniversité de MontpellierMontferrier‐sur‐Lez CedexFrance
| | - Jeanne Duhayer
- LabEx ECOFECT «Ecoevolutionary Dynamics of Infectious Diseases»Université de LyonLyonFrance
| | - Inazio Garin
- Department of Zoology and Animal Cell BiologyUniversity of the Basque CountryLeioaThe Basque Country
| | - Fiona Mathews
- College of Life SciencesUniversity of SussexFalmerUK
| | - Sébastien Puechmaille
- ISEMUniv MontpellierCNRSEPHEIRDMontpellierFrance
- Groupe Chiroptères de Midi‐Pyrénées (CREN‐GCMP)ToulouseFrance
| | - Nathalie Charbonnel
- CBGPINRACIRADIRDMontpellier SupAgroUniversité de MontpellierMontferrier‐sur‐Lez CedexFrance
| | - Dominique Pontier
- LabEx ECOFECT «Ecoevolutionary Dynamics of Infectious Diseases»Université de LyonLyonFrance
- CNRSLaboratoire de Biométrie et Biologie ÉvolutiveUMR5558Université Lyon 1Université de LyonVilleurbanneFrance
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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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15
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Chattopadhyay B, Garg KM, Ray R, Rheindt FE. Fluctuating fortunes: genomes and habitat reconstructions reveal global climate-mediated changes in bats' genetic diversity. Proc Biol Sci 2019; 286:20190304. [PMID: 31530139 PMCID: PMC6784725 DOI: 10.1098/rspb.2019.0304] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 08/23/2019] [Indexed: 12/21/2022] Open
Abstract
Over the last approximately 2.6 Myr, Earth's climate has been dominated by cyclical ice ages that have profoundly affected species' population sizes, but the impact of impending anthropogenic climate change on species' extinction potential remains a worrying problem. We investigated 11 bat species from different taxonomic, ecological and geographical backgrounds using combined information from palaeoclimatic habitat reconstructions and genomes to analyse biotic impacts of historic climate change. We discover tightly correlated fluctuations between species' historic distribution and effective population size, identify frugivores as particularly susceptible to global warming, pinpoint large insectivores as having overall low effective population size and flag the onset of the Holocene (approx. 10-12 000 years ago) as the period with the generally lowest effective population sizes across the last approximately 1 Myr. Our study shows that combining genomic and palaeoclimatological approaches reveals effects of climatic shifts on genetic diversity and may help predict impacts of future climate change.
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Affiliation(s)
| | - Kritika M. Garg
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Rajasri Ray
- Center for Ecological Sciences, Indian Institute of Science, Bangalore, 560012 Karnataka, India
- Centre for Studies in Ethnobiology, Biodiversity and Sustainability (CEiBa), BG Road, Mokdumpur, Malda-732103 West Bengal, India
| | - Frank E. Rheindt
- Department of Biological Sciences, National University of Singapore, Singapore
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16
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Zhao H, Wang H, Liu T, Liu S, Jin L, Huang X, Dai W, Sun K, Feng J. Gene expression vs. sequence divergence: comparative transcriptome sequencing among natural Rhinolophus ferrumequinum populations with different acoustic phenotypes. Front Zool 2019; 16:37. [PMID: 31528181 PMCID: PMC6743130 DOI: 10.1186/s12983-019-0336-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 09/04/2019] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Although the sensory drive hypothesis can explain the geographic variation in echolocation frequencies of some bat species, the molecular mechanisms underlying this phenomenon are still unclear. The three lineages of greater horseshoe bat (Rhinolophus ferrumequinum) in China (northeast, central-east, and southwest) have significant geographic variation in resting frequencies (RF) of echolocation calls. Because their cochleae have an acoustic fovea that is highly sensitive to a narrow range of frequencies, we reported the transcriptomes of cochleae collected from three genetic lineages of R. ferrumequinum, which is an ideal organism for studying geographic variation in echolocation signals, and tried to understand the mechanisms behind this bat phenomenon by analyzing gene expression and sequence variation. RESULTS A total of 8190 differentially expressed genes (DEGs) were identified. We identified five modules from all DEGs that were significantly related to RF or forearm length (FL). DEGs in the RF-related modules were significantly enriched in the gene categories involved in neural activity, learning, and response to sound. DEGs in the FL-related modules were significantly enriched in the pathways related to muscle and actin functions. Using 21,945 single nucleotide polymorphisms, we identified 18 candidate unigenes associated with hearing, five of which were differentially expressed among the three populations. Additionally, the gene ERBB4, which regulates diverse cellular processes in the inner ear such as cell proliferation and differentiation, was in the largest module. We also found 49 unigenes that were under positive selection from 4105 one-to-one orthologous gene pairs between the three R. ferrumequinum lineages and three other Chiroptera species. CONCLUSIONS The variability of gene expression and sequence divergence at the molecular level might provide evidence that can help elucidate the genetic basis of geographic variation in echolocation signals of greater horseshoe bats.
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Affiliation(s)
- Hanbo Zhao
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, 130117 China
| | - Hui Wang
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, 130117 China
| | - Tong Liu
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, 130117 China
| | - Sen Liu
- Institute of Resources & Environment, Henan Polytechnic University, Jiaozuo, 454000 China
| | - Longru Jin
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, 130117 China
| | - Xiaobin Huang
- Vector Laboratory, Institute of Pathogens and Vectors, Branch of Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali University, Dali, 671003 China
| | - Wentao Dai
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, 130117 China
| | - Keping Sun
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, 130117 China
| | - Jiang Feng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, 130117 China
- College of Life Science, Jilin Agricultural University, Changchun, 130118 China
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17
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Centeno‐Cuadros A, Razgour O, García‐Mudarra JL, Mingo‐Casas P, Sandonís V, Redondo A, Ibáñez C, Paz O, Martinez‐Alós S, Pérez Suarez G, Echevarría JE, Juste J. Comparative phylogeography and asymmetric hybridization between cryptic bat species. J ZOOL SYST EVOL RES 2019. [DOI: 10.1111/jzs.12318] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
| | - Orly Razgour
- Biological Sciences University of Southampton Southampton UK
| | | | | | | | - Adrián Redondo
- Departmento de Ecología Evolutiva Estación Biológica de Doñana (CSIC) Sevilla Spain
| | - Carlos Ibáñez
- Departmento de Ecología Evolutiva Estación Biológica de Doñana (CSIC) Sevilla Spain
| | - Oscar Paz
- Departamento de Ciencias de la Vida, Facultad de Ciencias Universidad de Alcalá Alcalá de Henares, Madrid Spain
| | - Susana Martinez‐Alós
- Departamento de Ciencias de la Vida, Facultad de Ciencias Universidad de Alcalá Alcalá de Henares, Madrid Spain
| | - Gonzalo Pérez Suarez
- Departamento de Ciencias de la Vida, Facultad de Ciencias Universidad de Alcalá Alcalá de Henares, Madrid Spain
| | - Juan E. Echevarría
- Instituto de Salud Carlos III Majadahonda, Madrid Spain
- CIBER de Epidemiología y Salud Pública, CIBERESP Madrid Spain
| | - Javier Juste
- Departmento de Ecología Evolutiva Estación Biológica de Doñana (CSIC) Sevilla Spain
- CIBER de Epidemiología y Salud Pública, CIBERESP Madrid Spain
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18
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Riddle BR, Jezkova T. How is phylogeography shaping our understanding of the geography of diversity, diversification, and range dynamics in mammals? J Mammal 2019. [DOI: 10.1093/jmammal/gyz027] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Brett R Riddle
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, USA
| | - Tereza Jezkova
- Department of Biology, Miami University of Ohio, Oxford, OH, USA
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19
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McKee CD, Krawczyk AI, Sándor AD, Görföl T, Földvári M, Földvári G, Dekeukeleire D, Haarsma AJ, Kosoy MY, Webb CT, Sprong H. Host Phylogeny, Geographic Overlap, and Roost Sharing Shape Parasite Communities in European Bats. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00069] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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20
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Contemporary and historical river connectivity influence population structure in western brook lamprey in the Columbia River Basin. CONSERV GENET 2018. [DOI: 10.1007/s10592-018-1137-9] [Citation(s) in RCA: 5] [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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21
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Andriollo T, Ashrafi S, Arlettaz R, Ruedi M. Porous barriers? Assessment of gene flow within and among sympatric long-eared bat species. Ecol Evol 2018; 8:12841-12854. [PMID: 30619587 PMCID: PMC6309003 DOI: 10.1002/ece3.4714] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 10/18/2018] [Accepted: 10/30/2018] [Indexed: 11/11/2022] Open
Abstract
Species are the basic units for measuring biodiversity and for comprehending biological interactions. Yet, their delineation is often contentious, especially in groups that are both diverse and phenotypically conservative. Three cryptic species of long-eared bats, Plecotus auritus, P. austriacus, and P. macrobullaris, co-occur over extensive areas of Western Europe. The latter is a fairly recent discovery, questioning the overall diversity of the entire Plecotus complex. Yet, high morphological and acoustic similarities compromise the reliable identification of long-eared bats in the field. We postulate that such extensive phenotypic overlap, along with the recurrent observation of morphologically intermediate individuals, may hide rampant interspecific hybridization. Based on a geographic sampling centered on areas of sympatry in the Alps and Corsica, we assessed the level of reproductive isolation of these three Plecotus species with mitochondrial and nuclear markers, looking at both inter- and intraspecific genetic population structuring. No sign of hybridization was detected between these three species that appear well separated biologically. Genetic structuring of populations, however, reflected different species-specific responses to environmental connectivity, that is, to the presence of orographic or sea barriers. While the Alpine range and the Ligurian Sea coincided with sharp genetic discontinuities in P. macrobullaris and P. austriacus, the more ubiquitous P. auritus showed no significant population structuration. There were clear phylogeographic discrepancies between microsatellite and mitochondrial markers at the intraspecific level, however, which challenges the reliance on simple barcoding approaches for the delineation of sound conservation units.
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Affiliation(s)
- Tommy Andriollo
- Department of Mammalogy and OrnithologyNatural History Museum of GenevaGenevaSwitzerland
- Section of Biology, Faculty of SciencesUniversity of GenevaGenevaSwitzerland
| | - Sohrab Ashrafi
- Department of Environmental Sciences, Faculty of Natural ResourcesUniversity of TehranKarajIran
| | - Raphaël Arlettaz
- Division of Conservation Biology, Institute of Ecology and EvolutionUniversity of BernBernSwitzerland
| | - Manuel Ruedi
- Department of Mammalogy and OrnithologyNatural History Museum of GenevaGenevaSwitzerland
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22
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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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23
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Stone GN, White SC, Csóka G, Melika G, Mutun S, Pénzes Z, Sadeghi SE, Schönrogge K, Tavakoli M, Nicholls JA. Tournament ABC analysis of the western Palaearctic population history of an oak gall wasp,Synergus umbraculus. Mol Ecol 2017; 26:6685-6703. [DOI: 10.1111/mec.14372] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 09/16/2017] [Accepted: 09/18/2017] [Indexed: 01/17/2023]
Affiliation(s)
- Graham N. Stone
- Institute of Evolutionary Biology; University of Edinburgh; Edinburgh UK
| | - Sarah C. White
- Institute of Evolutionary Biology; University of Edinburgh; Edinburgh UK
| | - György Csóka
- National Agricultural Research and Innovation Centre; Forest Research Institute; Mátrafüred Hungary
| | - George Melika
- Plant Health and Molecular Biology Laboratory; Directorate of Plant Protection, Soil Conservation and Agri-environment; Budapest Hungary
| | - Serap Mutun
- Department of Biology; Faculty of Science and Arts; Abant İzzet Baysal University; Bolu Turkey
| | - Zsolt Pénzes
- Department of Ecology; Faculty of Science and Informatics; University of Szeged; Szeged Hungary
| | - S. Ebrahim Sadeghi
- Agricultural Research, Education and Extension Organization (AREEO); Research Institute of Forests and Rangelands of Iran; Tehran Iran
| | | | - Majid Tavakoli
- Lorestan Agriculture and Natural Resources Research Center; Khorramabad Lorestan Iran
| | - James A. Nicholls
- Institute of Evolutionary Biology; University of Edinburgh; Edinburgh UK
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24
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Novel Alphacoronaviruses and Paramyxoviruses Cocirculate with Type 1 and Severe Acute Respiratory System (SARS)-Related Betacoronaviruses in Synanthropic Bats of Luxembourg. Appl Environ Microbiol 2017; 83:AEM.01326-17. [PMID: 28710271 DOI: 10.1128/aem.01326-17] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 07/05/2017] [Indexed: 01/21/2023] Open
Abstract
Several infectious disease outbreaks with high mortality in humans have been attributed to viruses that are thought to have evolved from bat viruses. In this study from Luxembourg, the genetic diversity and epidemiology of paramyxoviruses and coronaviruses shed by the bat species Rhinolophus ferrumequinum and Myotis emarginatus were evaluated. Feces collection (n = 624) was performed longitudinally in a mixed-species colony in 2015 and 2016. In addition, feces (n = 254) were collected cross-sectionally from six Myotis emarginatus colonies in 2016. By use of degenerate primers in a nested format, overall prevalences of 1.1% (10/878) and 4.9% (43/878) were determined for paramyxoviruses and coronaviruses. Sequences of the partial RNA-dependent RNA polymerase and spike glycoprotein genes of coronaviruses, as well as sequences of the partial L gene of paramyxoviruses, were obtained. Novel paramyxovirus and Alphacoronavirus strains were identified in different Myotis emarginatus colonies, and severe acute respiratory syndrome (SARS)-related Betacoronavirus strains were shed by Rhinolophus ferrumequinum Logistic regression revealed that the level of Alphacoronavirus shedding was highest in July (odds ratio, 2.8; P < 0.01), probably due to periparturient stress. Phylogenetic analyses point to close virus-host coevolution, and the high genetic similarity of the study strains suggests that the Myotis emarginatus colonies in Luxembourg are socially connected. Most interestingly, we show that bats also host Betacoronavirus1 strains. The high similarity of the spike gene sequences of these viruses with mammalian Betacoronavirus 1 strains may be of concern. Both the SARS-related and Betacoronavirus 1 strains detected in bats in Luxembourg may cross the species barrier after a host adaptation process.IMPORTANCE Bats are a natural reservoir of a number of zoonotic pathogens. Several severe outbreaks in humans (e.g., a Nipah virus outbreak in Malaysia in 1998, and the almost global spread of severe acute respiratory syndrome in 2003) have been caused by bat-borne viruses that were transmitted to humans mostly after virus adaptation (e.g., in intermediate animal hosts). Despite the indigenousness of bat species that host viruses with suspected zoonotic potential and despite the zoonotic transmission of European bat 1 lyssavirus in Luxembourg, knowledge about the diversity and epidemiology of bat viruses remains limited in this country. Moreover, in contrast to other European countries, bat viruses are currently not included in the national surveillance activities of this land-locked country. We suggest that this gap in disease surveillance should be addressed, since we show here that synanthropic bats host viruses that may be able to cross the species barrier.
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25
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Shahabi S, Akmali V, Sharifi M. Taxonomic Evaluation of the Greater Horseshoe Bat Rhinolophus ferrumequinum (Chiroptera: Rhinolophidae) in Iran Inferred from the Mitochondrial D-Loop Gene. Zoolog Sci 2017; 34:361-367. [DOI: 10.2108/zs170001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Saeed Shahabi
- Department of Biology, Faculty of Science, Razi University, Kermanshah, Iran
| | - Vahid Akmali
- Department of Biology, Faculty of Science, Razi University, Kermanshah, Iran
| | - Mozafar Sharifi
- Department of Biology, Faculty of Science, Razi University, Kermanshah, Iran
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26
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Where can introduced populations learn their tricks? Searching for the geographical source of a species introduction to the Galápagos archipelago. CONSERV GENET 2017. [DOI: 10.1007/s10592-017-0988-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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27
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Chan J, Li W, Hu X, Liu Y, Xu Q. Genetic diversity and population structure analysis of Qinghai-Tibetan plateau schizothoracine fish (Gymnocypris dobula) based on mtDNA D-loop sequences. BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2016.09.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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28
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Sun K, Kimball RT, Liu T, Wei X, Jin L, Jiang T, Lin A, Feng J. The complex evolutionary history of big-eared horseshoe bats (Rhinolophus macrotis complex): insights from genetic, morphological and acoustic data. Sci Rep 2016; 6:35417. [PMID: 27748429 PMCID: PMC5066199 DOI: 10.1038/srep35417] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 09/27/2016] [Indexed: 12/21/2022] Open
Abstract
Palaeoclimatic oscillations and different landscapes frequently result in complex population-level structure or the evolution of cryptic species. Elucidating the potential mechanisms is vital to understanding speciation events. However, such complex evolutionary patterns have rarely been reported in bats. In China, the Rhinolophus macrotis complex contains a large form and a small form, suggesting the existence of a cryptic bat species. Our field surveys found these two sibling species have a continuous and widespread distribution with partial sympatry. However, their evolutionary history has received little attention. Here, we used extensive sampling, morphological and acoustic data, as well as different genetic markers to investigate their evolutionary history. Genetic analyses revealed discordance between the mitochondrial and nuclear data. Mitochondrial data identified three reciprocally monophyletic lineages: one representing all small forms from Southwest China, and the other two containing all large forms from Central and Southeast China, respectively. The large form showed paraphyly with respect to the small form. However, clustering analyses of microsatellite and Chd1 gene sequences support two divergent clusters separating the large form and the small form. Moreover, morphological and acoustic analyses were consistent with nuclear data. This unusual pattern in the R. macrotis complex might be accounted for by palaeoclimatic oscillations, shared ancestral polymorphism and/or interspecific hybridization.
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Affiliation(s)
- Keping Sun
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Rebecca T Kimball
- Department of Biology, University of Florida, Gainesville, Florida, United States of America
| | - Tong Liu
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Xuewen Wei
- 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
| | - Tinglei Jiang
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Aiqing Lin
- 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
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Liu T, Sun K, Park YC, Feng J. Phylogenetic relationships and evolutionary history of the greater horseshoe bat, Rhinolophus ferrumequinum, in Northeast Asia. PeerJ 2016; 4:e2472. [PMID: 27761309 PMCID: PMC5068396 DOI: 10.7717/peerj.2472] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 08/22/2016] [Indexed: 11/20/2022] Open
Abstract
The greater horseshoe bat, Rhinolophus ferrumequinum, is an important model organism for studies on chiropteran phylogeographic patterns. Previous studies revealed the population history of R. ferrumequinum from Europe and most Asian regions, yet there continue to be arguments about their evolutionary process in Northeast Asia. In this study, we obtained mitochondrial DNA cyt b and D-loop data of R. ferrumequinum from Northeast China, South Korea and Japan to clarify their phylogenetic relationships and evolutionary process. Our results indicate a highly supported monophyletic group of Northeast Asian greater horseshoe bats, in which Japanese populations formed a single clade and clustered into the mixed branches of Northeast Chinese and South Korean populations. We infer that R. ferrumequinum in Northeast Asia originated in Northeast China and South Korea during a cold glacial period, while some ancestors likely arrived in Japan by flying or land bridge and subsequently adapted to the local environment. Consequently, during the warm Eemian interglaciation, the Korea Strait, between Japan and South Korea, became a geographical barrier to Japanese and inland populations, while the Changbai Mountains, between China and North Korea, did not play a significant role as a barrier between Northeast China and South Korea populations.
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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
| | - Yung Chul Park
- Department of Forest Environment Protection, College of Forest and Environmental Science, Kangwon National University , Chuncheon , South Korea
| | - Jiang Feng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University , Changchun , China
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30
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Mende MB, Bartel M, Hundsdoerfer AK. A comprehensive phylogeography of the Hyles euphorbiae complex (Lepidoptera: Sphingidae) indicates a 'glacial refuge belt'. Sci Rep 2016; 6:29527. [PMID: 27439775 PMCID: PMC4954964 DOI: 10.1038/srep29527] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 06/08/2016] [Indexed: 12/20/2022] Open
Abstract
We test the morphology based hypothesis that the Western Palaearctic spurge hawkmoths represent two species, the Eurasian H. euphorbiae and Afro-Macaronesian H. tithymali. It has been suggested that these species merged into several hybrid swarm populations, although a mitochondrial phylogeography revealed substructure with local differentiation. We analysed a three-gene mt-dataset (889 individuals) and 12 microsatellite loci (892 individuals). Microsatellite analyses revealed an overall weak differentiation and corroborated the superordinate division into two clusters. The data indicate that the populations studied belong to only one species according to the biological species concept, refuting the opening hypothesis. A future taxonomic revision appears necessary to reflect the division into two subgroups. Ancestral mitochondrial polymorphisms are retained in H. euphorbiae, indicating gene flow within a broad 'glacial refuge belt' and ongoing postglacial gene flow. Diverse patterns of extensive mito-nuclear discordance in the Mediterranean and the Middle East presumably evolved by more recent processes. This discordance indicates introgression of H. tithymali-related mitochondrial haplogroups, accompanied (to a lesser degree) by nuclear alleles, into Italian and Aegean H. euphorbiae populations as recently as the late Holocene. The complex mosaic of divergence and reintegration is assumed to have been influenced by locally differing environmental barriers to gene flow.
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Affiliation(s)
- Michael B Mende
- Senckenberg Naturhistorische Sammlungen Dresden, Museum für Tierkunde, Königsbrücker Landstraße 159, D-01109 Dresden, Germany.,Georg-August-Universität Göttingen, Johann-Friedrich-Blumenbach-Institut für Zoologie und Anthropologie, Abteilung für Morphologie, Systematik und Evolutionsbiologie, Berliner Str. 28, D-37073 Göttingen, Germany.,Biodiversität und Klima Forschungszentrum (BiK-F), Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
| | - Manuela Bartel
- Senckenberg Naturhistorische Sammlungen Dresden, Museum für Tierkunde, Königsbrücker Landstraße 159, D-01109 Dresden, Germany
| | - Anna K Hundsdoerfer
- Senckenberg Naturhistorische Sammlungen Dresden, Museum für Tierkunde, Königsbrücker Landstraße 159, D-01109 Dresden, Germany.,Biodiversität und Klima Forschungszentrum (BiK-F), Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
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31
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Behavioural response of the greater horseshoe bat to geographical variation in echolocation calls. Behav Ecol Sociobiol 2016. [DOI: 10.1007/s00265-016-2182-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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32
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Hornok S, Estrada-Peña A, Kontschán J, Plantard O, Kunz B, Mihalca AD, Thabah A, Tomanović S, Burazerović J, Takács N, Görföl T, Estók P, Tu VT, Szőke K, Fernández de Mera IG, de la Fuente J, Takahashi M, Yamauchi T, Takano A. High degree of mitochondrial gene heterogeneity in the bat tick species Ixodes vespertilionis, I. ariadnae and I. simplex from Eurasia. Parasit Vectors 2015; 8:457. [PMID: 26382218 PMCID: PMC4573304 DOI: 10.1186/s13071-015-1056-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 08/26/2015] [Indexed: 02/13/2024] Open
Abstract
Background Phylogeographical studies allow precise genetic comparison of specimens, which were collected over large geographical ranges and belong to the same or closely related animal species. These methods have also been used to compare ticks of veterinary-medical importance. However, relevant data are missing in the case of ixodid ticks of bats, despite (1) the vast geographical range of both Ixodes vespertilionis and Ixodes simplex, and (2) the considerable uncertainty in their taxonomy, which is currently unresolvable by morphological clues. Methods In the present study 21 ticks were selected from collections or were freshly removed from bats or cave walls in six European and four Asian countries. The DNA was extracted and PCRs were performed to amplify part of the cytochrome oxidase I (COI), 16S and 12S rDNA genes, followed by sequencing for identification and molecular-phylogenetic comparison. Results No morphological differences were observed between Ixodes vespertilionis specimens from Spain and from other parts of Europe, but corresponding genotypes had only 94.6 % COI sequence identity. An I. vespertilionis specimen collected in Vietnam was different both morphologically and genetically (i.e. with only 84.1 % COI sequence identity in comparison with I. vespertilionis from Europe). Two ticks (collected in Vietnam and in Japan) formed a monophyletic clade and shared morphological features with I. ariadnae, recently described and hitherto only reported in Europe. In addition, two Asiatic specimens of I. simplex were shown to differ markedly from European genotypes of the same species. Phylogenetic relationships of ticks showed similar clustering patterns with those of their associated bat host species. Conclusions Although all three ixodid bat tick species evaluated in the present study appear to be widespread in Eurasia, they exhibit pronounced genetic differences. Data of this study also reflect that I. vespertilionis may represent a species complex.
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Affiliation(s)
- Sándor Hornok
- Department of Parasitology and Zoology, Faculty of Veterinary Science, Szent István University, Budapest, Hungary.
| | | | - Jenő Kontschán
- Plant Protection Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary.
| | - Olivier Plantard
- INRA, Biologie, Epidémiologie et Analyse de Risque en santé animale, Nantes, France. .,LUNAM Université, Oniris, Ecole nationale vétérinaire, agroalimentaire et de l'alimentation Nantes-Atlantique, Nantes, France.
| | - Bernd Kunz
- Independent researcher, Langenburg, Germany.
| | - Andrei D Mihalca
- Department of Parasitology and Parasitic Diseases, University of Agricultural Sciences and Veterinary Medicine, Cluj-Napoca, Romania.
| | - Adora Thabah
- Solar View Cottage, Upper Mawprem, Shillong, Meghalaya, India.
| | - Snežana Tomanović
- Laboratory for Medical Entomology, Centre of Exellence for Food and Vector-Borne Zoonoses, Institute for Medical Research, University of Belgrade, Belgrade, Serbia.
| | - Jelena Burazerović
- Chair of Animal Ecology and Zoogeography, Institute of Zoology, Faculty of Biology, University of Belgrade, Belgrade, Serbia.
| | - Nóra Takács
- Department of Parasitology and Zoology, Faculty of Veterinary Science, Szent István University, Budapest, Hungary.
| | - Tamás Görföl
- Department of Zoology, Hungarian Natural History Museum, Budapest, Hungary. .,Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary.
| | - Péter Estók
- Department of Zoology, Eszterházy Károly College, Eger, Hungary.
| | - Vuong Tan Tu
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, Hanoi, Vietnam.
| | - Krisztina Szőke
- Department of Parasitology and Zoology, Faculty of Veterinary Science, Szent István University, Budapest, Hungary.
| | | | - José de la Fuente
- SaBio. Instituto de Investigación en Recursos Cinegéticos IREC, Ciudad Real, Spain. .,Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, USA.
| | - Mamoru Takahashi
- Department of Anesthesiology, Saitama Medical University, Iruma-gun, Japan.
| | | | - Ai Takano
- Department of Veterinary Medicine, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan.
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Luis AD, O'Shea TJ, Hayman DTS, Wood JLN, Cunningham AA, Gilbert AT, Mills JN, Webb CT. Network analysis of host-virus communities in bats and rodents reveals determinants of cross-species transmission. Ecol Lett 2015; 18:1153-1162. [PMID: 26299267 PMCID: PMC5014217 DOI: 10.1111/ele.12491] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 05/13/2015] [Accepted: 07/15/2015] [Indexed: 01/16/2023]
Abstract
Bats are natural reservoirs of several important emerging viruses. Cross‐species transmission appears to be quite common among bats, which may contribute to their unique reservoir potential. Therefore, understanding the importance of bats as reservoirs requires examining them in a community context rather than concentrating on individual species. Here, we use a network approach to identify ecological and biological correlates of cross‐species virus transmission in bats and rodents, another important host group. We show that given our current knowledge the bat viral sharing network is more connected than the rodent network, suggesting viruses may pass more easily between bat species. We identify host traits associated with important reservoir species: gregarious bats are more likely to share more viruses and bats which migrate regionally are important for spreading viruses through the network. We identify multiple communities of viral sharing within bats and rodents and highlight potential species traits that can help guide studies of novel pathogen emergence.
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Affiliation(s)
- Angela D Luis
- Department of Biology, Colorado State University, Fort Collins, CO, 80523, USA.,Fogarty International Center, National Institutes of Health, Bethesda, MD, 20892, USA.,Wildlife Biology Program, Department of Ecosystem and Conservation Sciences, University of Montana, Missoula, MT, 59812, USA
| | - Thomas J O'Shea
- U.S. Geological Survey (retired), Fort Collins Science Center, Fort Collins, CO, 80526, USA
| | - David T S Hayman
- Department of Biology, Colorado State University, Fort Collins, CO, 80523, USA.,Department of Biology, University of Florida, Gainesville, FL, 32611, USA.,mEpiLab, Infectious Disease Research Centre (IDReC), Hopkirk Research Institute, Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, Manawatu, 4442, New Zealand
| | - James L N Wood
- Department of Veterinary Medicine, Disease Dynamics Unit, University of Cambridge, Cambridge, CB3 0ES, UK
| | - Andrew A Cunningham
- Institute of Zoology, Zoological Society of London, Regents Park, London, NW1 4RY, UK
| | - Amy T Gilbert
- National Wildlife Research Center, U.S. Department of Agriculture, Fort Collins, CO, 80521, USA
| | - James N Mills
- Population Biology, Ecology, and Evolution Program, Emory University, Atlanta, GA, 30322, USA
| | - Colleen T Webb
- Department of Biology, Colorado State University, Fort Collins, CO, 80523, USA
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Andriollo T, Naciri Y, Ruedi M. Two Mitochondrial Barcodes for one Biological Species: The Case of European Kuhl's Pipistrelles (Chiroptera). PLoS One 2015; 10:e0134881. [PMID: 26241944 PMCID: PMC4524706 DOI: 10.1371/journal.pone.0134881] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 07/14/2015] [Indexed: 11/18/2022] Open
Abstract
The Kuhl's pipistrelle (Pipistrellus kuhlii) is a Western Palaearctic species of bat that exhibits several deeply divergent mitochondrial lineages across its range. These lineages could represent cryptic species or merely ancient polymorphism, but no nuclear markers have been studied so far to properly assess the taxonomic status of these lineages. We examined here two lineages occurring in Western Europe, and used both mitochondrial and nuclear markers to measure degrees of genetic isolation between bats carrying them. The sampling focused on an area of strict lineage sympatry in Switzerland but also included bats from further south, in North Africa. All individuals were barcoded for the COI gene to identify their mitochondrial lineages and five highly polymorphic microsatellite loci were used to cluster them according to their nuclear genotypes. Despite this low number of nuclear markers, all North African nuclear genotypes were grouped in a highly distinct subpopulation when compared with European samples sharing the same mitochondrial barcodes. The reverse situation prevailed in Switzerland where bats carrying distinct barcodes had similar nuclear genotypes. There was a weak east/west nuclear structure of populations, but this was independent of mitochondrial lineages as bats carrying either variant were completely admixed. Thus, the divergent mitochondrial barcodes present in Western Europe do not represent cryptic species, but are part of a single biological species. We argue that these distinct barcodes evolved in allopatry and came recently into secondary contact in an area of admixture north of the Alps. Historical records from this area and molecular dating support such a recent bipolar spatial expansion. These results also highlight the need for using appropriate markers before claiming the existence of cryptic species based on highly divergent barcodes.
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Affiliation(s)
- Tommy Andriollo
- Muséum d’histoire naturelle de la Ville de Genève, BP 6434, 1211 Geneva 6, Switzerland
- Université de Genève, Faculté des Sciences, Section de biologie, 1211 Geneva 4, Switzerland
- * E-mail:
| | - Yamama Naciri
- Université de Genève, Faculté des Sciences, Section de biologie, 1211 Geneva 4, Switzerland
- Conservatoire et Jardin botaniques de la Ville de Genève and University of Geneva, BP 60, 1292 Chambésy, Geneva, Switzerland
| | - Manuel Ruedi
- Muséum d’histoire naturelle de la Ville de Genève, BP 6434, 1211 Geneva 6, Switzerland
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35
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Bailey SE, Mao X, Struebig M, Tsagkogeorga G, Csorba G, Heaney LR, Sedlock J, Stanley W, Rouillard JM, Rossiter SJ. The use of museum samples for large-scale sequence capture: a study of congeneric horseshoe bats (family Rhinolophidae). Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12620] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Sebastian E. Bailey
- School of Biological and Chemical Sciences; Queen Mary University of London; London E1 4NS UK
| | - Xiuguang Mao
- School of Biological and Chemical Sciences; Queen Mary University of London; London E1 4NS UK
- SKLEC; Institute of Molecular Ecology and Evolution; East China Normal University; Shanghai 200062 China
| | - Monika Struebig
- School of Biological and Chemical Sciences; Queen Mary University of London; London E1 4NS UK
- The Genome Centre; John Vane Science Centre; Queen Mary University of London; Charterhouse Square London EC1M 6BQ UK
| | - Georgia Tsagkogeorga
- School of Biological and Chemical Sciences; Queen Mary University of London; London E1 4NS UK
| | - Gabor Csorba
- Hungarian Natural History Museum; Baross 13 1088 Budapest Hungary
| | - Lawrence R. Heaney
- The Field Museum of Natural History; 1400 S. Lake Shore Drive Chicago IL 60605-2496 USA
| | - Jodi Sedlock
- The Field Museum of Natural History; 1400 S. Lake Shore Drive Chicago IL 60605-2496 USA
| | - William Stanley
- The Field Museum of Natural History; 1400 S. Lake Shore Drive Chicago IL 60605-2496 USA
| | | | - Stephen J. Rossiter
- School of Biological and Chemical Sciences; Queen Mary University of London; London E1 4NS UK
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36
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Moussy C, Atterby H, Griffiths AGF, Allnutt TR, Mathews F, Smith GC, Aegerter JN, Bearhop S, Hosken DJ. Population genetic structure of serotine bats (Eptesicus serotinus) across Europe and implications for the potential spread of bat rabies (European bat lyssavirus EBLV-1). Heredity (Edinb) 2015; 115:83-92. [PMID: 25832817 PMCID: PMC4815494 DOI: 10.1038/hdy.2015.20] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 01/29/2015] [Accepted: 02/12/2015] [Indexed: 11/09/2022] Open
Abstract
Understanding of the movements of species at multiple scales is essential to appreciate patterns of population connectivity and in some cases, the potential for pathogen transmission. The serotine bat (Eptesicus serotinus) is a common and widely distributed species in Europe where it frequently harbours European bat lyssavirus type 1 (EBLV-1), a virus causing rabies and transmissible to humans. In the United Kingdom, it is rare, with a distribution restricted to south of the country and so far the virus has never been found there. We investigated the genetic structure and gene flow of E. serotinus across the England and continental Europe. Greater genetic structuring was found in England compared with continental Europe. Nuclear data suggest a single population on the continent, although further work with more intensive sampling is required to confirm this, while mitochondrial sequences indicate an east-west substructure. In contrast, three distinct populations were found in England using microsatellite markers, and mitochondrial diversity was very low. Evidence of nuclear admixture indicated strong male-mediated gene flow among populations. Differences in connectivity could contribute to the high viral prevalence on the continent in contrast with the United Kingdom. Although the English Channel was previously thought to restrict gene flow, our data indicate relatively frequent movement from the continent to England highlighting the potential for movement of EBLV-1 into the United Kingdom.
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Affiliation(s)
- C Moussy
- Centre for Ecology and Conservation, University of Exeter, Cornwall Campus, Cornwall, UK
| | - H Atterby
- Food and Environment Research Agency, York, UK
| | - A G F Griffiths
- Environment and Sustainability Institute, University of Exeter, Cornwall Campus, Cornwall, UK
| | - T R Allnutt
- Food and Environment Research Agency, York, UK
- CSIRO, Werribee, Victoria, Australia
| | - F Mathews
- Hatherly Laboratories, College of Life and Environmental Sciences, University of Exeter, Exeter, UK
| | - G C Smith
- National Wildlife Management Centre, Animal Health and Veterinary Laboratories Agency (AHVLA), York, UK
| | - J N Aegerter
- National Wildlife Management Centre, Animal Health and Veterinary Laboratories Agency (AHVLA), York, UK
| | - S Bearhop
- Centre for Ecology and Conservation, University of Exeter, Cornwall Campus, Cornwall, UK
| | - D J Hosken
- Centre for Ecology and Conservation, University of Exeter, Cornwall Campus, Cornwall, UK
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From the field to the lab: best practices for field preservation of bat specimens for molecular analyses. PLoS One 2015; 10:e0118994. [PMID: 25798819 PMCID: PMC4370412 DOI: 10.1371/journal.pone.0118994] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Accepted: 12/18/2014] [Indexed: 11/19/2022] Open
Abstract
Studies in molecular ecology depend on field-collected samples for genetic information, and the tissue sampled and preservation conditions strongly affect the quality of the DNA obtained. DNA yields from different tissue types have seldom been compared, and the relative performance of storage media has never been directly tested, even though these media may influence DNA degradation under field conditions. We analyzed DNA yield from buccal swabs and wing punches harvested from live bats using nucleic acid quantification as well as quantitative PCR for a single-copy nuclear locus. We also compared DNA yields from wing tissue preserved in three media: ethanol, NaCl-saturated dimethyl sulfoxide (DMSO), and silica desiccant. Wing punches yielded more total DNA than did buccal swabs, and wing tissues preserved in silica beads yielded significantly more total and nuclear DNA than those preserved in DMSO or ethanol. These results show that tissue type and preservation media strongly influence the quantity of DNA obtained from non-lethal genetic samples, and based on these effects we provide recommendations for field collection of tissues for genetic analyses.
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Li S, Sun K, Lu G, Lin A, Jiang T, Jin L, Hoyt JR, Feng J. Mitochondrial genetic differentiation and morphological difference of Miniopterus fuliginosus and Miniopterus magnater in China and Vietnam. Ecol Evol 2015; 5:1214-23. [PMID: 25859327 PMCID: PMC4377265 DOI: 10.1002/ece3.1428] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2014] [Revised: 01/24/2015] [Accepted: 01/28/2015] [Indexed: 01/09/2023] Open
Abstract
Because of its complicated systematics, the bent-winged bat is one of the most frequently studied bat species groups. In China, two morphologically similar bent-winged bat species, Miniopterus fuliginosus and Miniopterus magnater were identified, but their distribution range and genetic differentiation are largely unexplored. In this study, we applied DNA bar codes and two other mitochondrial DNA genes including morphological parameters to determine the phylogeny, genetic differentiation, spatial distribution, and morphological difference of the M. fuliginosus and M. magnater sampled from China and one site in Vietnam. Mitochondrial DNA gene genealogies revealed two monophyletic lineages throughout the Tropic of Cancer. According to DNA bar code divergences, one is M. fuliginosus corresponding to the Chinese mainland and the other is M. magnater corresponding to tropical regions including Hainan and Guangdong provinces of China and Vietnam. Their most recent common ancestor was dated to the early stage of the Quaternary glacial period (ca. 2.26 million years ago [Ma] on the basis of D-loop data, and ca. 1.69-2.37 Ma according to ND2). A population expansion event was inferred for populations of M. fuliginosus at 0.14 Ma. The two species probably arose in separate Pleistocene refugia under different climate zones. They significantly differed in forearm length, maxillary third molar width, and greatest length of the skull.
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Affiliation(s)
- Shi Li
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University Changchun, 130024, China ; College of Animal Science and Technology, Jilin Agricultural University Changchun, 130118, China
| | - Keping Sun
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University Changchun, 130024, China
| | - Guanjun Lu
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University Changchun, 130024, China ; College of Urban and Environment Sciences, Changchun Normal University Changchun, 130032, China
| | - Aiqing Lin
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University Changchun, 130024, China
| | - Tinglei Jiang
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University Changchun, 130024, China
| | - Longru Jin
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University Changchun, 130024, China
| | - Joseph R Hoyt
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, California, 95064, USA
| | - Jiang Feng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University Changchun, 130024, China
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Little genetic divergence of the greater horseshoe bat Rhinolophus ferrumequinum from far-eastern Asia, with a preliminary report on genetic differentiation of R. ferrumequinum from Eurasia and northern Africa examined from cytochrome b sequences. RUSSIAN JOURNAL OF THERIOLOGY 2014. [DOI: 10.15298/rusjtheriol.13.2.05] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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40
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Boston ESM, Puechmaille SJ, Clissmann F, Teeling EC. Further Evidence for Cryptic North-Western Refugia in Europe? Mitochondrial Phylogeography of the Sibling SpeciesPipistrellus pipistrellusandPipistrellus pygmaeus. ACTA CHIROPTEROLOGICA 2014. [DOI: 10.3161/150811014x687233] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Kuo HC, Chen SF, Fang YP, Flanders J, Rossiter SJ. Comparative rangewide phylogeography of four endemic Taiwanese bat species. Mol Ecol 2014; 23:3566-86. [DOI: 10.1111/mec.12838] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Accepted: 06/09/2014] [Indexed: 11/28/2022]
Affiliation(s)
- Hao-Chih Kuo
- School of Biological and Chemical Sciences; Queen Mary University of London; London E1 4NS UK
| | - Shiang-Fan Chen
- Center for General Education; National Taipei University; New Taipei City 23741 Taiwan
| | - Yin-Ping Fang
- Department of Biological Resources; National Chiayi University; Chiayi City 60004 Taiwan
| | - Jon Flanders
- School of Biological Sciences; University of Bristol; Bristol BS8 1UG UK
| | - Stephen J. Rossiter
- School of Biological and Chemical Sciences; Queen Mary University of London; London E1 4NS UK
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Dohms KM, Burg TM. Limited geographic genetic structure detected in a widespread Palearctic corvid, Nucifraga caryocatactes. PeerJ 2014; 2:e371. [PMID: 25024901 PMCID: PMC4081298 DOI: 10.7717/peerj.371] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 04/14/2014] [Indexed: 12/04/2022] Open
Abstract
The Eurasian or spotted nutcracker (Nucifraga caryocatactes) is a widespread resident corvid found throughout the Palearctic from Central Europe to Japan. Characterized by periodic bouts of irruptive dispersal in search of Pinus seed crops, this species has potential for high levels of gene flow across its range. Previous analysis of 11 individuals did not find significant range-wide population genetic structure. We investigated population structure using 924 base pairs of mitochondrial DNA control region sequence data from 62 individuals from 12 populations distributed throughout the nutcracker’s range. We complemented this analysis by incorporating additional genetic data from previously published sequences. High levels of genetic diversity and limited population genetic structure were detected suggesting that potential barriers to dispersal do not restrict gene flow in nutcrackers.
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Affiliation(s)
- Kimberly M Dohms
- Department of Biological Sciences, University of Lethbridge , Lethbridge, AB , Canada
| | - Theresa M Burg
- Department of Biological Sciences, University of Lethbridge , Lethbridge, AB , Canada
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Dool SE, Puechmaille SJ, Dietz C, Juste J, Ibáñez C, Hulva P, Roué SG, Petit EJ, Jones G, Russo D, Toffoli R, Viglino A, Martinoli A, Rossiter SJ, Teeling EC. Phylogeography and postglacial recolonization of Europe by Rhinolophus hipposideros: evidence from multiple genetic markers. Mol Ecol 2014; 22:4055-70. [PMID: 23889545 DOI: 10.1111/mec.12373] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Revised: 04/23/2013] [Accepted: 04/25/2013] [Indexed: 01/03/2023]
Abstract
The demographic history of Rhinolophus hipposideros (lesser horseshoe bat) was reconstructed across its European, North African and Middle-Eastern distribution prior to, during and following the most recent glaciations by generating and analysing a multimarker data set. This data set consisted of an X-linked nuclear intron (Bgn; 543 bp), mitochondrial DNA (cytb-tRNA-control region; 1630 bp) and eight variable microsatellite loci for up to 373 individuals from 86 localities. Using this data set of diverse markers, it was possible to determine the species' demography at three temporal stages. Nuclear intron data revealed early colonization into Europe from the east, which pre-dates the Quaternary glaciations. The mtDNA data supported multiple glacial refugia across the Mediterranean, the largest of which were found in the Ibero-Maghreb region and an eastern location (Anatolia/Middle East)-that were used by R. hipposideros during the most recent glacial cycles. Finally, microsatellites provided the most recent information on these species' movements since the Last Glacial Maximum and suggested that lineages that had diverged into glacial refugia, such as in the Ibero-Maghreb region, have remained isolated. These findings should be used to inform future conservation management strategies for R. hipposideros and show the power of using a multimarker data set for phylogeographic studies.
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Affiliation(s)
- Serena E Dool
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
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Lu G, Lin A, Luo J, Blondel DV, Meiklejohn KA, Sun K, Feng J. Phylogeography of the Rickett's big-footed bat, Myotis pilosus (Chiroptera: Vespertilionidae): a novel pattern of genetic structure of bats in China. BMC Evol Biol 2013; 13:241. [PMID: 24188176 PMCID: PMC4228257 DOI: 10.1186/1471-2148-13-241] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 10/29/2013] [Indexed: 12/03/2022] Open
Abstract
Background China is characterized by complex topographic structure and dramatic palaeoclimatic changes, making species biogeography studies particularly interesting. Previous researchers have also demonstrated multiple species experienced complex population histories, meanwhile multiple shelters existed in Chinese mainland. Despite this, species phylogeography is still largely unexplored. In the present study, we used a combination of microsatellites and mitochondrial DNA (mtDNA) to investigate the phylogeography of the east Asian fish-eating bat (Myotis pilosus). Results Phylogenetic analyses showed that M. pilosus comprised three main lineages: A, B and C, which corresponded to distinct geographic populations of the Yangtze Plain (YTP), Sichuan Basin (SCB) and North and South of China (NSC), respectively. The most recent common ancestor of M. pilosus was dated as 0.25 million years before present (BP). Population expansion events were inferred for populations of Clade C, North China Plain region, Clade B and YunGui Plateau region at 38,700, 15,900, 4,520 and 4,520 years BP, respectively. Conflicting results were obtained from mtDNA and microsatellite analyses; strong population genetic structure was obtained from mtDNA data but not microsatellite data. The microsatellite data indicated that genetic subdivision fits an isolation-by-distance (IBD) model, but the mtDNA data failed to support this model. Conclusions Our results suggested that Pleistocene climatic oscillations might have had a profound influence on the demographic history of M. pilosus. Spatial genetic structures of maternal lineages that are different from those observed in other sympatric bats species may be as a result of interactions among special population history and local environmental factors. There are at least three possible refugia for M. pilosus during glacial episodes. Apparently contradictory genetic structure patterns of mtDNA and microsatellite could be explained by male-mediated gene flow among populations. This study also provides insights on the necessity of conservation of M. pilosus populations to conserve this genetic biodiversity, especially in the areas of YTP, SCB and NSC regions.
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Affiliation(s)
| | | | | | | | | | - Keping Sun
- Jilin Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130117, China.
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Bartáková V, Reichard M, Janko K, Polačik M, Blažek R, Reichwald K, Cellerino A, Bryja J. Strong population genetic structuring in an annual fish, Nothobranchius furzeri, suggests multiple savannah refugia in southern Mozambique. BMC Evol Biol 2013; 13:196. [PMID: 24028633 PMCID: PMC4231482 DOI: 10.1186/1471-2148-13-196] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Accepted: 09/03/2013] [Indexed: 12/22/2022] Open
Abstract
Background Intraspecific genetic variation of African fauna has been significantly affected by pronounced climatic fluctuations in Plio-Pleistocene, but, with the exception of large mammals, very limited empirical data on diversity of natural populations are available for savanna-dwelling animals. Nothobranchius furzeri is an annual fish from south-eastern Africa, inhabiting discrete temporary savannah pools outside main river alluvia. Their dispersal is limited and population processes affecting its genetic structure are likely a combination of those affecting terrestrial and aquatic taxa. N. furzeri is a model taxon in ageing research and several populations of known geographical origin are used in laboratory studies. Here, we analysed the genetic structure, diversity, historical demography and temporal patterns of divergence in natural populations of N. furzeri across its entire distribution range. Results Genetic structure and historical demography of N. furzeri were analysed using a combination of mitochondrial (partial cytochrome b sequences, 687 bp) and nuclear (13 microsatellites) markers in 693 fish from 36 populations. Genetic markers consistently demonstrated strong population structuring and suggested two main genetic groups associated with river basins. The split was dated to the Pliocene (>2 Mya). The northern group inhabits savannah pools across the basin of the intermittent river Chefu in south-western Mozambique and eastern Zimbabwe. The southern group (from southernmost Mozambique) is subdivided, with the River Limpopo forming a barrier (maximum divergence time 1 Mya). A strong habitat fragmentation (isolated temporary pools) is reflected in significant genetic structuring even between adjacent pools, with a major influence of genetic drift and significant isolation-by-distance. Analysis of historical demography revealed that the expansion of both groups is ongoing, supported by frequent founder effects in marginal parts of the range and evidence of secondary contact between Chefu and Limpopo populations. Conclusions We demonstrated: (1) ancient (pre-Pleistocene) divergence between the two main N. furzeri lineages, their recent secondary contact and lack of reproductive isolation; (2) important genetic structuring attributed to the fragmented nature of their environment and isolation-by-distance, suggesting that dispersal is limited, occurs over short distances and is not directly associated with river routes; (3) an apparent role of the River Limpopo as a barrier to dispersal and gene flow.
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Affiliation(s)
- Veronika Bartáková
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Květná 8, Brno 603 65, Czech Republic.
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46
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Sun K, Luo L, Kimball RT, Wei X, Jin L, Jiang T, Li G, Feng J. Geographic variation in the acoustic traits of greater horseshoe bats: testing the importance of drift and ecological selection in evolutionary processes. PLoS One 2013; 8:e70368. [PMID: 23950926 PMCID: PMC3738568 DOI: 10.1371/journal.pone.0070368] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2013] [Accepted: 06/17/2013] [Indexed: 11/19/2022] Open
Abstract
Patterns of intraspecific geographic variation of signaling systems provide insight into the microevolutionary processes driving phenotypic divergence. The acoustic calls of bats are sensitive to diverse evolutionary forces, but processes that shape call variation are largely unexplored. In China, Rhinolophus ferrumequinum displays a diverse call frequency and inhabits a heterogeneous landscape, presenting an excellent opportunity for this kind of research. We quantified geographic variation in resting frequency (RF) of echolocation calls, estimated genetic structure and phylogeny of R. ferrumequinum populations, and combined this with climatic factors to test three hypotheses to explain acoustic variation: genetic drift, cultural drift, and local adaptation. Our results demonstrated significant regional divergence in frequency and phylogeny among the bat populations in China's northeast (NE), central-east (CE) and southwest (SW) regions. The CE region had higher frequencies than the NE and SW regions. Drivers of RF divergence were estimated in the entire range and just the CE/NE region (since these two regions form a clade). In both cases, RF divergence was not correlated with mtDNA or nDNA genetic distance, but was significantly correlated with geographic distance and mean annual temperature, indicating cultural drift and ecological selection pressures are likely important in shaping RF divergence among different regions in China.
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Affiliation(s)
- Keping Sun
- Jilin Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
- Key Laboratory for Wetland Ecology and Vegetation Restoration of National Environmental Protection, Northeast Normal University, Changchun, China
- Department of Biology, University of Florida, Gainesville, Florida, United States of America
| | - Li Luo
- Jilin Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Rebecca T. Kimball
- Department of Biology, University of Florida, Gainesville, Florida, United States of America
| | - Xuewen Wei
- Jilin Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Longru Jin
- Jilin Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Tinglei Jiang
- Jilin Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Guohong Li
- Jilin Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
- School of Life Science, Guizhou Normal University, Guiyang, China
| | - Jiang Feng
- Jilin Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
- Key Laboratory for Wetland Ecology and Vegetation Restoration of National Environmental Protection, Northeast Normal University, Changchun, China
- * E-mail:
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47
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Mao X, Thong VD, Bates PJJ, Jones G, Zhang S, Rossiter SJ. Multiple cases of asymmetric introgression among horseshoe bats detected by phylogenetic conflicts across loci. Biol J Linn Soc Lond 2013. [DOI: 10.1111/bij.12138] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
| | - Vu D. Thong
- Institute of Ecology and Biological Resources; 18 Hoang Quoc Viet Road; Cau Giay District; Hanoi; Vietnam
| | - Paul J. J. Bates
- Harrison Institute; Centre for Systematics and Biodiversity Research; Bowerwood House; St Botolph's Road; Sevenoaks; Kent; TN13 3AQ; UK
| | - Gareth Jones
- School of Biological Sciences; University of Bristol; Woodland Road; Bristol; BS8 1UG; UK
| | - Shuyi Zhang
- Institute of Molecular Ecology and Evolution; Institute for Advanced Studies in Multidisciplinary Science and Technology; East China Normal University; Shanghai; 200062; China
| | - Stephen J. Rossiter
- School of Biological and Chemical Sciences; Queen Mary University of London; London; E1 4NS; UK
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48
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Říčanová Š, Koshev Y, Říčan O, Ćosić N, Ćirović D, Sedláček F, Bryja J. Multilocus phylogeography of the European ground squirrel: cryptic interglacial refugia of continental climate in Europe. Mol Ecol 2013; 22:4256-4269. [PMID: 23879230 DOI: 10.1111/mec.12382] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Revised: 05/07/2013] [Accepted: 05/09/2013] [Indexed: 11/30/2022]
Abstract
The theory of classical and cryptic Pleistocene refugia is based mainly on historical changes in temperature, and the refugia are usually defined within a latitudinal gradient. However, the gradient of oceanic-continental climate (i.e. longitudinal) was also significantly variable during glacial cycles with important biotic consequences. Range-wide phylogeography of the European ground squirrel (EGS) was used to interpret the evolutionary and palaeogeographical history of the species in Europe and to shed light on its glacial-interglacial dynamic. The EGS is a steppe-inhabiting species and the westernmost member of the genus in the Palaearctic region. We have analysed 915 specimens throughout the present natural range by employing mitochondrial DNA sequences (cytochrome b gene) and 12 nuclear microsatellite markers. The reconstructed phylogeography divides the species into two main geographical groups, with deep substructuring within both groups. Bulgaria is the centre of the ancestral area, and it also has the highest genetic diversity within the species. The northernmost group of the EGS survived in the southern part of Pannonia throughout several glacial-interglacial cycles. Animals from this population probably repeatedly colonized areas further to the north and west during the glacial periods, while in the interglacial periods, the EGS distribution contracted back to this Pannonian refugium. The EGS thus represents a species with a glacial expansion/interglacial contraction palaeogeographical dynamics, and the Pannonian and southeastern Balkanian steppes are supported as cryptic refugia of continental climate during Pleistocene interglacials.
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Affiliation(s)
- Štěpánka Říčanová
- Faculty of Science, University of South Bohemia, Branišovská 31, 370 05, České Budějovice, Czech Republic.,Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Květná 8, 603 65, Brno, Czech Republic
| | - Yordan Koshev
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Science, 1 Tzar Osvoboditel blvb, 1000, Sofia, Bulgaria
| | - Oldřich Říčan
- Faculty of Science, University of South Bohemia, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - Nada Ćosić
- Institute for Biological Research Siniša Stanković, University of Belgrade, Bulevar despota Stefana 142, 11000, Belgrade, Serbia
| | - Duško Ćirović
- Faculty of Biology, University of Belgrade, Studentski trg 16, 11000, Belgrade, Serbia
| | - František Sedláček
- Faculty of Science, University of South Bohemia, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - Josef Bryja
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Květná 8, 603 65, Brno, Czech Republic.,Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic
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49
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Mao X, He G, Zhang J, Rossiter SJ, Zhang S. Lineage divergence and historical gene flow in the Chinese horseshoe bat (Rhinolophus sinicus). PLoS One 2013; 8:e56786. [PMID: 23451086 PMCID: PMC3581519 DOI: 10.1371/journal.pone.0056786] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Accepted: 01/15/2013] [Indexed: 11/18/2022] Open
Abstract
Closely related taxa living in sympatry provide good opportunities to investigate the origin of barriers to gene flow as well as the extent of reproductive isolation. The only two recognized subspecies of the Chinese rufous horseshoe bat Rhinolophus sinicus are characterized by unusual relative distributions in which R. s. septentrionalis is restricted to a small area within the much wider range of its sister taxon R. s. sinicus. To determine the history of lineage divergence and gene flow between these taxa, we applied phylogenetic, demographic and coalescent analyses to multi-locus datasets. MtDNA gene genealogies and microsatellite-based clustering together revealed three divergent lineages of sinicus, corresponding to Central China, East China and the offshore Hainan Island. However, the central lineage of sinicus showed a closer relationship with septentrionalis than with other lineages of R. s. sinicus, in contrary to morphological data. Paraphyly of sinicus could result from either past asymmetric mtDNA introgression between these two taxa, or could suggest septentrionalis evolved in situ from its more widespread sister subspecies. To test between these hypotheses, we applied coalescent-based phylogenetic reconstruction and Approximate Bayesian Computation (ABC). We found that septentrionalis is likely to be the ancestral taxon and therefore a recent origin of this subspecies can be ruled out. On the other hand, we found a clear signature of asymmetric mtDNA gene flow from septentrionalis into central populations of sinicus yet no nuclear gene flow, thus strongly pointing to historical mtDNA introgression. We suggest that the observed deeply divergent lineages within R. sinicus probably evolved in isolation in separate Pleistocene refugia, although their close phylogeographic correspondence with distinct eco-environmental zones suggests that divergent selection might also have promoted broad patterns of population genetic structure.
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Affiliation(s)
- Xiuguang Mao
- Institute of Molecular Ecology and Evolution, Institute for Advanced Studies in Multidisciplinary Science and Technology, East China Normal University, Shanghai, China
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Guimei He
- Institute of Molecular Ecology and Evolution, Institute for Advanced Studies in Multidisciplinary Science and Technology, East China Normal University, Shanghai, China
| | - Junpeng Zhang
- Institute of Molecular Ecology and Evolution, Institute for Advanced Studies in Multidisciplinary Science and Technology, East China Normal University, Shanghai, China
| | - Stephen J. Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
- * E-mail: (SJR); (SZ)
| | - Shuyi Zhang
- Institute of Molecular Ecology and Evolution, Institute for Advanced Studies in Multidisciplinary Science and Technology, East China Normal University, Shanghai, China
- * E-mail: (SJR); (SZ)
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50
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Patriquin KJ, Palstra F, Leonard ML, Broders HG. Female northern myotis (Myotis septentrionalis) that roost together are related. Behav Ecol 2013. [DOI: 10.1093/beheco/art012] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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