Published January 24, 2024
| Version v1
Journal article
Restricted
Phylogenetic relationships among horseshoe bats within the Rhinolophus ferrumequinum group (Mammalia, Chiroptera)
Authors/Creators
- 1. Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic & Department of Zoology, National Museum, Prague, Czech Republic
Description
Uvizl, Marek, Varadínová, Zuzana Kotyková, Benda, Petr (2024): Phylogenetic relationships among horseshoe bats within the Rhinolophus ferrumequinum group (Mammalia, Chiroptera). Zoologica Scripta 53 (3): 249-266, DOI: 10.1111/zsc.12650, URL: https://doi.org/10.1111/zsc.12650
Files
Restricted
The record is publicly accessible, but files are restricted. Log in to check if you have access.
Linked records
Additional details
Identifiers
- LSID
- urn:lsid:plazi.org:pub:4B05FFA68854FFB5FFD36851FF8E0356
- URL
- http://publication.plazi.org/id/4B05FFA68854FFB5FFD36851FF8E0356
References
- Aellen, V. (1959). Contribution a l'etude de la faune d'Afghanistan 9. Chiropteres. Revue Suisse de Zoologie, 66, 353-386.
- Aellen, V., & Brosset, A. (1968). Chiropteres du sud du Congo (Brazzaville). Revue Suisse de Zoologie, 75(14), 435-458.
- Andersen, K. (1904). LXII.-On von Heuglin's, Ruppell's, and Sundevall's types of African Rhinolophi. Annals and Magazine of Natural History, 14(84), 451-458. https://doi.org/10.1080/ 03745480409443035
- Andersen, K. (1905). XXXI.-On the bats of the Rhinolophus macrotis group, with descriptions of two new forms. Annals and Magazine of Natural History, 16(93), 289-292. https://doi.org/ 10.1080/03745480509442864
- Anisimova, M., Gil, M., Dufayard, J. F., Dessimoz, C., & Gascuel, O. (2011). Survey of branch support methods demonstrates accuracy, power, and robustness of fast likelihood-based approximation schemes. Systematic Biology, 60(5), 685-699. https://doi. org/10.1093/sysbio/syr041
- Asouti, E., Kabukcu, C., White, C. E., Kuijt, I., Finlayson, B., & Makarewicz, C. (2015). Early Holocene woodland vegetation and human impacts in the arid zone of the southern Levant. The Holocene, 25(10), 1565-1580.
- Bachtrog, D., Thornton, K., Clark, A., & Andolfatto, P. (2006). Extensive introgression of mitochondrial DNA relative to nuclear genes in the drosophila yakuba species group. Evolution, 60, 292-302. https://doi.org/10.1111/j.0014-3820.2006.tb01107. x
- Bailey, S. E., Mao, X., Struebig, M., Tsagkogeorga, G., Csorba, G., Heaney, L. R., Sedlock, J., Stanley, W., Rouillard, J.-M., & Rossiter, S. J. (2016).The use of museum samples for large-scale sequence capture: A study of congeneric horseshoe bats (family Rhinolophidae). Biological Journal of the Linnean Society, 117(1), 58-70. https://doi.org/10.1111/bij.12620
- Bauer, K. (1963). Ergebnisse der Zoologischen Nubien-Expedition 1962, Teil 19: Saugertiere. Annalen Des Naturhistorischen Museums in Wien, 66, 495-506.
- Benda, P., Andreas, M., Kock, D., Lucan, R. K., Munclinger, P., Nova, P., Jan, O., Ochman, K., Antonin, R., Marcel, U., & Weinfurtova, D. (2006). Bats (Mammalia: Chiroptera) of the eastern Mediterranean. Part 4. Bat fauna of Syria: Distribution, systematics, ecology. Acta Societatis Zoologicae Bohemicae, 70, 1-329.
- Benda, P., Faizolahi, K., Andreas, M., Obuch, J., Reiter, A., Sevcik, M., Uhrin, M., Vallo, P., & Ashrafi, S. (2012). Bats (Mammalia: Chiroptera) of the Eastern Mediterranean and Middle East. Part 10. Bat fauna of Iran. Acta Societatis Zoologicae Bohemicae, 76, 163-582.
- Benda, P., & Gaisler, J. (2015). Bats (Mammalia: Chiroptera) of the Eastern Mediterranean and Middle East. Part 12. Bat fauna of Afghanistan: Revision of distribution and taxonomy. Acta Societatis Zoologicae Bohemicae, 79(4), 267-458.
- Benda, P., Lucan, R. K., Obuch, J., Reiter, A., Andreas, M., Backor, P., Bohnenstengel, T., Eid, E. K., Sevcik, M., Vallo, M., & Amr, Z. S. (2010). Bats (Mammalia: Chiroptera) of the Eastern Mediterranean and Middle East. Part 8. Bats of Jordan: fauna, ecology, echolocation, ectoparasites. Acta Societatis Zoologicae Bohemicae, 74(3-4), 185-353.
- Benda, P., Nasher, A. K., Van Damme, K., Vallo, P., & Reiter, A. (2017). Bats (Mammalia: Chiroptera) of the Eastern
- Benda, P., Uvizl, M., Skliba, J., Mazoch, V., & Cerveny, J. (2022). African bats in the collection of the National Museum, Prague (Chiroptera). I. Bats from Zambia. Lynx, 53, 291-332.
- Benda, P., Uvizl, M., Vallo, P., Reiter, A., & Uhrin, M. (2022). A revision of the Rhinolophus hipposideros group (Chiroptera: Rhinolophidae) with definition of an additional species from the Middle East. Acta Chiropterologica, 24(2), 269-298. https:// doi.org/10.3161/15081109ACC2022.24.2.001
- Benda, P., & Vallo, P. (2012). New look on the geographical variation in Rhinolophus clivosus with description of a new horseshoe bat species from Cyrenaica, Libya. Vespertilio, 16, 69-96.
- Berthier, P., Excoffier, L., & Ruedi, M. (2006). Recurrent replacement of mtDNA and cryptic hybridization between two sibling bat species Myotis myotis and Myotis blythii. Proceedings of the Royal Society B: Biological Sciences, 273(1605), 3101-3123. https://doi.org/10.1098/rspb.2006.3680
- Bobrinskij, N. A. (1925). Materialy dla fauny letucih mysej Turkenstanskogo kraa (Ruskij Turkestan s Semirecenskoj i Zakaspijskoj oblast'ami, Hiva i Buhara). Bulleten' Moskovskogo Obsestva Izpytatelej Prirody, Otdel Biologiceskij, 34, 330-374.
- Bogdanowicz, W. (1992). Phenetic relationships among bats of the family Rhinolophidae. Acta Theriologica, 37(3), 213-240.
- Bryant, D., & Moulton, V. (2004). Neighbor-net: An agglomerative method for the construction of phylogenetic networks. Molecular Biology and Evolution, 21(2), 255-265. https://doi. org/10.1093/MOLBEV/MSH018
- Burgin, C. J. (2019). Genus Rhinolophus Lacepede, 1799. In D. E. Wilson & R. A. Mittermeier (Eds.), Handbook of the mammals of the world. 9. Bats (pp. 280-332). Lynx Edicions.
- Burgin, C. J., Colella, J. P., Kahn, P. L., & Upham, N. S. (2018). How many species of mammals are there? Journal of Mammalogy, 99(1), 1-14. https://doi.org/10.1093/jmammal/gyx147
- Castresana, J. (2000). Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Molecular Biology and Evolution, 17(4), 540-552. https://doi.org/10.1093/ oxfordjournals.molbev.a026334
- Chernomor, O., von Haeseler, A., & Minh, B. (2016). Terrace aware data structure for phylogenomic inference from supermatrices. Systematic Biology, 65(6), 997-1008. https://doi.org/10.1093/ sysbio/syw037
- Corbet, G. (1978). The mammals of the palaearctic region: A taxonomic review. British Museum (Natural History).
- Corbet, G., & Hill, J. (1992). The mammals of the Indomalayan region: A systematic review. Natural History Museum Publications.
- Cotterill, F. P. D. (2002). A new species of horseshoe bat (Microchiroptera: Rhinolophidae) from south-central Africa: With comments on its affinities and evolution, and the characterization of rhinolophid species. Journal of Zoology (London), 256(2), 165-179. https://doi.org/10.1017/s0952 836902000201
- Cretzschmar, P. J. (1826-1830). Atlas zu der Reise im Nordlichen Afrika von Eduard Ruppel, Saugetiere. Senckenbergische Naturforschende Gesellschaft.
- Csorba, G., Ujhelyi, P., & Thomas, N. (2003). Horseshoe bats of the world (Chiroptera: Rhinolophidae). Alana Books.
- Curran, M., Kopp, M., Ruedi, M., & Bayliss, J. (2022). A new species of horseshoe bat (Chiroptera: Rhinolophidae) from Mount Namuli, Mozambique. Acta Chiropterologica, 24(1), 19-40. https://doi.org/10.3161/15081109ACC2022.24.1.002
- Currat, M., Ruedi, M., Petit, R. J., & Excoffier, L. (2008). The hidden side of invasions: Massive introgression by local genes. Evolution, 62(8), 1908-1920. https://doi.org/10.1111/j.1558- 5646.2008.00413.x
- Demos, T. C., Webala, P. W., Goodman, S. M., Kerbis Peterhans, J. C., Bartonjo, M., & Patterson, B. D. (2019). Molecular phylogenetics of the African horseshoe bats (Chiroptera: Rhinolophidae): Expanded geographic and taxonomic sampling of the Afrotropics. BMC Evolutionary Biology, 19(1), 1-14. https://doi. org/10.1186/s12862-019-1485-1
- Dobson, G. (1876). Monograph of the Asiatic chiroptera and catalogue of the species of bats in the collection of the Indian Museum, Calcutta. Taylor and Francis.
- Dool, S. E., Puechmaille, S. J., Foley, N. M., Allegrini, B., Bastian, A., Mutumi, G. L., Maluleke, T. G., Odendaal, L. J., Teeling, E. C., & Jacobs, D. S. (2016). Nuclear introns outperform mitochondrial DNA in inter-specific phylogenetic reconstruction: Lessons from horseshoe bats (Rhinolophidae: Chiroptera). Molecular Phylogenetics and Evolution, 97, 196-212. https://doi.org/10. 1016/j.ympev.2016.01.003
- Dulic, B., & Mutere, F. A. (1974). The chromosomes of two bats from East Africa: Rhinolophus clivosus Cretzschmar, 1828 and Hipposideros caffer (Sundevall, 1846). Periodicum Biologorum, 76(1), 31-34.
- Edwards, C. J., Suchard, M., Lemey, P., Welch, J. J., Barnes, I., Fulton, T. L., Barnett, R., O'Connell, T. C., Coxon, P., Monaghan, N., Valdiosera, C. E., Lorenzen, E. D., Willerslev, E., Baryshnikov, G. F., Rambaut, A., Thomas, M. G., Bradley, D. G., & Shapiro, B. (2011). Ancient hybridization and an Irish origin for the modern polar bear matriline. Current Biology, 21, 1251-1258.
- Ellerman, J. R., & Morrison-Scott, T. C. S. (1951). Checklist of Palaearctic and Indian mammals 1758 to 1946. National Museum (Natural History).
- Felten, H., Spitzenberger, F., & Storch, G. (1977). Zur Kleinsaugerfauna West-Anatoliens. Teil IIIa. Senckenbergiana Biologica, 58, 1-44.
- Flanders, J., Jones, G., Benda, P., Dietz, C., Zhang, S., Li, G., Sharifi, M., & Rossiter, S. J. (2009). Phylogeography of the greater horseshoe bat, Rhinolophus ferrumequinum: Contrasting results from mitochondrial and microsatellite data. Molecular Ecology, 18(2), 306-318. https://doi.org/10.1111/j.1365-294X. 2008.04021.x
- Flanders, J., Wei, L., Rossiter, S. J., & Zhang, S. (2011). Identifying the effects of the Pleistocene on the greater horseshoe bat, Rhinolophus ferrumequinum, in East Asia using ecological niche modelling and phylogenetic analyses. Journal of Biogeography, 38(3), 439-452. https://doi.org/10.1111/j.1365- 2699.2010.02411.x
- Foley, N. M., Thong, V. D., Soisook, P., Goodman, S. M., Armstrong, K. N., Jacobs, D. S., Puechmaille, S. J., & Teeling, E. C. (2015). How and why overcome the impediments to resolution: Lessons from rhinolophid and hipposiderid bats. Molecular Biology and Evolution, 32(2), 313-333. https://doi.org/10.1093/ molbev/msu329
- Funk, D. J., & Omland, K. E. (2003). Species-level paraphyly and polyphyly: Frequency, causes, and consequences, with insights from animal mitochondrial DNA. Annual Review of Ecology, Evolution, and Systematics, 34(1), 397-423. https://doi.org/10. 1146/annurev.ecolsys.34.011802.132421
- Gernhard, T. (2008). The conditioned reconstructed process. Journal of Theoretical Biology, 253(4), 769-778. https://doi.org/10. 1016/j.jtbi.2008.04.005
- Guillen-Servent, A., Francis, C. M., & Ricklefs, R. E. (2003). Phylogeny and biogeography of the horseshoe bats. In G. Csorba, P. Ujhelyi, & N. Thomas (Eds.), Horseshoe bats of the world (Chiroptera: Rhinolophidae) (pp. xii -xxiv). Alana Books.
- Guindon, S., Dufayard, J.-F., Lefort, V., Anisimova, M., Hordijk, W., & Gascuel, O. (2010). New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of PhyML 3.0. Systematic Biology, 59(3), 307-321. https://doi. org/10.1093/sysbio/syq010
- Hanak, V. (1969). Zur Kenntnis von Rhinolophus bocharicus Kastchenko et Akimov, 1917 (Mammalia: Chiroptera). Vestnik Ceskoslovenske Spolecnosti Zoologicke, 33, 315-327.
- Hoang, D., Chernomor, O., von Haeseler, A., & Minh, B. (2018). UFBoot2: Improving the ultrafast bootstrap approximation. Molecular Biology and Evolution, 35(2), 518-522. https://doi. org/10.1093/molbev/msx281
- Horacek, I., Hanak, V., & Gaisler, J. (2000). Bats of the Palearctic region: A taxonomic and biogeographic review. In B. W. Woloszyn (Ed.), Proceedings of the VIIIth EBRS. CIC ISEZ PAN.
- Huson, D., & Bryant, D. (2006). Application of phylogenetic networks in evolutionary studies. Molecular Biology and Evolution, 23(2), 254-267. https://doi.org/10.1093/molbev/msj030
- Ikeda, Y., Jiang, T., Oh, H., Csorba, G., & Motokawa, M. (2020). Geographic variations of skull morphology in the Rhinolophus ferrumequinum species complex (Mammalia: Chiroptera). Zoologischer Anzeiger, 288, 125-138. https://doi.org/10.1016/j. jcz.2020.08.004
- Ikeda, Y., & Motokawa, M. (2021). Phylogeography of the Japanese greater horseshoe bat Rhinolophus nippon (Mammalia: Chiroptera) in Northeast Asia: New insight into the monophyly of the Japanese populations. Ecology and Evolution, 11(24), 18181-18195. https://doi.org/10.1002/ece3.8414
- Jacobs, D. S., Babiker, H., Bastian, A., Kearney, T., van Eeden, R., & Bishop, J. M. (2013). Phenotypic convergence in genetically distinct lineages of a Rhinolophus species complex (Mammalia, Chiroptera). PLoS One, 8(12), e82614.
- Jiang, T., Wang, J., Wu, H., Csorba, G., Puechmaille, S. J., Benda, P., Boireau, J., Toffoli, R., Courtois, J.-Y., Nyssen, P., Colombo, R., & Feng, J. (2019). The patterns and possible causes of global geographical variation in the body size of the greater horseshoe bat (Rhinolophus ferrumequinum). Journal of Biogeography, 46(10), 2363-2377. https://doi.org/10.1111/jbi.13658
- Juste, J., Benda, P., Garcia-Mudarra, J. L., & Ibanez, C. (2013). Phylogeny and systematics of Old World serotine bats (genus Eptesicus, Vespertilionidae, Chiroptera): An integrative approach. Zoologica Scripta, 42, 441-457. https://doi.org/10.1111/ asc.12020
- Kalyaanamoorthy, S., Minh, B. Q., Wong, T. K. F., von Haeseler, A., & Jermiin, L. S. (2017). ModelFinder: Fast model selection for accurate phylogenetic estimates. Nature Methods, 14(6), 587-589. https://doi.org/10.1038/nmeth.4285
- Kapli, P., Lutteropp, S., Zhang, J., Kobert, K., Pavlidis, P., Stamatakis, A., & Flouri, T. (2017). Phylogenetics multi-rate Poisson tree processes for single-locus species delimitation under maximum likelihood and Markov chain Monte Carlo. Bioinformatics, 33(11), 1630-1638. https://doi.org/10.1093/bioinformatics/ btx025
- Katoh, K., & Standley, D. (2013). MAFFT multiple sequence alignment software version 7: Improvements in performance and usability. Molecular Biology and Evolution, 30(4), 772-780. https://doi.org/10.1093/molbev/mst010
- Klymus, K. E., Humfeld, S. C., Marshall, V. T., Cannatella, D., & Gerhardt, H. C. (2010). Molecular patterns of differentiation in canyon treefrogs (Hyla arenicolor): Evidence for introgressive hybridization with the Arizona treefrog (H. wrightorum) and correlations with advertisement call differences. Journal of Evolutionary Biology, 23, 1425-1435. https://doi.org/10.1111/j. 1420-9101.2010.02008.x
- Koh, H. S., Jo, J. E., Oh, J. G., Kweon, G. H., Ahn, N. H., Sin, W. H., & Sin, D. S. (2014). 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, 13(2), 97-103. https://doi.org/10.15298/rusjtheriol.13.2.05
- Koopman, K. F. (1966). Taxonomic and distributional notes on southern African bats. The Puku, 4, 155-165.
- Koopman, K. F. (1994). Chiroptera: Systematics. In J. Niethammer, H. Schliemann, & D. Starck (Eds.), Handbuch der Zoologie. Band VIII. Mammalia. Teilband 60 (pp. 1-217). Walter de Gruyter.
- Krystufek, B. (1993). Geographic variation in the greater horseshoe bat Rhinolophus ferrumequinum in south-eastern Europe. Acta Theriologica, 38(1), 67-79.
- Kus, P. (2008). Molekularne geneticka studie vrapencu vychodniho Stredomori (Chiroptera: Rhinolophidae: Rhinolophus) [Molecular genetic study of horseshoe bats of the Eastern Mediterranean (Chiroptera: Rhinolophidae: Rhinolophus)]. MSc Thesis, Charles University, Prague. [In Czech].
- Leache, A. D., & Fujita, M. K. (2010). Bayesian species delimitation in West African forest geckos (Hemidactylus fasciatus). Proceedings of the Royal Society B: Biological Sciences, 277(1697), 3071-3077. https://doi.org/10.1098/rspb.2010.0662
- Mammal Diversity Database. (2023). Mammal diversity database. https://doi.org/10.5281/zenodo.7830771
- Mao, X., & Rossiter, S. J. (2020). Genome-wide data reveal discordant mitonuclear introgression in the intermediate horseshoe bat (Rhinolophus affinis). Molecular Phylogenetics and Evolution, 150, 106886. https://doi.org/10.1016/j.ympev.2020.106886
- Mao, X., Thong, V. D., Bates, P. J. J., Jones, G., Zhang, S., & Rossiter, S. J. (2013). Multiple cases of asymmetric introgression among horseshoe bats detected by phylogenetic conflicts across loci. Biological Journal of the Linnean Society, 110(2), 346-361. https://doi.org/10.1111/bij.12138
- Mao, X., Zhang, J., Zhang, S., & Rossiter, S. J. (2010). Historical malemediated introgression in horseshoe bats revealed by multilocus DNA sequence data. Molecular Ecology, 19(7), 1352-1366. https://doi.org/10.1111/j.1365-294X.2010.04560.x
- Melo-Ferreira, J., Alves, P. C., Freitas, H., Ferrand, N., & Boursot, P. (2009). The genomic legacy from the extinct Lepus timidus to the three hare species of Iberia: Contrast between mtDNA, sex chromosomes and autosomes. Molecular Ecology, 18, 2643- 2658. https://doi.org/10.1111/j.1365-294X.2009.04221.x
- Mendelssohn, H., & Yom-Tov, Y. (1999). A report of birds and mammals which have increased their distribution and abundance in Israel due to human activity. Israel Journal of Zoology, 45(1), 35-47.
- Mendez-Rodriguez, A., Juste, J., Centeno-Cuadros, A., Rodriguez Gomez, F., Serrato-Diaz, A., Garcia-Mundarra, J. L., Guevara- Chumacero, L. M., & Lopez-Wilchis, R. (2021). Species along their contact zone in Central America. Diversity, 13, 194. https://doi.org/10.3390/d13050194
- Miebach, A., Stolzenberger, S., Wacker, L., Hense, A., & Litt, T. (2019). A new Dead Sea pollen record reveals the last glacial paleoenvironment of the southern Levant. Quaternary Science Reviews, 214, 98-116.
- Miller, M. A., Pfeiffer, W., & Schwartz, T. (2010). Creating the CIPRES science gateway for inference of large phylogenetic trees. Gateway Computing Environments Workshop (GCE), 1-8. https://doi. org/10.1109/GCE.2010.5676129
- Nesi, N., Kadjo, B., Pourrut, X., Leroy, E., Pongombo Shongo, C., Cruaud, C., & Hassanin, A. (2013). Molecular systematics and phylogeography of the tribe Myonycterini (Mammalia, Pteropodidae) inferred from mitochondrial and nuclear markers. Molecular Phylogenetics and Evolution, 66(1), 126-137. https://doi.org/10.1016/j.ympev.2012.09.028
- Nguyen, L., Schmidt, H., von Haeseler, A., & Minh, B. (2015). IQ- TREE: A fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Molecular Biology and Evolution, 32(1), 268-274. https://doi.org/10.1093/molbev/ msu300
- Ognev, S. I. (1927). A synopsis of the Russian bats. Journal of Mammalogy, 8(2), 140-157.
- Palumbi, S. R., Cipriano, F., & Hare, M. P. (2001). Predicting nuclear gene coalescence from mitochondrial data: The three-times rule. Evolution, 55(5), 859-868. https://doi.org/10.1111/j.0014- 3820.2001.tb00603.x
- Puechmaille, S. J., Gouilh, M. A., Piyapan, P., Yokubol, M., Mie, K. M., Bates, P. J., & Teeling, E. C. (2011). The evolution of sensory divergence in the context of limited gene flow in the bumblebee bat. Nature Communications, 2(1), 573. https://doi.org/10. 1038/ncomms1582
- Qumsiyeh, M. B. (1985). The bats of Egypt (Vol. 23, pp. 1-101). Special Publications, The Museum Texas Tech University.
- Rambaut, A., Suchard, M. A., Xie, D., & Drummond, A. (2015). Tracer v1. 6. http://beast.bio.ed.ac.uk/Tracer
- Rannala, B., & Yang, Z. (2003). Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics, 164(4), 1645-1656.
- Ransome, R. (2020). Greater Horseshoe Bat Rhinolophus ferrumequinum (Schreber, 1774). In K. Hacklander & F. E. Zachos (Eds.), Handbook of the mammals of Europe. Handbook of the mammals of Europe. Springer. https://doi.org/10.1007/978-3- 319-65038-8_38-1
- Ronquist, F., & Huelsenbeck, J. (2003). MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 19(12), 1572-1574. https://doi.org/10.1093/bioinformatics/btg180
- Rossiter, S. J., Benda, P., Dietz, C., Zhang, S., & Jones, G. (2007). Rangewide phylogeography in the greater horseshoe bat inferred from microsatellites: Implications for population history, taxonomy and conservation. Molecular Ecology, 16(22), 4699-4714. https://doi.org/10.1111/j.1365-294X.2007.03546.x
- Salicini, I., Ibanez, C., & Juste, J. (2011). Multilocus phylogeny and species delimitation within the Natterer's bat species complex in the Western Palearctic. Molecular Phylogenetics and Evolution, 61(3), 888-898. https://doi.org/10.1016/j.ympev.2011.08.010
- Sano, A. (2015). Rhinolophus ferrumequinum (Schreber, 1774). In S. D. Ohdachi, Y. Ishibashi, M. A. Iwasa, D. Fukui, & T. Saitoh (Eds.), The wild mammals of Japan (2nd ed., pp. 58-60). Shoukadoh Book Sellers.
- Senn, H. V., & Pemberton, J. M. (2009). Variable extent of hybridization between invasive sika (Cervus nippon) and native red deer (C. elaphus) in a small geographical area. Molecular Ecology, 18, 862-876. https://doi.org/10.1111/j.1365-294X.2008.04051.x
- Simmons, N. B. (2005). Order Chiroptera. In D. E. Wilson & M. D. Reeder (Eds.), Mammal species of the world. A taxonomic and geographic reference (3rd ed., pp. 312-529). Johns Hopkins University Press.
- Simmons, N. B., & Cirranello, A. L. (2023). Bat species of the World: A taxonomic and geographic database. Version 1.4.
- Sinha, Y. P. (1973). Taxonomic studies on the Indian horseshoe bats of the genus Rhinolophus Lacepede. Mammalia, 37(4), 603- 630. https://doi.org/10.1515/MAMM.1973.37.4.603/HTML
- Stoffberg, S., Jacobs, D. S., Mackie, I. J., & Matthee, C. A. (2010). Molecular phylogenetics and historical biogeography of Rhinolophus bats. Molecular Phylogenetics and Evolution, 54(1), 1-9. https://doi.org/10.1016/j.ympev.2009.09.021
- Strelkov, P. P. (1971). Bolsie (Rhinolophus ferrumequinum) i buharskie (Rh. bocharicus) podkovonosy (Chiroptera) iz pustyni Karakumy [Greater (Rhinolophus ferrumequinum) and Bukhara (Rh. bocharicus) horseshoe bats (Chiroptera) from the Karakum desert]. Zoologiceskij Zurnal, 50, 893-907.
- Stundlova, J., Smid, J., Nguyen, P., & Stahlavsky, F. (2019). Cryptic diversity and dynamic chromosome evolution in Alpine scorpions (Euscorpiidae: Euscorpius). Molecular Phylogenetics and Evolution, 134, 152-163. https://doi.org/10.1016/j.ympev.2019. 02.002
- Sukumaran, J., & Knowles, L. L. (2017). Multispecies coalescent delimits structure, not species. Proceedings of the National Academy of Sciences of the United States of America, 114(7), 1607-1611. https://doi.org/10.1073/pnas.1607921114
- Sun, K., Kimball, R. T., Liu, T., Wei, X., Jin, L., Jiang, T., Lin, A., & Feng, J. (2016). The complex evolutionary history of big-eared horseshoe bats (Rhinolophus macrotis complex): Insights from genetic, morphological and acoustic data. Scientific Reports, 6, 35417. https://doi.org/10.1038/srep35417
- Tamura, K., Stecher, G., & Kumar, S. (2021). MEGA11: Molecular evolutionary genetics analysis version 11. Molecular Biology and Evolution, 38(7), 3022-3027. https://doi.org/10.1093/molbev/msab120
- Tate, G. H. H., & Archbold, R. (1939). Results of the Archbold expeditions. No. 24. Oriental Rhinolophus, with special reference to material from the Archbold collections. American Museum Novitates, 1036, 1-12.
- Taylor, P. J., MacDonald, A., Goodman, S. M., Kearney, T., Cotterill, F. P. D., Stoffberg, S., Monadjem, A., Schoeman, M. C., Guyton, J., Naskrecki, P., & Richards, L. R. (2018). Integrative taxonomy resolves three new cryptic species of small southern African horseshoe bats (Rhinolophus). Zoological Journal of the Linnean Society, 184, 1249-1276.
- Teeling, E. C., Springer, M. S., Madsen, O., Bates, P. J. J., Brien, S. J. O., & Murphy, W. J. (2005). A molecular phylogeny for bats illuminates biogeography and the fossil record. Science, 307, 580-584. https://doi.org/10.1126/science.1105113
- Thomas, N. M. (1997). A systematic review of selected Afro-Asiatic Rhinolophidae (Mammalia: Chiroptera): An evaluation of taxonomic methodologies. PhD Thesis. The University of Aberdeen.
- Thong, V. D., Puechmaille, S. J., Denzinger, A., Bates, P. J. J., Dietz, C., Csorba, G., Soisook, P., Teeling, E. C., Matsumura, S., Furey, N. M., & Schnitzler, H.-U. (2012). Systematics of the Hipposideros turpis complex and a description of a new subspecies from Vietnam. Mammal Review, 42, 166-192. https://doi. org/10.1111/j.1365-2907.2011.00202.x
- Toews, D. P. L., & Brelsford, A. (2012). The biogeography of mitochondrial and nuclear discordance in animals. Molecular Ecology, 21(16), 3907-3930. https://doi.org/10.1111/j.1365- 294X.2012.05664.x
- Trifinopoulos, J., Nguyen, L.-T., von Haeseler, A., & Quang Minh, B. (2016). W-IQ-TREE: A fast online phylogenetic tool for maximum likelihood analysis. Nucleic Acids Research, 44(W1), W232-W235. https://doi.org/10.1093/nar/gkw256
- Vallo, P., Benda, P., Cerveny, J., & Koubek, P. (2012). Conflicting mitochondrial and nuclear paraphyly in small-sized West African house bats (Vespertilionidae). Zoologica Scripta, 42, 1-12. https://doi.org/10.1111/j.1463-6409.2012.00563.x
- Yang, Z., & Rannala, B. (2010). Bayesian species delimitation using multilocus sequence data. Proceedings of the National Academy of Sciences of the United States of America, 107(20), 9264-9269. https://doi.org/10.1073/pnas.0913022107
- Yoshiyuki, M. (1989). A systematic study of the Japanese Chiroptera. National Science Museum Monographs, 7, 1-242.
- Yule, G. (1925). II.-A mathematical theory of evolution, based on the conclusions of Dr. J. C. Willis, F. R. S. Philosophical transactions of the Royal Society of London Series B, Containing Papers of a Biological Character, 213(402-410), 21-87. https://doi.org/ 10.1098/RSTB.1925.0002
- Zhang, J., Kapli, P., Pavlidis, P., & Stamatakis, A. (2013). A general species delimitation method with applications to phylogenetic placements. Bioinformatics, 29(22), 2869-2876. https://doi.org/ 10.1093/BIOINFORMATICS/BTT499
- Zhou, Z. M., Guillen-Servent, A., Lim, B. K., Eger, J. L., Wang, Y. X., & Jiang, X. L. (2009). A new species from southwestern China in the Afro-Palearctic lineage of the horseshoe bats (Rhinolophus). Journal of Mammalogy, 90(1), 57-73. https:// doi.org/10.1644/08-MAMM-A-048.1
- Zohary, M. (1973). Geobotanical foundations of the Middle East. Gustav Fischer Verlag.