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Olgun Karacan G, Çolak R, Çolak E. The roles of possible geographic barriers and geological events on the phylogeographic structure of the Eastern broad toothed field mouse ( Apodemus mystacinus). MAMMALIA 2021. [DOI: 10.1515/mammalia-2020-0017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
The Eastern broad toothed field mouse, Apodemus mystacinus, is a rodent species distributed in Turkey, the Middle East, and a few Aegean Islands. The aim of this study is to analyse the phylogeographic structure of A. mystacinus and possible causes of its differentiation, on the basis of mitochondrial and nuclear DNA sequences using a large number of new samples from Turkey. In this context, partial mitochondrial sequences of cytochrome b (Cytb), control region (D-loop) and a nuclear interphotoreceptor retinoid-binding protein (IRBP) gene were used to reveal the geographical differentiation among A. mystacinus populations and the validity of its subspecies. The estimated divergence times revealed that the first separation of A. mystacinus into three distinct groups (subspecies of A. mystacinus: A. m. mystacinus, A. m. smyrnensis, and A. m. euxinus) begun 0.641 Mya. The possible physical barriers in Anatolia such as high mountains and rivers could interrupt the gene flow between A. mystacinus populations. The results of the present study indicated that A. mystacinus might have used the high rocky areas along the Anatolian Diagonal as a dispersal way. Moreover, mitochondrial data in this study suggested for the first time that A. m. rhodius is synonymous with the nominative subspecies A. m. mystacinus.
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Affiliation(s)
- Gül Olgun Karacan
- Department of Medical Services and Techniques , Vocational School of Health Services, Aksaray University , Aksaray 68100 , Turkey
| | - Reyhan Çolak
- Department of Biology , Faculty of Science, Ankara University , Ankara , Turkey
| | - Ercüment Çolak
- Department of Biology , Faculty of Science, Ankara University , Ankara , Turkey
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Mohammadi Z, Ghorbani F, Kami HG, Khajeh A, Olsson U. Molecular Phylogeny of the Subgenus Karstomys Reveals Genetic Signature of Post-Glacial Colonization of Apodemus mystacinus (Rodentia: Muridae) in the Zagros Mountains from Different Refugia. Zoolog Sci 2021; 38:72-81. [PMID: 33639721 DOI: 10.2108/zs200065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 09/10/2020] [Indexed: 11/17/2022]
Abstract
Eastern broad-toothed field mouse, Apodemus mystacinus, is a rocky habitat dwelling rodent distributed in Asia Minor, the Levant, the Caucasus, and the Zagros Mountains. In this study, we investigated the phylogenetic relationship between different populations of A. mystacinus throughout its range, based on the mitochondrial cytb marker. Phylogenetic analyses revealed the existence of five separately evolving lineages within A. mystacinus, of which two previously unrecognized lineages were identified in the Zagros Mountains and the Levant. Divergence between two major clades of the subgenus Karstomys, corresponding to A. mystacinus and Apodemus epimelas, is inferred to coincide with the Messinian Salinity Crisis (Late Miocene), whereas the splits between major lineages of A. mystacinus are inferred to have occurred during the Pleistocene. Colonization of the Zagros may have occurred from different refugia via eastward migration of the Turkish population and then again by a more recent colonization from the Caucasus, after reopening of the land corridor between the Caucasus and the Zagros Mountains during the Holocene drought.
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Affiliation(s)
- Zeinolabedin Mohammadi
- Department of Biology, Faculty of Sciences, Golestan University, Gorgan, 39361-79142, Golestan, Iran, .,Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad 9177948974, Iran
| | - Fatemeh Ghorbani
- Department of Biology, Faculty of Sciences, Golestan University, Gorgan, 39361-79142, Golestan, Iran
| | - Haji Gholi Kami
- Department of Biology, Faculty of Sciences, Golestan University, Gorgan, 39361-79142, Golestan, Iran
| | - Asghar Khajeh
- Department of Crop Productions Technology, Faculty of Agriculture, Higher Educational Complex of Saravan, Saravan 99516-34145, Iran
| | - Urban Olsson
- University of Gothenburg, Department of Biology and Environmental Sciences, Systematics and Biodiversity, SE-405 30 Göteborg, Sweden.,Gothenburg Global Biodiversity Centre, SE-405 30 Göteborg, Sweden
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Hanazaki K, Tomozawa M, Suzuki Y, Kinoshita G, Yamamoto M, Irino T, Suzuki H. Estimation of Evolutionary Rates of Mitochondrial DNA in Two Japanese Wood Mouse Species Based on Calibrations with Quaternary Environmental Changes. Zoolog Sci 2019; 34:201-210. [PMID: 28589839 DOI: 10.2108/zs160169] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Reliable estimates of evolutionary rates of mitochondrial DNA might allow us to build realistic evolutionary scenarios covering broad time scales based on phylogenetic inferences. In the present study, we sought to obtain estimates of evolutionary rates in murine rodents using calibrations against historical biogeographic events. We first assumed that land-bridge-like structures that appeared intermittently at glacial maxima with 100,000-year intervals shaped the divergence patterns of cytochrome b (Cytb) sequences (1140 bp) of the larger Japanese wood mouse Apodemus speciosus. The comparison of sequences from peripheral remote islands that are separated from one another by deep straits allowed us to estimate mitochondrial DNA evolutionary rates (substitutions/site/million years) to be 0.027 to 0.036, with presumed calibrations from 140,000, 250,000, 350,000, and 440,000 years ago. Second, we addressed rapid expansion events inferred from analyses of the Cytb sequences of the lesser Japanese wood mouse A. argenteus. We detected five expansion signals in the dataset and established three categories based on the expansion parameter tau values: 3.9, 5.6-5.7, and 7.8-8.1. Considering that the climate became warmer 15,000, 53,000, and 115,000 years ago after preceding periods of rapid cooling, we calculated evolutionary rates to be 0.114, 0.047, and 0.031, respectively. This preliminary concept of the evolutionary rates on a time scale from 15,000 to 440,000 years ago for the wood mouse should be refined and tested in other species of murine rodents, including mice and rats.
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Affiliation(s)
- Kaori Hanazaki
- 1 Graduate School of Environmental Science, Hokkaido University, Kita-ku, Sapporo 060-0810, Japan
| | | | - Yutaro Suzuki
- 1 Graduate School of Environmental Science, Hokkaido University, Kita-ku, Sapporo 060-0810, Japan
| | - Gohta Kinoshita
- 1 Graduate School of Environmental Science, Hokkaido University, Kita-ku, Sapporo 060-0810, Japan
| | - Masanobu Yamamoto
- 1 Graduate School of Environmental Science, Hokkaido University, Kita-ku, Sapporo 060-0810, Japan
| | - Tomohisa Irino
- 1 Graduate School of Environmental Science, Hokkaido University, Kita-ku, Sapporo 060-0810, Japan
| | - Hitoshi Suzuki
- 1 Graduate School of Environmental Science, Hokkaido University, Kita-ku, Sapporo 060-0810, Japan
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Balasanyan V, Yavruyan E, Somerová B, Abramjan A, Landová E, Munclinger P, Frynta D. High Diversity of mtDNA Haplotypes Confirms Syntopic Occurrence of Two Field Mouse Species Apodemus uralensis and A. witherbyi (Muridae: Apodemus) in Armenia. RUSS J GENET+ 2018. [DOI: 10.1134/s1022795418060030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Neumann K, Yiğit N, Fritzsche P, Çolak E, Feoktistova N, Surov A, Michaux J. Genetic structure of the Turkish hamster ( Mesocricetus brandti ). Mamm Biol 2017. [DOI: 10.1016/j.mambio.2017.06.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Çolak R, Olgun Karacan G, Kandemir I, Çolak E, Kankiliç T, Yigit N, Michaux J. Genetic variations of Turkish bank vole, Myodes glareolus (Mammalia: Rodentia) inferred from mtDNA. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:4372-4379. [PMID: 26540489 DOI: 10.3109/19401736.2015.1089537] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The bank vole, Myodes glareolus, lives in deciduous forests throughout the Palearctic region. In Turkey, this species is distributed only in northern Anatolia (the Black Sea region) where these forests exist. This study reveals genetic differentiation among bank vole populations based on two regions of mitochondrial DNA (cytochrome b and D-loop). Populations in northern Anatolia are divided into two genetic lineages (the "eastern" and "western Black Sea" lineages) by the Kızılırmak Valley. While the western Black Sea lineage is close to the Balkan lineage, in accordance with their geographical proximities, surprisingly, the Uludag lineage, also situated in Western Turkey appears related to the eastern Black Sea population. The divergence time analyses suggest a separation between the Balkan and Turkish groups around 0.26 Mya, whereas the split between the eastern and western Black sea lineages appeared a little bit later (0.20 Mya). Our results suggest that regional refuges existed for this species in Turkey and that small-scale habitat fragmentations led to genetic differentiations between Myodes populations.
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Affiliation(s)
- Reyhan Çolak
- a Department of Biology , Faculty of Science, Ankara University , Tandoğan, Ankara , Turkey
| | - Gül Olgun Karacan
- b Department of Biology , Faculty of Science and Letters, Aksaray University , Aksaray , Turkey
| | - Irfan Kandemir
- a Department of Biology , Faculty of Science, Ankara University , Tandoğan, Ankara , Turkey
| | - Ercüment Çolak
- a Department of Biology , Faculty of Science, Ankara University , Tandoğan, Ankara , Turkey
| | - Teoman Kankiliç
- c Department of Biology , Faculty of Arts and Sciences, Niğde University , Niğde , Turkey , and
| | - Nuri Yigit
- a Department of Biology , Faculty of Science, Ankara University , Tandoğan, Ankara , Turkey
| | - Johan Michaux
- d Conservation Genetics Unit, Botany Institute (Bat. 22), University of Liège , Liège , Belgium
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Suzuki Y, Tomozawa M, Koizumi Y, Tsuchiya K, Suzuki H. Estimating the molecular evolutionary rates of mitochondrial genes referring to Quaternary ice age events with inferred population expansions and dispersals in Japanese Apodemus. BMC Evol Biol 2015; 15:187. [PMID: 26373638 PMCID: PMC4571126 DOI: 10.1186/s12862-015-0463-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 08/21/2015] [Indexed: 11/22/2022] Open
Abstract
Background Determining reliable evolutionary rates of molecular markers is essential in illustrating historical episodes with phylogenetic inferences. Although emerging evidence has suggested a high evolutionary rate for intraspecific genetic variation, it is unclear how long such high evolutionary rates persist because a recent calibration point is rarely available. Other than using fossil evidence, it is possible to estimate evolutionary rates by relying on the well-established temporal framework of the Quaternary glacial cycles that would likely have promoted both rapid expansion events and interisland dispersal events. Results We examined mitochondrial cytochrome b (Cytb) and control region (CR) gene sequences in two Japanese wood mouse species, Apodemus argenteus and A. speciosus, of temperate origin and found signs of rapid expansion in the population from Hokkaido, the northern island of Japan. Assuming that global warming after the last glacial period 7–10 thousand years before present (kyr BP) was associated with the expansion, the evolutionary rates (sites per million years, myr) of Cytb and CR were estimated as 11–16 % and 22–32 %, respectively, for A. argenteus, and 12–17 % and 17–24 %, respectively, for A. speciosus. Additionally, the significant signature of rapid expansion detected in the mtDNA sequences of A. speciosus from the remaining southern main islands, Honshu, Shikoku, and Kyushu, provided an estimated Cytb evolutionary rate of 3.1 %/site/myr under the assumption of a postglacial population expansion event long ago, most probably at 130 kyr BP. Bayesian analyses using the higher evolutionary rate of 11–17 %/site/myr for Cytb supported the recent demographic or divergence events associated with the Last Glacial Maximum. However, the slower evolutionary rate of 3.1 %/site/myr would be reasonable for several divergence events that were associated with glacial periods older than 130 kyr BP. Conclusions The faster and slower evolutionary rates of Cytb can account for divergences associated with the last and earlier glacial maxima, respectively, in the phylogenetic inference of murine rodents. The elevated evolutionary rate seemed to decline within 100,000 years.
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Affiliation(s)
- Yutaro Suzuki
- Laboratory of Ecology and Genetics, Graduate School of Environmental Science, Hokkaido University, Sapporo, 060-0810, Japan.
| | | | - Yuki Koizumi
- Laboratory of Ecology and Genetics, Graduate School of Environmental Science, Hokkaido University, Sapporo, 060-0810, Japan.
| | - Kimiyuki Tsuchiya
- Laboratory of Bioresources, Ooyo Seibutsu Co. Ltd., Tokyo, 107-0062, Japan.
| | - Hitoshi Suzuki
- Laboratory of Ecology and Genetics, Graduate School of Environmental Science, Hokkaido University, Sapporo, 060-0810, Japan.
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Phylogenetic Relationships of Apodemus Kaup, 1829 (Rodentia: Muridae) Species in the Eastern Mediterranean Inferred from Mitochondrial DNA, with Emphasis on Iranian Species. J MAMM EVOL 2015. [DOI: 10.1007/s10914-015-9294-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Poulakakis N, Kapli P, Lymberakis P, Trichas A, Vardinoyiannis K, Sfenthourakis S, Mylonas M. A review of phylogeographic analyses of animal taxa from the Aegean and surrounding regions. J ZOOL SYST EVOL RES 2014. [DOI: 10.1111/jzs.12071] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nikos Poulakakis
- Natural History Museum of Crete; University of Crete; Iraklion Greece
- Biology Department; University of Crete; Iraklion Greece
| | - Paschalia Kapli
- Natural History Museum of Crete; University of Crete; Iraklion Greece
- Biology Department; University of Crete; Iraklion Greece
| | - Petros Lymberakis
- Natural History Museum of Crete; University of Crete; Iraklion Greece
| | - Apostolos Trichas
- Natural History Museum of Crete; University of Crete; Iraklion Greece
| | | | | | - Moisis Mylonas
- Natural History Museum of Crete; University of Crete; Iraklion Greece
- Biology Department; University of Crete; Iraklion Greece
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Wang Y, Zhao LM, Fang FJ, Liao JC, Liu NF. Intraspecific molecular phylogeny and phylogeography of theMeriones meridianus(Rodentia: Cricetidae) complex in northern China reflect the processes of desertification and the Tianshan Mountains uplift. Biol J Linn Soc Lond 2013. [DOI: 10.1111/bij.12123] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Ying Wang
- School of Life Sciences; Lanzhou University; Lanzhou; Gansu; 730000; China
| | - Li-Ming Zhao
- School of Life Sciences; Lanzhou University; Lanzhou; Gansu; 730000; China
| | - Feng-Jie Fang
- School of Life Sciences; Lanzhou University; Lanzhou; Gansu; 730000; China
| | - Ji-Cheng Liao
- School of Life Sciences; Lanzhou University; Lanzhou; Gansu; 730000; China
| | - Nai-Fa Liu
- School of Life Sciences; Lanzhou University; Lanzhou; Gansu; 730000; China
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Tu T, Volis S, Dillon MO, Sun H, Wen J. Dispersals of Hyoscyameae and Mandragoreae (Solanaceae) from the New World to Eurasia in the early Miocene and their biogeographic diversification within Eurasia. Mol Phylogenet Evol 2010; 57:1226-37. [PMID: 20858548 DOI: 10.1016/j.ympev.2010.09.007] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2010] [Revised: 09/08/2010] [Accepted: 09/09/2010] [Indexed: 10/19/2022]
Abstract
The cosmopolitan Solanaceae contains 21 tribes and has the greatest diversity in South America. Hyoscyameae and Mandragoreae are the only tribes of this family distributed exclusively in Eurasia with two centers of diversity: the Mediterranean-Turanian (MT) region and the Tibetan Plateau (TP). In this study, we examined the origins and biogeographical diversifications of the two tribes based on the phylogenetic framework and chronogram inferred from a combined data set of six plastid DNA regions (the atpB gene, the ndhF gene, the rps16-trnK intergenic spacer, the rbcL gene, the trnC-psbM region and the psbA-trnH intergenic spacer) with two fossil calibration points. Our data suggest that Hyoscyameae and Mandragoreae each forms a monophyletic group independently derived from different New World lineages in the early Miocene. Phylogenetic relationships within both tribes are generally well resolved. All genera of Hyoscyameae are found to be monophyletic and they diversified in middle to late Miocene. At nearly the same time, Mandragoreae split into two clades, corresponding to the MT region and the TP region, respectively. Both the phylogenetic relationships and the estimated ages of Hyoscyameae and Mandragoreae support two independent dispersal events of their ancestors from the New World into Eurasia. After their arrivals in Eurasia, the two tribes diversified primarily in the MT region and in the TP region via multiple biogeographic processes including vicariance, dispersal, recolonization or being preserved as relicts, from the mid Miocene to the late Quaternary.
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Affiliation(s)
- Tieyao Tu
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academic of Sciences, Kunming 650204, PR China
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Jung GL, Lee SJ, Kim CK, Lee H, Kim CB. A Phylogenetic Study of Korean Rodents (Muridae, Sciuridae) Based on Mitochondrial and Nuclear DNA. ANIMAL SYSTEMATICS, EVOLUTION AND DIVERSITY 2010. [DOI: 10.5635/kjsz.2010.26.2.099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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Castiglia R, Annesi F, Kryštufek B, Filippucci MG, Amori G. The evolutionary history of a mammal species with a highly fragmented range: the phylogeography of the European snow vole. J Zool (1987) 2009. [DOI: 10.1111/j.1469-7998.2009.00612.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Geography and host biogeography matter for understanding the phylogeography of a parasite. Mol Phylogenet Evol 2008; 47:538-54. [DOI: 10.1016/j.ympev.2008.01.028] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2007] [Revised: 01/15/2008] [Accepted: 01/24/2008] [Indexed: 11/23/2022]
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Tomozawa M, Suzuki H. A Trend of Central Versus Peripheral Structuring in Mitochondrial and Nuclear Gene Sequences of the Japanese Wood Mouse, Apodemus speciosus. Zoolog Sci 2008; 25:273-85. [DOI: 10.2108/zsj.25.273] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2007] [Accepted: 12/09/2007] [Indexed: 11/17/2022]
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Suzuki H, Filippucci MG, Chelomina GN, Sato JJ, Serizawa K, Nevo E. A Biogeographic View of Apodemus in Asia and Europe Inferred From Nuclear and Mitochondrial Gene Sequences. Biochem Genet 2008; 46:329-46. [DOI: 10.1007/s10528-008-9149-7] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2007] [Revised: 11/12/2007] [Accepted: 11/12/2007] [Indexed: 11/24/2022]
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Renaud S, Chevret P, Michaux J. Morphological vs. molecular evolution: ecology and phylogeny both shape the mandible of rodents. ZOOL SCR 2007. [DOI: 10.1111/j.1463-6409.2007.00297.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Hoofer SR, Gaschak S, Dunina-Barkovskaya Y, Makluk J, Meeks HN, Wickliffe JK, Baker RJ. New Information for Systematics, Taxonomy, and Phylogeography of the Rodent GenusApodemus(Sylvaemus) in Ukraine. J Mammal 2007. [DOI: 10.1644/06-mamm-a-218r1.1] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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