Phylogenetic relationships and divergence times of the genus Tokudaia within Murinae (Muridae; Rodentia) inferred from the nucleotide sequences encoding the Cytb gene, RAG 1, and IRBP

2004 ◽  
Vol 82 (8) ◽  
pp. 1343-1351 ◽  
Author(s):  
Jun J Sato ◽  
Hitoshi Suzuki
Keyword(s):  
Phylogenetic Relationships ◽  
Divergence Time ◽  
Nucleotide Sequences ◽  
Ryukyu Islands ◽  
Mitochondrial Cytochrome B ◽  
Short Period ◽  
The Ryukyu Islands ◽  
Codon Positions ◽  
Recombination Activating Gene ◽  
Rag 1

The phylogenetic relationships of six genera of Murinae (Apodemus, Diplothrix, Micromys, Mus, Rattus, and Tokudaia) were examined using the nucleotide sequences for the mitochondrial cytochrome b (Cytb), as well as the nuclear recombination activating gene 1 (RAG1) and interphotoreceptor retinoid-binding protein (IRBP), with special emphasis on the position of the genus Tokudaia, which is endemic to the Ryukyu Islands. Compared with Cytb at all codon positions, the first and second codon positions of Cytb, RAG1 (1002 base pairs (bp)), and IRBP (1586 bp) sequences were less prone to saturation. Close affinity between the genera Tokudaia and Apodemus was observed in the analyses using the IRBP (1586 bp) and combined nuclear (2588 bp; RAG1 + IRBP) sequences. The divergence time for the Tokudaia–Apodemus clade was estimated at approximately 6.5–8.0 Ma, which is more recent than previously reported, thereby indicating the recent colonization of the Ryukyu Islands by the genus Tokudaia. The other relationships among the main genera were highly ambiguous, owing either to saturation or insufficient phylogenetic information. The radiation of the main genera within a relatively short period of evolutionary time may explain the unresolved topologies, although molecular sources that are less subject to saturation are required to resolve the outstanding issues.

scholarly journals Phylogenetic relationships among Callosciurus squirrels in the Indochina Peninsula: phylogenetic position of C. pygerythrus from Myanmar

2021 ◽  
Vol 67 (1) ◽  
pp. 87-98
Author(s):  
Tatsuo Oshida ◽  
Wynn Than ◽  
Thida Oo ◽  
Khin Yu Yu Swe ◽  
Hiroaki Saito ◽  
...  
Keyword(s):  
Cytochrome B ◽  
Phylogenetic Relationships ◽  
Divergence Time ◽  
Divergence Times ◽  
Phylogenetic Position ◽  
Mitochondrial Cytochrome ◽  
Indochina Peninsula ◽  
Mitochondrial Cytochrome B ◽  
Global Cooling ◽  
Mitochondrial Cytochrome B Gene

The phylogenetic relationships among seven Callosciurus species from the Indochina Peninsula, including the C. honkhoaiensis which is endemic to Hon Khoai Island, were studied using complete mitochondrial cytochrome b gene sequences (1140 bases). We primarily focused on the phylogenetic position of C. pygerythrus, which is distributed in the western part of the peninsula. We identified two main lineages: 1) C. caniceps, C. honkhoaiensis, C. inornatus, C. phayrei and C. pygerythrus, and 2) C. erythraeus and C. finlaysonii. Estimated divergence time between the two lineages was at the junction of the Zanclean and Piacenzian in the Pliocene. Within the first linage, the divergence time of sub-lineages corresponded to the Pliocene-Pleistocene boundary, although phylogenetic relationships were unclear. These two divergence times estimated in the present study correspond to episodes of global cooling, suggesting that climate may have contributed to the divergence of these Callosciurus squirrels.

scholarly journals Low-Frequency Earthquakes along the Ryukyu Islands Triggered by Teleseismic Earthquakes

2021 ◽  
Author(s):  
Ayumi Kinjo ◽  
Mamoru Nakamura
Keyword(s):  
Surface Waves ◽  
Low Frequency ◽  
Stress Sensitivity ◽  
Peak Ground Velocity ◽  
Ryukyu Islands ◽  
Plate Interface ◽  
Okinawa Island ◽  
Short Period ◽  
Ryukyu Arc ◽  
The Ryukyu Islands

Abstract Tremors and low-frequency earthquakes (LFEs), which occur in the plate interface, can provide useful information about the state of aseismic stress transfer in mega-earthquake fault zones. We estimated the distribution of stress sensitivity in the subducted plate interface by using triggered LFEs. Specifically, we detected LFEs in the Ryukyu Trench triggered by the surface waves of large teleseismic earthquakes by using the waveform records of broadband and short-period seismometers installed in the Ryukyu Arc. We selected a total of 45 teleseismic earthquakes with magnitudes of more than 7.5, which occurred between 2004 and 2017, for the analysis. We could detect the triggered LFEs for five teleseismic earthquakes. Then, we determined the hypocenters of LFEs by using the relative arrival times of LFEs for each station. The LFEs were distributed in the south of Okinawa Island and the Yaeyama area. Moreover, they were distributed around the source fault of the slow slip events. These were almost the same as the position of LFEs accompanying very low-frequency earthquakes (VLFEs). However, the epicenters of the triggered LFEs were concentrated near the locations of the most active LFE clusters accompanying VLFEs. This suggests that the sensitivity for inducing LFEs was higher near the most active clusters of the LFEs accompanying the VLFEs. The amplitudes of the triggered LFEs were proportional to the peak ground velocity of the surface waves. This indicates that the LFEs accompanying VLFEs are activated by stress acceleration in the Yaeyama and Okinawa areas and the triggered LFEs observed in these areas can be a result of the activation of the ambient tremors due to increased stress.

scholarly journals Phylogenetic Relationships between the Tideland Snails Batillaria flectosiphonata in the Ryukyu Islands and B. multiformis in the Japanese Islands

2003 ◽  
Vol 20 (11) ◽  
pp. 1423-1433 ◽  
Author(s):  
Shigeaki Kojima ◽  
Satomi Kamimura ◽  
Taeko Kimura ◽  
Ikuo Hayashi ◽  
Akiko Iijima ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Ryukyu Islands ◽  
The Ryukyu Islands ◽  
Japanese Islands

A molecular phylogeny of the genus Psittacula sensu lato (Aves: Psittaciformes: Psittacidae: Psittacula, Psittinus, Tanygnathus, †Mascarinus) with taxonomic implications 

Zootaxa ◽  
2019 ◽  
Vol 4563 (3) ◽  
pp. 547 ◽  
Author(s):  
MICHAEL P. BRAUN ◽  
THOMAS DATZMANN ◽  
THOMAS ARNDT ◽  
MATTHIAS REINSCHMIDT ◽  
HEINZ SCHNITKER ◽  
...  
Keyword(s):  
Molecular Phylogeny ◽  
Genetic Markers ◽  
Related Species ◽  
Phylogenetic Relationships ◽  
Nucleotide Sequences ◽  
Monophyletic Group ◽  
Closely Related Species ◽  
Psittacula Krameri ◽  
Taxonomic Implications ◽  
Rag 1

The long-tailed parakeets of the genus Psittacula Cuvier, 1800 have thus far been regarded as a homogeneous and monophyletic group of parrots. We used nucleotide sequences of two genetic markers (mitochondrial CYTB, nuclear RAG-1) to reconstruct the phylogenetic relationships of Psittacula and closely related species. We found that the Asian genus Psittacula is apparently paraphyletic because two genera of short-tailed parrots, Psittinus Blyth, 1842 and Tanygnathus Wagler, 1832, cluster within Psittacula, as does †Mascarinus Lesson, 1830. To create monophyletic genera, we propose recognition of the following genera: Himalayapsitta Braun, 2016 for P. himalayana, P. finschii, P. roseata, and P. cyanocephala; Nicopsitta Braun, 2016 for P. columboides and P. calthrapae; Belocercus S. Müller, 1847 for P. longicauda; Psittacula Cuvier, 1800 for P. alexandri and P. derbiana; Palaeornis Vigors, 1825 for †P. wardi and P. eupatria; and Alexandrinus Braun, 2016 for P. krameri, †P. exsul, and P. (eques) echo. Additionally, Psittacula krameri and P. alexandri are paraphyletic species, which should be split to form monophyletic species. 

scholarly journals Phylogenomic insights into the divergent history and hybridization within the East Asian endemic Abelia (Caprifoliaceae)

2021 ◽  
Author(s):  
Qinghui Sun ◽  
Diego F Morales-Briones ◽  
Hongxin Wang ◽  
Jacob F. Landis ◽  
Jun Wen ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
East Asian ◽  
Network Evolution ◽  
Disjunct Distribution ◽  
Ryukyu Islands ◽  
Last Interglacial ◽  
Niche Modelling ◽  
Range Contraction ◽  
Biogeographic History ◽  
The Ryukyu Islands

Background and Aims Abelia (Caprifoliaceae) is a small genus with five species (including one artificial hybrid). The genus has a disjunct distribution across mainland China, Taiwan and the Ryukyu Islands, providing a model system to explore species dispersal mechanisms of the East Asian flora. However, the current phylogenetic relationships within Abelia remain controversial. Methods In this study, we reconstructed the phylogenetic relationships within Abelia using nuclear loci generated by target enrichment and the cpDNA from genome skimming. Key Results: We found large cytonuclear discordance across the genus. Based on the nuclear and chloroplast phylogenies we proposed to merge A. schumannii into A. macrotera, and A. macrotera var. mairei into A. uniflora. Divergence time estimation, ancestral area reconstruction, and ecological niche modelling (ENM) were used to examine the biogeographic history of Abelia. Our results showed that Abelia originated in Southwest China, and diversification began in the Early Eocene, followed by A. chinensis var. ionandra colonizing Taiwan in the Middle Miocene. The ENM results suggested an expansion of climatically suitable areas during the Last Glacial Maximum and range contraction during the Last Interglacial. Disjunction between the Himalaya-Hengduan Mountain region (HHM) and Taiwan is most likely the consequence of topographic isolation and postglacial contraction. Conclusions Overall, our results supports that postglacial range contraction together with topographic heterogeneity resulted in the Taiwan and China mainland disjunction. Furthermore, when we using genome data to reconstruct the phylogeny of related species, branch evolution and network evolution should be considered, as well as gene flow in historical periods. This research provide new insights for the speciation process and taxonomy of Abelia.

scholarly journals Low-frequency earthquakes along the Ryukyu Islands triggered by teleseismic earthquakes

2021 ◽  
Vol 73 (1) ◽  
Author(s):  
Ayumi Kinjo ◽  
Mamoru Nakamura
Keyword(s):  
Low Frequency ◽  
Stress Transfer ◽  
Ryukyu Islands ◽  
Plate Interface ◽  
Okinawa Island ◽  
Slow Slip Events ◽  
Arrival Times ◽  
Short Period ◽  
Ryukyu Arc ◽  
The Ryukyu Islands

AbstractTremors and low-frequency earthquakes (LFEs), which occur in the plate interface, can provide useful information about the state of aseismic stress transfer in mega-earthquake fault zones. We estimated the distribution of triggered LFEs in the subducted plate interface. Specifically, we detected LFEs in the Ryukyu Trench triggered by the surface waves of large teleseismic earthquakes by using the waveform records of broadband and short-period seismometers installed in the Ryukyu Arc. We selected a total of 45 teleseismic earthquakes with magnitudes of more than 7.5, which occurred between 2004 and 2017, for the analysis. We could detect the triggered LFEs for five teleseismic earthquakes. Then, we determined the hypocenters of LFEs by using the relative arrival times of LFEs for each station. The LFEs were distributed in the south of Okinawa Island and the Yaeyama area. Moreover, they were distributed around the source fault of the slow slip events. These were almost the same as and concentrated near to the locations of the most active LFE clusters accompanying very low-frequency earthquakes, suggesting higher sensitivity of inducing LFEs near these clusters. This indicates that the LFEs accompanying VLFEs are activated by stress acceleration in the Yaeyama and Okinawa areas.

Phylogeographic structure and gene flow of Himalayan snowcock (Tetraogallus himalayensis)

2010 ◽  
Vol 60 (4) ◽  
pp. 449-465
Author(s):  
Wen Longying ◽  
Zhang Lixun ◽  
An Bei ◽  
Luo Huaxing ◽  
Liu Naifa ◽  
...  
Keyword(s):  
Demographic History ◽  
Phylogenetic Analyses ◽  
Divergence Time ◽  
Population Expansion ◽  
Population History ◽  
Tibet Plateau ◽  
Phylogeographic Structure ◽  
Mitochondrial Cytochrome B ◽  
History Of ◽  
Qinghai Tibet Plateau

AbstractWe have used phylogeographic methods to investigate the genetic structure and population history of the endangered Himalayan snowcock (Tetraogallus himalayensis) in northwestern China. The mitochondrial cytochrome b gene was sequenced of 102 individuals sampled throughout the distribution range. In total, we found 26 different haplotypes defined by 28 polymorphic sites. Phylogenetic analyses indicated that the samples were divided into two major haplogroups corresponding to one western and one eastern clade. The divergence time between these major clades was estimated to be approximately one million years. An analysis of molecular variance showed that 40% of the total genetic variability was found within local populations, 12% among populations within regional groups and 48% among groups. An analysis of the demographic history of the populations suggested that major expansions have occurred in the Himalayan snowcock populations and these correlate mainly with the first and the second largest glaciations during the Pleistocene. In addition, the data indicate that there was a population expansion of the Tianshan population during the uplift of the Qinghai-Tibet Plateau, approximately 2 million years ago.

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