scholarly journals Odonata Timetree; Exponentially Increased Base Substitution Rate Toward The Recent and Within the Carboniferous

2020 ◽  
Author(s):  
Soichi Osozawa ◽  
John Wakabayashi
Keyword(s):  
Substitution Rate ◽  
Sequence Data ◽  
Atmospheric Co2 ◽  
Base Substitution ◽  
Ryukyu Islands ◽  
28S Rrna ◽  
Terrestrial Plants ◽  
Quaternary Glaciation ◽  
The Ryukyu Islands ◽  
Base Substitution Rate

Abstract Using BEAST v1.X, we constructed a credible timetree of 115 specimens of Odonata and five species of Ephemeroptera (Paleoptera; Pterygota) and two species of Archaeognatha and three species of Zygentoma (Apterygota). 88 specimens we ourselves analyzed were collected from the Ryukyu islands, Taiwan, Japan, and China, and the resting sequence data were mostly from whole mitochondrial data found in GenBank / DDJB. The combined gene (not concatenated gene) analysis of the mitochondrial COI (795 bp), COII (548 bp), and 16S rRNA (517 bp), and the nuclear 28S rRNA (825 bp) were performed. Using the calibration function of BEAST v1.X, the timetree was constructed by applying a 1.55 Ma geological event (isolation of the Ryukyu islands from China), in addition to chronologically robust fossil dates ranging from 400 Ma for Archaeognatha, 300 Ma for Ephemeroptera, and 200 Ma for Odonata and to 1.76 Ma for Calopterygidae, for a total of 13 calibration points (event: 6, fossil: 12; Quaternary 7, pre Quaternary 11). The resultant timetree showed that molecular clock was not uniformly progressed, and the base substitution rate has exponentially increased from ca. 20 Ma to the Recent by over an order of magnitude. Our new and attractive finding indicates that the Quaternary severe climatic change including a start of glacial and interglacial cycle might have resulted in the extensive radiation and speciation of Odonata, and consequently increased the biodiversity. C4 pores generated in the Miocene effectively decreased atmospheric CO2, and triggered the Quaternary glaciation. Another peak of base substitution rate was found in the Carboniferous time around 320 Ma, and this may be analogous to the late Paleozoic icehouse. This glaciation has been triggered by the development of terrestrial plants to form thick coal layers, because this process also reduced the atmospheric CO2.

Evaluation of single-base substitution rate in DNA by affinity capillary electrophoresis

2008 ◽  
Vol 619 (1) ◽  
pp. 101-109 ◽  
Author(s):  
Naoki Kanayama ◽  
Tohru Takarada ◽  
Hideaki Shibata ◽  
Ayumi Kimura ◽  
Mizuo Maeda
Keyword(s):  
Capillary Electrophoresis ◽  
Substitution Rate ◽  
Single Base Substitution ◽  
Base Substitution ◽  
Affinity Capillary Electrophoresis ◽  
Single Base ◽  
Base Substitution Rate

scholarly journals Cicada timetree by BEAST v1.X verified the recently and exponentially increasing base substitution rates

2020 ◽  
Author(s):  
Soichi Osozawa ◽  
John Wakabayashi
Keyword(s):  
Substitution Rate ◽  
Phylogenetic Trees ◽  
Base Substitution ◽  
C4 Grasses ◽  
Calibration Function ◽  
Clock Model ◽  
Exponential Increase ◽  
Geological Event ◽  
Relaxed Clock ◽  
Base Substitution Rate

AbstractFollowing the recent publication of global cicada phylogenetic trees by Marshall et al. (2018), Łukasik et al. (2018), and Simon et al. (2019), we developed a new dated tree incorporating mostly endemic east Asian cicada data for totally 113 specimens, using the mostly advanced BEAST v1.X software applied the relaxed clock model. Fossil calibrations as old as Triassic were adopted after Moulds (2018), and a Quaternary geological event calibration was adopted following Osozawa et al. (2012), applying the calibration function of BEAST. Our timetree suggests that Tettigarctidae had cicada basal lineage as old as 200 Ma, and Derotettiginae was next as old as 100 Ma. Tibicininae was a sister of the resting Cicadidae, and Tettigomyiinae, Cicadettinae, and Cicadina started simultaneous branching and radiation around 40 Ma. We made a base substitution rate vs age diagram based on the timetree using the BEAST function, and it strongly suggested an exponential increase of base substitution rate approaching the present. The consequent increased cicada biodiversity including generation of cryptic species might have been driven by the generation and spreading of C4 grasses and the following Quaternary glaciations and severe environmental change.

scholarly journals Post-Triassic Spermatophyta Timetree Adding the Quaternary Radiated Asarum Wild Gingers

2020 ◽  
Author(s):  
Soichi Osozawa ◽  
Cunio Nackejima ◽  
John Wakabayashi
Keyword(s):  
Adaptive Radiation ◽  
Substitution Rate ◽  
Evolutionary History ◽  
Base Substitution ◽  
C4 Grasses ◽  
Glacial Period ◽  
Fossil Calibration ◽  
Geologic Time ◽  
Exponential Increase ◽  
Base Substitution Rate

Abstract BackgroundAngiospermae radiation was known as the mid-Cretaceous event, but adaptive radiation of Asarum is also expected in the Quaternary. In order to know such the Angiospermae evolutionary history through the time, we constructed a whole Spermatophyta timetree employing BEAST v1. X associated with robust fossil calibration function.ResultsWe successfully and precisely dated the Spermatophyta phylogeny, and the Angiospermae topology was concordant to the APG system. Using another function of BEAST, we discovered the exponential increase in base substitution rate in recent geologic time, and another rise of rate at the mid-Cretaceous time. These increasing events correspond to the Quaternary and mid-Cretaceous Angiospermae radiations.ConclusionsA probable cause of the recently increasing rate and the consequent radiation was ultimately generation of C4 grasses, reduction of atomospheric CO2, and the start of the Quaternary glacial period. Mid-Cretaceous event was explained by co-radiation with insect beetles as the food plant.

scholarly journals Geologically calibrated mammalian tree and the corresponding global events, including birth of human

2021 ◽  
Author(s):  
Soichi Osozawa ◽  
John Wakabayashi
Keyword(s):  
Carbon Fixation ◽  
Homo Sapiens ◽  
Base Substitution ◽  
Ryukyu Islands ◽  
C4 Grasses ◽  
Calibration Function ◽  
Fossil Calibration ◽  
The Ryukyu Islands ◽  
Mammalian Fossil ◽  
Atmospheric Co2 Concentrations

Abstract The robust timetree could be constructed using a calibration function of BEAST v1. X released in 2018 simply by applying times of the most recent (= the latest) common ancestors (tMRCAs) for specific monophyletic species groups (clades). The present research is probably the first trial to fully use the calibration function in BEAST X. The specific node age (child tMRCA) in BEAST X = “minimum age” in conventional MCMCTree, but the “maximum age” in MCMCTree can be equivalent to, e.g., the parent node age (parent tMRCA) in BEAST X. We applied 19 mammalian fossil calibration ages considering Benton et al. (2015; solely their minimum ages), including those of fossil Gorilla and Pan + one geologic event calibration age for otters (= Quaternary isolation time of the Ryukyu islands and start of vicariant speciation), and we estimated our targeted splitting age of Homo and Pan at 5.69 Ma (calibration dates by Benton et al., 2015 were incorrect). After the initial rifting at 120 Ma, the Atlantic Ocean spread over 500 km on Chron 34 (84 Ma), and Afrotheria (Africa) and Xenarthra (South America) started vicariant speciation at this time (~ 70 Ma), reflecting the progressed continental isolation. Ordinal-level differentiations started just after the K-Pg boundary (66.0 Ma), and this timing reconfirmed that mammalian radiation occurred by rapidly filling the niches left vacant by the non-avian dinosaurs. In addition, we made a base substitution rate vs age diagram using the BEAST X function and showed that the rate exponentially increased and accelerated toward the Holocene, other than having the 55 Ma mild peak reflecting the post K-Pg mammalian explosion. The increased rate might have consequently increased the biodiversity, and extensive adaptive radiation might have ultimately birthed Homo sapiens. The basic factor of radiation might be the generation and spreading of C4 grasses since 20 Ma, which has been linked to increasing carbon fixation, decreasing atmospheric CO2 concentrations, cooling Earth, and triggering the Quaternary (2.58 Ma ~) glacier-inter glacier cycle and severe climatic change. Note that Perissodactyla and Cetartiodactyla (Laurasiatheria) feed on C4 grasses (savanna), and Carnivora (also Laurasiatheria) is the predator, also suggesting coevolutions since 20 Ma.

Monthly Water Exchange through the Ryukyu Islands Revealed by Salinity Structural Changes

2013 ◽  
Vol 864-867 ◽  
pp. 2335-2339
Author(s):  
Ya Pan Liu ◽  
Jian Cheng Kang ◽  
Jiong Zhu ◽  
Qin Chen Han
Keyword(s):  
Structural Changes ◽  
Water Exchange ◽  
High Salinity ◽  
World Ocean ◽  
Core Layer ◽  
Ryukyu Islands ◽  
High Salinity Water ◽  
The Ryukyu Islands ◽  
Salinity Water ◽  
World Ocean Atlas

Using salinity database of World Ocean Atlas 2009 (WOA09) issued by NOAA in 2010, refer the range of high-salinity tongue to indicate the strength about high-salinity water, from the perspective of structural changes of salinity; the water exchange through Ryukyu Islands upper 500 m have been analyzed, the results show that: due to Ryukyu Trough, currents on both sides of Ryukyu Islands occur exchange, for upper 500 m, high-salinity water in east of the Ryukyu Islands mainly invade the west waterthe Kuroshio in East China Sea; the intrusion strength is powerful from the depth of 100 m to 200 m, and the 150 m layer is the core layer of high-salinity water intrusion; the high-salinity water at the east of Ryukyu Islands invades the Kuroshio are stronger in March, May, June, September, October and November, are weaker in April and December.

The comparative yields of two types of leucaena (Peruvian v. Hawaiian) grown for forage production in Ryukyu Islands

1986 ◽  
Vol 106 (3) ◽  
pp. 623-624 ◽  
Author(s):  
Y. Kitamura
Keyword(s):  
Leucaena Leucocephala ◽  
Ryukyu Islands ◽  
Forage Production ◽  
High Quality ◽  
The Ryukyu Islands

Leucaena leucocephala (Lam.) de Wit, a leguminous shrub, has come into use as a fodder plant for animals in the Ryukyu Islands as it provides highly palatable, high quality feed (Kitamura, 1985). It is superior to other feeds available in this regard (Higashiohmine, Aramoto & Yamashiro, 1971; Isa et al. 1982).

Carbon and Oxygen Isotope Records of Tridacna squamosa Shells from two Different Latitudes in the Ryukyu Islands

2021 ◽  
Vol 25 (2) ◽  
Author(s):  
Satoshi Kodama ◽  
Hideko Takayanagi ◽  
Kosuke Yoshii ◽  
Thuy Thi Nhu Ha ◽  
Ryuji Asami ◽  
...  
Keyword(s):  
Oxygen Isotope ◽  
Ryukyu Islands ◽  
Carbon And Oxygen Isotope ◽  
The Ryukyu Islands ◽  
Tridacna Squamosa

A taxonomic review of the genus Physopelta (Hemiptera: Heteroptera: Largidae) from Japan, Korea, and Taiwan, with a new record of Ph. parviceps from China

Zootaxa ◽  
2021 ◽  
Vol 4951 (3) ◽  
pp. 461-491
Author(s):  
JUN SOUMA ◽  
TADASHI ISHIKAWA
Keyword(s):  
New Species ◽  
New Record ◽  
Guangdong Province ◽  
Zhejiang Province ◽  
Ryukyu Islands ◽  
Taxonomic Review ◽  
The Ryukyu Islands ◽  
Two New Species ◽  
Central Taiwan ◽  
First Time

In this paper, we revised the physopeltine genus Physopelta Amyot & Serville, 1843 (Hemiptera: Heteroptera: Largidae) from Japan, Korea, and Taiwan. Five species were recognized and diagnosed, including two new species, Ph. (Neophysopelta) lutaspidata sp. nov. from northern and central Taiwan and Ph. (N.) fusciscutellata sp. nov. from the Ryukyu Islands, Japan and Taiwan, and three known species, Ph. (N.) gutta gutta (Burmeister, 1834), Ph. (N.) parviceps Blöte, 1931, and Ph. (N.) quadriguttata Bergroth, 1894. Physopelta (Neophysopelta) fusciscutellata sp. nov., was previously regarded as either of the two species, Ph. (N.) cincticollis Stål, 1863 and Ph. (N.) parviceps, for populations from Taiwan. Previous records of Ph. (N.) cincticollis from Japan proper and Korea, and Ph. (N.) slanbuschii (Fabricius, 1787) from the Ryukyu Islands were considered as misidentifications of Ph. parviceps. A key to facilitate the identification of the five species known in Japan, Korea, and Taiwan is provided. Additionally, Ph. (N.) parviceps is recorded from China (Guangdong Province and Zhejiang Province) for the first time. 

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