Complete Mitochondrial Genome of Piophila casei (Diptera: Piophilidae): Genome Description and Phylogenetic Implications

Bi, Shenghui; Song, Yan-Fei; Liu, Linggao; Wan, Jing; Zhou, Ying; Zhu, Qiujin; Liu, Jianfeng

doi:10.3390/genes14040883

Cited by 9 publications

(2 citation statements)

References 58 publications

(64 reference statements)

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“…This raised the question of whether the apparently slow rate reflected mutation saturation, so I examined the relation between pairwise distance and number of transitions or transversions for whole mitochondrial gene, using the additional function in MEGA 11 (Tamura et al, 2021; Figure 4). Similar approaches by alternative software are found in recent publications of Yuan et al (2022) and Bi et al (2023).…”

Section: Recovering Ancient Base Substitution Ratessupporting

confidence: 79%

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Geologically calibrated mammalian tree and its correlation with global events, including the emergence of humans

Osozawa

2023

Ecology and Evolution

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A robust timetree for Mammalia was constructed using the time calibration function of BEAST v1.10.4 and MEGA 11. The analysis involved the application of times of the most recent common ancestors, including a total of 19 mammalian fossil calibration ages following Benton et al. (Palaeontologia Electronica, 2015, 1–106) for their minimum ages. Additionally, fossil calibration ages for Gorilla, Pan, and a geologic event calibration age for otters were incorporated. Using these calibration ages, I constructed a geologically calibrated tree that estimates the age of the Homo and Pan splitting to be 5.69 Ma. The tree carries several significant implications. First, after the initial rifting at 120 Ma, the Atlantic Ocean expanded by over 500 km around Chron 34 (84 Ma), and vicariant speciation between Afrotheria (Africa) and Xenarthra (South America) appears to have commenced around 70 Ma. Additionally, ordinal level differentiations began immediately following the K–Pg boundary (66.0 Ma), supporting previous hypothesis that mammalian radiation rapidly filled ecological niches left vacant by non‐avian dinosaurs. I constructed a diagram depicting the relationship between base substitution rate and age using an additional function in BEAST v1.10.4. The diagram reveals an exponential increase in the base substitution rate approaching recent times. This increased base substitution rate during the Neogene period may have contributed to the expansion of biodiversity, including the extensive adaptive radiation that led to the evolution of Homo sapiens. One significant driving factor behind this radiation could be attributed to the emergence and proliferation of C4 grasses since 20 Ma. These grasses have played a role in increasing carbon fixation, reducing atmospheric CO2 concentration, inducing global cooling, and initiating Quaternary glacial–interglacial cycles, thereby causing significant climatic changes.

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Section: Recovering Ancient Base Substitution Ratessupporting

confidence: 79%

“…Phylogenetic research employing complete mitochondrial data has experienced notable advancements, enabling the construction of highly resolved and accurate phylogenetic trees (Bi et al., 2023 ; Łukasik et al., 2018 ; Yuan et al., 2022 ; Zhang et al., 2021 ).…”

Section: Methodsmentioning

confidence: 99%

Geologically calibrated mammalian tree and its correlation with global events, including the emergence of humans

Osozawa

2023

Ecology and Evolution

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Paleopteran molecular clock: Time drift and recent acceleration

Osozawa,

Nel

2024

Ecology and Evolution

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Applying BEAST v1.10.4, we constructed a Bayesian Inference tree comprising 322 taxa, primarily representing Paleoptera (Odonata and Ephemeroptera; Pterygota), Zygentoma and Archaeognatha (Apterygota; paraphyly), and Neoptera (Plecoptera; Pterygota), based on a 2685 bp sequence dataset. Our analyses revealed that robust dating required the incorporation of both Quaternary and pre‐Quaternary dates. To achieve this, our dating incorporated a 1.55 Ma (Quaternary) geological event (the formation of the Ryukyu Islands) and a set of chronologically well‐founded fossil dates, spanning from up to 400 Ma (Devonian) for the stem Archaeognatha, 320 Ma (Carboniferous) for the crown of Paleoptera, 300 Ma (Carboniferous) for the crown Ephemeroptera, and 280 Ma (Permian) for the crown Odonata, down to 1.76 Ma (Quaternary) for Calopteryx japonica, encompassing a total of 22 calibration points (events: 6, fossils: 16; Quaternary: 7, pre‐Quaternary: 15). The resulting dated tree aligns with previous research, albeit with some dates being overestimated. This overestimation was mainly due to the lack of Quaternary calibration and the exclusive dependence on pre‐Quaternary calibration, though the application of maximum age constraints also played a role. Our minimum age dating demonstrates that the molecular clock did not uniformly progress, rendering rate dating an inapplicable approach. We observed that the base substitution rate is time‐dependent, with an exponential increase evident from around 20 Ma (Miocene) to the present time, exceeding an order of magnitude. The extensive radiation and speciation of Insecta and Paleoptera, potentially resulting from the severe climatic changes associated with the Quaternary, including the commencement of glacial and interglacial cycles, may have significantly contributed to this increase in base substitution rates. Additionally, we identified a potential peak in base substitution rates during the Carboniferous period, around 320 million years ago, possibly corresponding to the Late Paleozoic Ice Age.

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Application of omics techniques in forensic entomology research

Shao

Yang

et al. 2023

Acta Tropica

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Complete Mitochondrial Genome of Piophila casei (Diptera: Piophilidae): Genome Description and Phylogenetic Implications

Cited by 9 publications

References 58 publications

Geologically calibrated mammalian tree and its correlation with global events, including the emergence of humans

Geologically calibrated mammalian tree and its correlation with global events, including the emergence of humans

Paleopteran molecular clock: Time drift and recent acceleration

Application of omics techniques in forensic entomology research

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