The Complete Mitochondrial Genome of Platysternon megacephalum peguense and Molecular Phylogenetic Analysis

Platysternon megacephalum is the only living representative species of Platysternidae and only three subspecies remain: P. m. megalorcephalum, P. m. shiui, and P. m. peguense. However, previous reports implied that P. m. peguense has distinct morphological and molecular features. The characterization of the mitogenome has been accepted as an efficient means of phylogenetic and evolutionary analysis. Hence, this study first determined the complete mitogenome of P. m. peguense with the aim to identify the structure and variability of the P. m. peguense mitogenome through comparative analysis. Furthermore, the phylogenetic relationship of the three subspecies was tested. Based on different tRNA gene loss and degeneration of these three subspecies, their rearrangement pathways have been inferred. Phylogenetic analysis showed that P. m. peguense is a sister group to (P. m. megalorcephalum and P. m. shiui). Furthermore, the divergence time estimation of these three subspecies coincided with the uplift of the Tibetan Plateau. This study shows that the genetic distances between P. m. peguense and the other two subspecies are comparable to interspecific genetic distances, for example within Mauremys. In general, this study provides new and meaningful insights into the evolution of the three Platysternidae subspecies.

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Genetic Differentiation and Divergence Time of Chinese Parnassius (Lepidoptera: Papilionidae) Species Based on Nuclear Internal Transcribed Spacer (ITS) Sequence Data

Journal of Entomological Science ◽

10.18474/0749-8004-55.4.520 ◽

2020 ◽

Vol 55 (4) ◽

pp. 520-546

Author(s):

Chengcai Si ◽

Keke Chen ◽

Ruisong Tao ◽

Chengyong Su ◽

Junye Ma ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Genetic Differentiation ◽

Species Identification ◽

Internal Transcribed Spacer ◽

Sequence Data ◽

Divergence Time ◽

Time Estimation ◽

Western China ◽

Tibet Plateau ◽

Divergence Time Estimation

Abstract Parnassius (Lepidoptera: Papilionidae) is a genus of attractive butterflies mainly distributed in the mountainous areas of Central Asia, the Himalayas, and western China. In this study, we used the internal transcribed spacer (ITS1 and ITS2) sequence data as DNA barcodes to characterize the genetic differentiation and conduct the phylogenetic analysis and divergence time estimation of the 17 Parnassius species collected in China. Species identification and genetic differentiation analysis suggest that the ITS barcode is an effective marker for Parnassius species identification; additionally, a relatively high level of genetic diversity and low level of gene flow were detected in the five Parnassius species with diverse geographic populations. Phylogenetic analysis indicates that the 17 species studied were clustered in six clades (subgenera), with subgenus Parnassius at the basal position in the phylogenetic trees. Bayesian divergence time estimation shows that the genus originated about 18 million years ago during the early Miocene, correlated with orogenic events in the distribution region, probably southwestern China about 20–10 million years ago. Our estimated phylochronology also suggests that the Parnassius interspecific and intraspecific divergences were probably related with the rapid rising of the Qinghai-Tibet Plateau, the Tibet Movement, the Kunlun-Yellow River Tectonic Movement, and global cooling associated with intensified glaciation in the region during the Quaternary Period.

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Comparative chloroplast genomics between the invasive weed Mikania micrantha and its indigenous congener Mikania cordata: Structure variation, identification of highly divergent regions, divergence time estimation, and phylogenetic analysis

Molecular Phylogenetics and Evolution ◽

10.1016/j.ympev.2018.04.015 ◽

2018 ◽

Vol 126 ◽

pp. 181-195 ◽

Cited By ~ 6

Author(s):

Yingjuan Su ◽

Lu Huang ◽

Zhen Wang ◽

Ting Wang

Keyword(s):

Phylogenetic Analysis ◽

Divergence Time ◽

Time Estimation ◽

Invasive Weed ◽

Structure Variation ◽

Mikania Micrantha ◽

Divergence Time Estimation

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Phylogenetic analysis of colubrid snakes based on 12S rDNA reveals distinct lineages of Dendrelaphis pictus (Gmelin, 1789) populations in Sumatra and Java

Biodiversitas Journal of Biological Diversity ◽

10.13057/biodiv/d190141 ◽

2018 ◽

Vol 19 (1) ◽

pp. 303-310 ◽

Cited By ~ 2

Author(s):

FITRA ARYA DWI NUGRAHA ◽

FATCHIYAH FATCHIYAH ◽

NIA KURNIAWAN ◽

ERIC NELSON SMITH

Keyword(s):

Phylogenetic Analysis ◽

Phylogenetic Analyses ◽

Divergence Time ◽

Time Estimation ◽

Limited Data ◽

Divergence Time Estimation ◽

12S Rdna ◽

The Subject ◽

Molecular Relationships ◽

Inference Methods

Nugraha FAD, Fatchiyah F, Smith EN, Nia Kurniawan N. 2018. Phylogenetic analysis of colubrid snakes based on 12S rDNA reveals distinct lineages of Dendrelaphis pictus (Gmelin, 1789) populations in Sumatra and Java. Biodiversitas 19: 303-310. The phylogenetic relationship among the major colubrid snakes, particularly those of the subfamily Colubrinae, has been the subject of much debate. Also, there was limited data on the molecular relationships of Sundaland colubrid snakes. This study aimed to examine the relationships among colubrid snakes from Sumatra and Java based on fragments of 12S rDNA gene. We sequenced 17 specimens of colubrid snakes representing 5 genera and 2 subfamilies: Colubrinae and Ahaetullinae. We used maximum likelihood, maximum parsimony and Bayesian inference methods for inferring phylogenetic relationships. The result of our phylogenetic analyses is in line with the previous findings for the separation between Colubrinae and Ahaetullinae. Interestingly, we found two distinct clades of Dendrelaphis pictus species with the high genetic divergence between them where D. pictus from Sumatra and West Java separated from Central and East Java clade. Our divergence time estimation showed that the differentiation between these clades of D. pictus occurred in the late Miocene epoch (8.9 Ma) when Sumatra and Java separated after being inundated in the early Miocene epoch.

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A ‘living fossil’ eel (Anguilliformes: Protanguillidae, fam. nov.) from an undersea cave in Palau

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2011.1289 ◽

2011 ◽

Vol 279 (1730) ◽

pp. 934-943 ◽

Cited By ~ 40

Author(s):

G. David Johnson ◽

Hitoshi Ida ◽

Jiro Sakaue ◽

Tetsuya Sado ◽

Takashi Asahida ◽

...

Keyword(s):

Evolutionary History ◽

Divergence Time ◽

Time Estimation ◽

Sister Group ◽

Morphological Characters ◽

Morphological Evidence ◽

Living Fossil ◽

Divergence Time Estimation ◽

New Family ◽

Republic Of Palau

We report the discovery of an enigmatic, small eel-like fish from a 35 m-deep fringing-reef cave in the western Pacific Ocean Republic of Palau that exhibits an unusual suite of morphological characters. Many of these uniquely characterize the Recent members of the 19 families comprising the elopomorph order Anguilliformes, the true eels. Others are found among anguilliforms only in the Cretaceous fossils, and still others are primitive with respect to both Recent and fossil eels. Thus, morphological evidence explicitly places it as the most basal lineage (i.e. the sister group of extant anguilliforms). Phylogenetic analysis and divergence time estimation based on whole mitogenome sequences from various actinopterygians, including representatives of all eel families, demonstrate that this fish represents one of the most basal, independent lineages of the true eels, with a long evolutionary history comparable to that of the entire Anguilliformes (approx. 200 Myr). Such a long, independent evolutionary history dating back to the early Mesozoic and a retention of primitive morphological features (e.g. the presence of a premaxilla, metapterygoid, free symplectic, gill rakers, pseudobranch and distinct caudal fin rays) warrant recognition of this species as a ‘living fossil’ of the true eels, herein described as Protanguilla palau genus et species nov. in the new family Protanguillidae.

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Out of the Qinghai-Tibetan Plateau (QTP) and rapid radiation across Eurasia for Allium section Daghestanica (Amaryllidaceae)

AoB Plants ◽

10.1093/aobpla/plab017 ◽

2021 ◽

Author(s):

Min-Jie Li ◽

Huan-Xi Yu ◽

Xian-Lin Guo ◽

Xing-Jin He

Keyword(s):

Evolutionary History ◽

Divergence Time ◽

Time Estimation ◽

Adjacent Region ◽

Rapid Radiation ◽

Divergence Time Estimation ◽

Species Diversification ◽

The Third ◽

Evolutionary Line ◽

History Of

Abstract The disjunctive distribution (Europe-Caucasus-Asia) and species diversification across Eurasia for the genus Allium sect. Daghestanica has fascinating attractions for researchers aiming to understanding the development and history of the modern Eurasia flora. However, no any studies have been carried out to address the evolutionary history of this section. Based on the nrITS and cpDNA fragments (trnL-trnF and rpl32-trnL), the evolutionary history of the third evolutionary line (EL3) of the genus Allium was reconstructed and we further elucidate the evolutionary line of sect. Daghestanica under this background. Our molecular phylogeny recovered two highly supported clades in sect. Daghestanica: the Clade I includes Caucasian-European species and Asian A. maowenense, A. xinlongense and A. carolinianum collected in Qinghai; the Clade II comprises Asian yellowish tepal species, A. chrysanthum, A. chrysocephalum, A. herderianum, A. rude and A. xichuanense. The divergence time estimation and biogeography inference indicated that Asian ancestor located in the QTP and the adjacent region could have migrated to Caucasus and Europe distributions around the Late Miocene and resulted in further divergence and speciation; Asian ancestor underwent the rapid radiation in the QTP and the adjacent region most likely due to the heterogeneous ecology of the QTP resulted from the orogeneses around 4–3 Mya. Our study provides a picture to understand the origin and species diversification across Eurasia for sect. Daghestanica.

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