scholarly journals Ancient Mitogenomes Suggest Stable Mitochondrial Clades of the Siberian Roe Deer

Genes ◽  
2022 ◽  
Vol 13 (1) ◽  
pp. 114
Author(s):  
Miao-Xuan Deng ◽  
Bo Xiao ◽  
Jun-Xia Yuan ◽  
Jia-Ming Hu ◽  
Kyung Seok Kim ◽  
...  
Keyword(s):  
Population Dynamics ◽  
Evolutionary History ◽  
Roe Deer ◽  
Phylogenetic Analyses ◽  
Northeastern China ◽  
Early Pleistocene ◽  
Population Increase ◽  
Mitochondrial Genomes ◽  
Siberian Roe Deer ◽  
Complete Mitochondrial Genomes

The roe deer (Capreolus spp.) has been present in China since the early Pleistocene. Despite abundant fossils available for detailed morphological analyses, little is known about the phylogenetic relationships of the fossil individuals to contemporary roe deer. We generated near-complete mitochondrial genomes for four roe deer remains from Northeastern China to explore the genetic connection of the ancient roe deer to the extant populations and to investigate the evolutionary history and population dynamics of this species. Phylogenetic analyses indicated the four ancient samples fall into three out of four different haplogroups of the Siberian roe deer. Haplogroup C, distributed throughout Eurasia, have existed in Northeastern China since at least the Late Pleistocene, while haplogroup A and D, found in the east of Lake Baikal, emerged in Northeastern China after the Mid Holocene. The Bayesian estimation suggested that the first split within the Siberian roe deer occurred approximately 0.34 million years ago (Ma). Moreover, Bayesian skyline plot analyses suggested that the Siberian roe deer had a population increase between 325 and 225 thousand years ago (Kya) and suffered a transient decline between 50 and 18 Kya. This study provides novel insights into the evolutionary history and population dynamics of the roe deer.

scholarly journals Evolutionary History of Chimpanzees Inferred from Complete Mitochondrial Genomes

2010 ◽  
Vol 28 (1) ◽  
pp. 615-623 ◽  
Author(s):  
A. Bjork ◽  
W. Liu ◽  
J. O. Wertheim ◽  
B. H. Hahn ◽  
M. Worobey
Keyword(s):  
Evolutionary History ◽  
Mitochondrial Genomes ◽  
History Of ◽  
Complete Mitochondrial Genomes

scholarly journals Evolutionary history of inversions in the direction of architecture-driven mutational pressures in crustacean mitochondrial genomes

2020 ◽  
Author(s):  
Dong Zhang ◽  
Hong Zou ◽  
Jin Zhang ◽  
Gui-Tang Wang ◽  
Ivan Jakovlić
Keyword(s):  
Evolutionary History ◽  
Phylogenetic Analyses ◽  
Branch Length ◽  
Mitochondrial Genomes ◽  
Close Attention ◽  
Mtdna Sequences ◽  
Mitochondrial Data ◽  
Gc Skew ◽  
History Of ◽  
Taxonomic Approach

AbstractInversions of the origin of replication (ORI) of mitochondrial genomes produce asymmetrical mutational pressures that can cause artefactual clustering in phylogenetic analyses. It is therefore an absolute prerequisite for all molecular evolution studies that use mitochondrial data to account for ORI events in the evolutionary history of their dataset. The number of ORI events in crustaceans remains unknown; several studies reported ORI events in some crustacean lineages on the basis of fully inversed (e.g. negative vs. positive) GC skew patterns, but studies of isolated lineages could have easily overlooked ORI events that produced merely a reduction in the skew magnitude. In this study, we used a comprehensive taxonomic approach to systematically study the evolutionary history of ORI events in crustaceans using all available mitogenomes and combining signals from lineage-specific skew magnitude and direction (+ or -), cumulative skew diagrams, and gene rearrangements. We inferred 24 putative ORI events (14 of which have not been proposed before): 17 with relative confidence, and 7 speculative. Most of these were located at lower taxonomic levels, but there are indications of ORIs that occurred at or above the order-level: Copepoda, Isopoda, and putatively in Branchiopoda and Poecilostomatida+Cyclopoida. Several putative ORI events did not result in fully inversed skews. In many lineages skew plots were not informative for the prediction of replication origin and direction of mutational pressures, but inversions of the mitogenome fragment comprising the ancestral CR (rrnS-CR-trnI) were rather good predictors of skew inversions. We also found that skew plots can be a useful tool to indirectly infer the relative strengths of mutational/purifying pressures in some crustacean lineages: when purifying pressures outweigh mutational, GC skew plots are strongly affected by the strand distribution of genes, and when mutational > purifying, GC skew plots can be even completely (apparently) unaffected by the strand distribution of genes. This observation has very important repercussions for phylogenetic and evolutionary studies, as it implies that not only the relatively rare ORI events, but also much more common gene strand switches and same-strand rearrangements can produce mutational bursts, which in turn affect phylogenetic and evolutionary analyses. We argue that such compositional biases may produce misleading signals not only in phylogenetic but also in other types of evolutionary analyses (dN/dS ratios, codon usage bias, base composition, branch length comparison, etc.), and discuss several such examples. Therefore, all studies aiming to study the evolution of mtDNA sequences should pay close attention to architectural rearrangements.

Phylogeny of Terrestrial Isopods Based on the Complete Mitochondrial Genomes, Subvert the Monophyly of Oniscidea

2020 ◽  
Author(s):  
Rui Zhang ◽  
Ruru Chen ◽  
Jianmei An ◽  
Carlos A. Santamaria
Keyword(s):  
Phylogenetic Analyses ◽  
Soil Formation ◽  
Taxonomic Status ◽  
Mitochondrial Genomes ◽  
Phylogenetic Hypothesis ◽  
Terrestrial Isopods ◽  
The Family ◽  
Complete Mitochondrial Genomes

Abstract Background: Oniscidea is the only truly terrestrial taxon within the Crustacea, and vital to soil formation. However, the monophyly of suborder Oniscidea has been in dispute since 1995, with different studies disagreeing on whether the coastal Ligiidae are included within the suborder. To clarify the phylogenetic hypothesis of suborder Oniscidea, we sequenced the complete mitochondrial genomes of Ligia exotica (Roux, 1828) and Mongoloniscus sinensis (Dollfus, 1901).Results: Like most metazoan, the complete mitogenomes of two species with circular double strands. The structure and characters of mitogenomes of these two species are analyzed. The constructed phylogenetic analyses show that Oniscidea is polyphyletic group, with Ligia being more closely related to marine isopods (Valvifera + Cymothoida + Sphaeromatidea).Conclusions: We elevate the taxonomic status of the family Ligiidae to the suborder Ligiaidea which are with parallel rank with Oniscidea. Ligiaidea is much primitive than other exact terrestrial isopods. Crinocheta are strongly monophyly, family Agnaridae is more closely related to Porcellionidae rather than Armadillididae.

scholarly journals The Complete Mitochondrial Genome of One Breeding Strain of Asian Swamp Eel (Monopterus albus, Zuiew 1793) Using PacBio and Illumina Sequencing Technologies and Phylogenetic Analysis in Synbranchiformes

Genes ◽  
2021 ◽  
Vol 12 (10) ◽  
pp. 1567
Author(s):  
Haifeng Tian ◽  
Qiaomu Hu ◽  
Hongyi Lu ◽  
Zhong Li
Keyword(s):  
Mitochondrial Genome ◽  
Illumina Sequencing ◽  
Phylogenetic Relationships ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Genomes ◽  
Sequencing Technologies ◽  
Asian Swamp Eel ◽  
Swamp Eel ◽  
Complete Mitochondrial Genomes

Asian swamp eel (Monopterus albus, Zuiew 1793) is a commercially important fish due to its nutritional value in Eastern and Southeastern Asia. One local strain of M. albus distributed in the Jianghan Plain of China has been subjected to a selection breeding program because of its preferred body color and superiority of growth and fecundity. Some members of the genus Monopterus have been reclassified into other genera recently. These classifications require further phylogenetic analyses. In this study, the complete mitochondrial genomes of the breeds of M. albus were decoded using both PacBio and Illumina sequencing technologies, then phylogenetic analyses were carried out, including sampling of M. albus at five different sites and 14 species of Synbranchiformes with complete mitochondrial genomes. The total length of the mitogenome is 16,621 bp, which is one nucleotide shorter than that of four mitogenomes of M. albus sampled from four provinces in China, as well as one with an unknown sampling site. The gene content, gene order, and overall base compositions are almost identical to the five reported ones. The results of maximum likelihood (ML) and Bayesian inference analyses of the complete mitochondrial genome and 13 protein-coding genes (PCGs) were consistent. The phylogenetic trees indicated that the selecting breed formed the deepest branch in the clade of all Asian swamp eels, confirmed the phylogenetic relationships of four genera of the family Synbranchidae, also providing systematic phylogenetic relationships for the order Synbranchiformes. The divergence time analyses showed that all Asian swamp eels diverged about 0.49 million years ago (MYA) and their common ancestor split from other species about 45.96 MYA in the middle of the Miocene epoch. Altogether, the complete mitogenome of this breed of M. albus would serve as an important dataset for germplasm identification and breeding programs for this species, in addition to providing great help in identifying the phylogenetic relationships of the order Synbranchiformes.

Two complete mitochondrial genomes of Crocodylus and implications for crocodilians phylogeny

2010 ◽  
Vol 31 (3) ◽  
pp. 299-309 ◽  
Author(s):  
Peng Yan ◽  
Ge Feng ◽  
Xiaoqiang Li ◽  
Xiaobing Wu
Keyword(s):  
Phylogenetic Analyses ◽  
Sister Group ◽  
Molecular Data ◽  
Mitochondrial Genomes ◽  
Trna Genes ◽  
Nucleotide Level ◽  
Protein Coding ◽  
Genome Features ◽  
Gavialis Gangeticus ◽  
Complete Mitochondrial Genomes

AbstractThe complete mitochondrial (mt) genomes of two crocodilians: Crocodylus palustris and Crocodylus mindorensis, were sequenced in order to examine their gene and genome features. Additionally, we intended to increase the amount of molecular data suitable for phylogenetic analysis. Their gene orders conform to other crocodilians that have been sequenced, except the arrangement of two tRNA genes differ from other vertebrates, showing that the gene order of crocodilians is remarkably conserved. Phylogenetic analyses (maximum likelihood, Bayesian inference) based on the mt protein-coding genes at the nucleotide level were performed among crocodilians for which complete mt genomes were available. The results suggest that the gharial (Gavialis gangeticus) joins the false gharial (Tomistoma schlegelii) on a common branch, that constitutes a sister group to traditional Crocodylidae. In this report, Mecistops cataphractus is evidently most closely related to Osteolaemus tetraspis. They are isolated as sister taxon from the main clades in Crocodylus. Regarding Paleosuchus, it appears as sister group to Caiman within the Alligatoridae. In particular, relationships among species of Crocodylus (true crocodiles) are discussed.

scholarly journals Comparative Characterization of the Complete Mitochondrial Genomes of the Three Apple Snails (Gastropoda: Ampullariidae) and the Phylogenetic Analyses

2018 ◽  
Vol 19 (11) ◽  
pp. 3646 ◽  
Author(s):  
Huirong Yang ◽  
Jia-en Zhang ◽  
Jun Xia ◽  
Jinzeng Yang ◽  
Jing Guo ◽  
...  
Keyword(s):  
Control Strategies ◽  
Phylogenetic Analyses ◽  
Mitochondrial Protein ◽  
Evolutionary Process ◽  
Economic Losses ◽  
Mitochondrial Genomes ◽  
Pomacea Canaliculata ◽  
Bayesian Phylogenetic Analysis ◽  
D Loop ◽  
Complete Mitochondrial Genomes

The apple snails Pomacea canaliculata, Pomacea diffusa and Pomacea maculate (Gastropoda: Caenogastropoda: Ampullariidae) are invasive pests causing massive economic losses and ecological damage. We sequenced and characterized the complete mitochondrial genomes of these snails to conduct phylogenetic analyses based on comparisons with the mitochondrial protein coding sequences of 47 Caenogastropoda species. The gene arrangements, distribution and content were canonically identical and consistent with typical Mollusca except for the tRNA-Gln absent in P. diffusa. An identifiable control region (d-loop) was absent. Bayesian phylogenetic analysis indicated that all the Ampullariidae species clustered on the same branch. The genus Pomacea clustered together and then with the genus Marisa. The orders Architaenioglossa and Sorbeoconcha clustered together and then with the order Hypsogastropoda. Furthermore, the intergenic and interspecific taxonomic positions were defined. Unexpectedly, Ceraesignum maximum, Dendropoma gregarium, Eualetes tulipa and Thylacodes squamigerus, traditionally classified in order Hypsogastropoda, were isolated from the order Hypsogastropoda in the most external branch of the Bayesian inference tree. The divergence times of the Caenogastropoda indicated that their evolutionary process covered four geological epochs that included the Quaternary, Neogene, Paleogene and Cretaceous periods. This study will facilitate further investigation of species identification to aid in the implementation of effective management and control strategies of these invasive species.

scholarly journals Characterization of the Complete Mitochondrial Genomes from Two Nitidulid Pests with Phylogenetic Implications

Insects ◽  
2020 ◽  
Vol 11 (11) ◽  
pp. 779
Author(s):  
Xiaoxiao Chen ◽  
Qing Song ◽  
Min Huang
Keyword(s):  
Tandem Repeats ◽  
Stop Codon ◽  
Phylogenetic Analyses ◽  
Sister Group ◽  
Start Codon ◽  
Mitochondrial Genomes ◽  
Sister Group Relationship ◽  
Rich Region ◽  
Phylogenetic Implications ◽  
Complete Mitochondrial Genomes

The complete mitochondrial genomes of Xenostrongylusvariegatus and Epuraea sp. were sequenced and analyzed. The total genome lengths are 17,657 and 16,641 bp, with an A+T content of 77.2% and 76.4%, respectively. Each mitochondrial genome consists of 37 coding genes and a non-coding (AT-rich) region. All protein-coding genes (PCGs) start with the standard start codon, ATN, and end with complete stop codons, TAA and TAG, or an incomplete stop codon, T. All tRNAs can be folded into the typical clover-leaf secondary structure, with the exception of trnS1 in both species with a reduced dihydrouridine (DHU) arm. The AT-rich region has tandem repeats differing in both number and length. Genetic distance and Ka/Ks analyses show that nad6 has a higher variability and more rapid evolutionary rate than other PCGs. Both maximum likelihood and Bayesian inference phylogenetic analyses based on 13 PCGs and 2 ribosome DNAs (rDNAs) agree with the previous phylogenies in supporting the Nitidulidae monophyly and the sister-group relationship of Kateretidae + (Monotomidae + Nitidulidae).

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