Phylogenetic analyses and improved resolution of the family Bovidae based on complete mitochondrial genomes

2013 ◽  
Vol 48 ◽  
pp. 136-143 ◽  
Author(s):  
Chengzhong Yang ◽  
Changkui Xiang ◽  
Wenhua Qi ◽  
Shan Xia ◽  
Feiyun Tu ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Mitochondrial Genomes ◽  
The Family ◽  
Complete Mitochondrial Genomes

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 Three Complete Mitochondrial Genomes of Erotylidae (Coleoptera: Cucujoidea) with Higher Phylogenetic Analysis

Insects ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 524
Author(s):  
Jing Liu ◽  
Yuyu Wang ◽  
Ruyue Zhang ◽  
Chengmin Shi ◽  
Weicheng Lu ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Genomic Analysis ◽  
Sister Group ◽  
Mitochondrial Genomes ◽  
Protein Coding ◽  
Transfer Rnas ◽  
Next Generation Sequencing Technology ◽  
The Family ◽  
Mt Genome ◽  
Complete Mitochondrial Genomes

The family Erotylidae belongs to the superfamily Cucujoidea, which are phytophagous and mycophagous. So far, only two representative complete mitochondrial (mt) genomes of Erotylidae have been sequenced. Mitochondrial genomes of Tritoma metasobrina, Neotriplax arisana, and Episcapha opaca, which all belong to the subfamily Erotylinae, were sequenced using next-generation sequencing technology to better understand the diversity of mt genomes of Erotylidae. A comparative mt genomic analysis was conducted on the three sequenced representatives of Erotylinae and Languriinae sp. (Languriinae). The size of the complete mt genome of the 4 species ranged from 15,581 bp to 16,502 bp in length, including 37 genes (13 protein-coding genes, 22 transfer RNAs, and 2 ribosomal RNAs) and the control region. The arrangements of their mt genomes are highly consistent with other Coleoptera species. The start codons of two PCGs (ND1 and ND5) and the stop codons of one PCG (ATP8) were illustrated differences between Languriinae sp. and the other three species. All tRNAs of these 4 species exhibited cloverleaf secondary structures except that the dihydorouridine (DHU) arm of tRNASer(AGN) was absent. The phylogenetic analyses using both Bayesian inference (BI) and maximum likelihood (ML) methods all supported that Erotylidae as monophyletic. Erotylinae was monophyletic being the sister group to Xenocelinae. Languriinae was closely related to ‘Erotylinae-Xenocelinae’. Our results recovered Languriinae nested within Erotylidae.

scholarly journals Complete Mitochondrial Genomes of Three Nuthatches From the Genus Sitta (Aves: Passeriformes: Sittidae) and Mitogenome-Based Phylogenetic Analysis

2021 ◽  
Author(s):  
Qing-Miao Yuan ◽  
Xu Luo ◽  
Jing Cao ◽  
Yu-Bao Duan
Keyword(s):  
Phylogenetic Analyses ◽  
Taxonomic Status ◽  
Sister Group ◽  
Gene Arrangement ◽  
Phylogenetic Position ◽  
Mitochondrial Genomes ◽  
Phylogenetic Relations ◽  
Genome Data ◽  
The Family ◽  
Complete Mitochondrial Genomes

Abstract Background Nuthatches (genus Sitta) comprise a group of Passeriformes. With the publication of more mitochondrial genome data, there has been considerable focus on the taxonomic status of the nuthatches. To understand the phylogenetic position of Sitta and phylogenetic relations within this genus, we sequenced and analyzed the complete mitochondrial genomes of three species, S. himalayensis, S. nagaensis and S. yunnanensis, making this the first account of complete mitochondrial genomes (mitogenomes) for this genus. Results The mitochondrial genomes of three Sitta species are 16,822-16,830 bp in length and consisted of 37 genes and a control region. This study recovered the same gene arrangement found in the mitogenomes of Gallus gallus, which is considered the typical ancestral avian gene order. All tRNAs were predicted to form the typical cloverleaf secondary structures. Bayesian inference and maximum likelihood phylogenetic analyses of sequences of 18 species obtained a well-supported topology. The family Sittidae is the sister-group of Troglodytidae, and the genus Sitta can be divided into 3 major clades. We demonstrated the phylogenetic relationships within genus Sitta (S. carolinensis + (S. villosa + S. yunnanensis + (S. himalayensis + (S. europaea + S. nagaensis)))).

scholarly journals Gene Rearrangements in the Mitochondrial Genomes of Whiteflies (Hemiptera: Aleyrodinae): Plesiomorphies, Synapomorphies and Autapomorphies

2021 ◽  
Author(s):  
Avas Pakrashi ◽  
VIKAS KUMAR ◽  
Dhirti Banerjee ◽  
Kaomud Tyagi ◽  
C. M. Kalleshwaraswamy
Keyword(s):  
Phylogenetic Analyses ◽  
Species Level ◽  
Individual Species ◽  
Mitochondrial Genomes ◽  
Gene Rearrangements ◽  
Gene Block ◽  
Level Data ◽  
The Family ◽  
Codon Positions ◽  
Complete Mitogenome

Abstract Mitochondrial genome rearrangements have been used for defining historical relationships, but there have been incidences of convergences at different taxonomic levels. Here, we sequenced complete mitogenome of Aleurodicus rugioperculatus (Aleyrodidae: Aleurodicinae) to examine gene rearrangements and phylogenetic relationships within the family Aleyrodidae. We identified five gene blocks (I-V) in the whitefly ancestor that are shared plesiomorphies retained in different whitefly lineages. Gene block I is conserved in all whiteflies except three species (Tetraleurodes acaciae and two Bemisia species). Conversely, we detected 83 derived gene boundaries within the family. Mapping these gene boundaries onto a phylogenetic tree revealed that 16 were symplesiomorphies for two subfamilies; 9 were synapomorphies at different taxonomic levels, and 28 autapomorphies for individual species. Bayesian Inference (BI) and Maximum Likelihood (ML) phylogenetic analyses yielded similar topologies supporting the monophyly of Aleyrodinae and Aleurodicinae. Exclusion of PCG third codon positions from phylogenetic analyses improved both node support and consistency with prior analyses. To understand the significance of gene order convergence on phylogeny of the whiteflies, more species-level data is required.

scholarly journals Comparative Mitogenomic Analysis of the Eurydema Genus in the Context of Representative Pentatomidae (Hemiptera: Heteroptera) Taxa

2019 ◽  
Vol 19 (6) ◽  
Author(s):  
Wanqing Zhao ◽  
Qing Zhao ◽  
Min Li ◽  
Jiufeng Wei ◽  
Xianhong Zhang ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Sister Group ◽  
Mitochondrial Genomes ◽  
Rna Structures ◽  
Protein Coding ◽  
Transfer Rnas ◽  
The Family ◽  
Maximum Likelihood Methods

Abstract The family Pentatomidae, the largest within the superfamily Pentatomoidae, comprises about 5,000 species; many of which are economically important pests. Although the phylogeny of Pentatomidae species has been studied using various molecular markers, their phylogenetic relationships remain controversial. Recently, mitochondrial genomes (mitogenomes) have been extensively employed to examine the phylogenetics and evolution of different insects, and in this study, we sequenced complete/near-complete mitochondrial genomes from five shield bug species of Eurydema to gain a better understanding of phylogenetic relationships in the Pentatomidae. The five mitogenomes ranged in length from 15,500 to 16,752 bp and comprised 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), 2 ribosomal RNAs (rRNAs), and a control region. We compared mitogenomic characteristics of the Pentatomidae and constructed phylogenetic trees using Bayesian inference and maximum likelihood methods. Our results showed that gene arrangements, base composition, start/stop codons, gene overlaps, and RNA structures were conserved within the Pentatomidae and that congeneric species shared more characteristics. Saturation and heterogeneity analyses revealed that our PCGs and PCGRNA datasets were valid for phylogenetic analysis. Phylogenetic analyses showed consistent topologies based on BI and ML methods. These analyses strongly supported that Eurydema species belong to the tribe Strachiini, and formed a sister group with Pentatomini. The relationships among Eurydema species were shown to be consistent with their morphological features. (Strachiini + Pentatomini) was found to be a stable sibling of the clade comprising Cappaeini, Graphosomini, and Carpocorini. Furthermore, our results indicated that Graphosoma rubrolineatum (Heteroptera: Pentatomidae) belongs to the Pentatominae and not the Podopinae.

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.

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.

Sign in / Sign up

Export Citation Format

Share Document