scholarly journals A molecular phylogeny of Schizothoracinae (Teleostei: Cypriniformes: Cyprinidae) based on 12 protein-coding mitochondrial genes and RAG1 gene analysis

2019 ◽  
Author(s):  
Yurong Du ◽  
Ting Wang ◽  
Delin Qi ◽  
Desheng Qi ◽  
Weilin Li ◽  
...  
Keyword(s):  
Molecular Phylogeny ◽  
Phylogenetic Relationships ◽  
Divergence Time ◽  
Sister Group ◽  
Mitochondrial Genes ◽  
Tibet Plateau ◽  
Divergence Times ◽  
Protein Coding ◽  
Rag1 Gene ◽  
The Times

AbstractThe ever-increasing interest in the investigation of origin and speciation of schizothoracine fishes can be dated to 20th century. However, molecular phylogeny of Schizothoracinae and their phylogenetic relationships, as well as the divergence times still remain controversial. In this study, two DNA sets consisting of 12 protein-coding mitochondrial genes from 254 individuals and RAG1 gene from 106 individuals were used to reconstruct the phylogenetic relationships and calculate the divergence times among the subfamily schizothoracinae. Our results indicated that both of the data sets supported a non-monophyletic relationship due to involving of species of Barbinae. However, the phylogenetic relationships based on mtDNA genes were more reliable than that inferred from RAG1 gene. The highly specialized grade formed a monophyletic group, together with Ptychobarbus as a sister group of Diptychus and Gymnodiptychus, which was belonging to specialized grade, indicating that Ptychobarbus may be transition species to involve to highly specialized schizothoracianae. In addition, the primitive grade clustered with Percocypris pingi, a species of Barbinae. Based on mtDNA gene, the speciation time of Schizothoracinae was 66 Ma, and the divergence time of the primitive grade and Percocypris pingi was 64 Ma. The speciation times of the three grades Schizothoracinae were 57 Ma, 51 Ma and 43 Ma, respectively; and the divergence time of specialized and highly specialized grade was 46 Ma. The divergence times of three grades were not consistent with the three stages of uplift of Qinghai-Tibet Plateau, which is older than the times.

scholarly journals An integrative phylogenomic approach illuminates the evolutionary history of cockroaches and termites (Blattodea)

2019 ◽  
Vol 286 (1895) ◽  
pp. 20182076 ◽  
Author(s):  
Dominic A. Evangelista ◽  
Benjamin Wipfler ◽  
Olivier Béthoux ◽  
Alexander Donath ◽  
Mari Fujita ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Divergence Time ◽  
Sister Group ◽  
Divergence Times ◽  
Sister Group Relationship ◽  
Time Analysis ◽  
The Social ◽  
History Of ◽  
Egg Care ◽  
Phylogenomic Study

Phylogenetic relationships among subgroups of cockroaches and termites are still matters of debate. Their divergence times and major phenotypic transitions during evolution are also not yet settled. We addressed these points by combining the first nuclear phylogenomic study of termites and cockroaches with a thorough approach to divergence time analysis, identification of endosymbionts, and reconstruction of ancestral morphological traits and behaviour. Analyses of the phylogenetic relationships within Blattodea robustly confirm previously uncertain hypotheses such as the sister-group relationship between Blaberoidea and remaining Blattodea, and Lamproblatta being the closest relative to the social and wood-feeding Cryptocercus and termites. Consequently, we propose new names for various clades in Blattodea: Cryptocercus + termites = Tutricablattae; Lamproblattidae + Tutricablattae = Kittrickea; and Blattoidea + Corydioidea = Solumblattodea. Our inferred divergence times contradict previous studies by showing that most subgroups of Blattodea evolved in the Cretaceous, reducing the gap between molecular estimates of divergence times and the fossil record. On a phenotypic level, the blattodean ground-plan is for egg packages to be laid directly in a hole while other forms of oviposition, including ovovivipary and vivipary, arose later. Finally, other changes in egg care strategy may have allowed for the adaptation of nest building and other novelties.

Genetic evidence supports Sylvilagus mansuetus (Lagomorpha: Leporidae) as a subspecies of S. bachmani

Zootaxa ◽  
2016 ◽  
Vol 4196 (2) ◽  
pp. 289
Author(s):  
SERGIO TICUL ÁLVAREZ-CASTAÑEDA ◽  
CONSUELO LORENZO
Keyword(s):  
Phylogenetic Relationships ◽  
Morphological Traits ◽  
Nuclear Gene ◽  
Sister Group ◽  
Genetic Distances ◽  
Mitochondrial Genes ◽  
The Other ◽  
Cyt B ◽  
San Jose ◽  
Allopatric Distribution

Since Sylvilagus bachmani (Lagomorpha: Leporidae) from the Baja California Peninsula and S. mansuetus from San Jose Island, Mexico, display an allopatric distribution and are closely related, their taxonomy is unclear. The phylogenetic relationships among specimens of both species were evaluated using two mitochondrial genes (Cyt b, COI) and the beta-fibrinogen nuclear gene intron 7 (β-fib I7). The genetic analyses revealed that S. mansuetus was included within the S. bachmani clade as the sister-group of S. b. cerrosensis. The genetic distances among S. b. cerrosensis and mansuetus were relatively low (1.3% with Cyt b), similar to intraspecific distances observed within other species of Sylvilagus. We consider mansuetus to be a subspecies of S. bachmani, and the morphological traits previously used to differentiate the two taxa should be used to distinguish S. b. mansuetus from the other subspecies of S. bachmani. 

scholarly journals Phylogenomics Based on Transcriptome Data Provides Evidence for the Internal Phylogenetic Relationships and Potential Terrestrial Evolutionary Genes of Lungfish

2021 ◽  
Vol 8 ◽  
Author(s):  
Linlin Zhao ◽  
Shouqiang Wang ◽  
Fangrui Lou ◽  
Tianxiang Gao ◽  
Zhiqiang Han
Keyword(s):  
Phylogenetic Relationships ◽  
Genetic Information ◽  
Divergence Time ◽  
Sister Group ◽  
Terrestrial Environment ◽  
Phylogenetic Structure ◽  
Terrestrial Vertebrates ◽  
Genome Wide ◽  
Crucial Information ◽  
Related Stress

The evolutionary relationships of lungfish can provide crucial information on the transition from Sarcopterygii to tetrapods. Phylogenomics is necessary to explore accurate internal phylogenetic relationships among all lungfish species. In the context of the lack of genome-wide genetic information for Protopterus amphibious, we are the first to systematically report the transcriptome of P. amphibius and these sequences can be used to enrich the genome-wide genetic information of lungfish. Meanwhile, we also found significant differences in the expression levels of 3,189 genes between the lung and heart of P. amphibious. Based on phylogenomics, 1,094 shared orthologous genes were identified and then applied to reconstruct the internal phylogenetic structure of lungfish species. The reconstructed phylogenetic relationships provide evidence that lungfish is the sister group of terrestrial vertebrates and that Neoceratodus forsteri is the most primitive lungfish. Moreover, the divergence time between the most primitive lungfish and other lungfish species is between 186.11 and 195.36 MYA. Finally, 43 protein metabolism-related, stress response-related, and skeletogenesis-related genes were found to have undergone positive selection and fast evolution in N. forsteri. We suspected that these genes possibly helped ancient fish adapt to the new terrestrial environment and ultimately contributed to its spreading to land.

scholarly journals Phylogenetic relationships among Callosciurus squirrels in the Indochina Peninsula: phylogenetic position of C. pygerythrus from Myanmar

2021 ◽  
Vol 67 (1) ◽  
pp. 87-98
Author(s):  
Tatsuo Oshida ◽  
Wynn Than ◽  
Thida Oo ◽  
Khin Yu Yu Swe ◽  
Hiroaki Saito ◽  
...  
Keyword(s):  
Cytochrome B ◽  
Phylogenetic Relationships ◽  
Divergence Time ◽  
Divergence Times ◽  
Phylogenetic Position ◽  
Mitochondrial Cytochrome ◽  
Indochina Peninsula ◽  
Mitochondrial Cytochrome B ◽  
Global Cooling ◽  
Mitochondrial Cytochrome B Gene

The phylogenetic relationships among seven Callosciurus species from the Indochina Peninsula, including the C. honkhoaiensis which is endemic to Hon Khoai Island, were studied using complete mitochondrial cytochrome b gene sequences (1140 bases). We primarily focused on the phylogenetic position of C. pygerythrus, which is distributed in the western part of the peninsula. We identified two main lineages: 1) C. caniceps, C. honkhoaiensis, C. inornatus, C. phayrei and C. pygerythrus, and 2) C. erythraeus and C. finlaysonii. Estimated divergence time between the two lineages was at the junction of the Zanclean and Piacenzian in the Pliocene. Within the first linage, the divergence time of sub-lineages corresponded to the Pliocene-Pleistocene boundary, although phylogenetic relationships were unclear. These two divergence times estimated in the present study correspond to episodes of global cooling, suggesting that climate may have contributed to the divergence of these Callosciurus squirrels.

Molecular phylogeny of the spoonbills (Aves: Threskiornithidae) based on mitochondrial DNA

Zootaxa ◽  
2010 ◽  
Vol 2603 (1) ◽  
pp. 53 ◽  
Author(s):  
R. TERRY CHESSER ◽  
CAROL K. L. YEUNG ◽  
CHENG-TE YAO ◽  
XIU-HUA TIAN ◽  
SHOU-HSIEN LI
Keyword(s):  
Mitochondrial Dna ◽  
Maximum Likelihood ◽  
Molecular Phylogeny ◽  
Phylogenetic Trees ◽  
Strong Support ◽  
Sister Group ◽  
Molecular Data ◽  
Mitochondrial Genes ◽  
Bayesian Analyses ◽  
Limited Sampling

Spoonbills (genus Platalea) are a small group of wading birds, generally considered to constitute the subfamily Plataleinae (Aves: Threskiornithidae). We reconstructed phylogenetic relationships among the six species of spoonbills using variation in sequences of the mitochondrial genes ND2 and cytochrome b (total 1796 bp). Topologies of phylogenetic trees reconstructed using maximum likelihood, maximum parsimony, and Bayesian analyses were virtually identical and supported monophyly of the spoonbills. Most relationships within Platalea received strong support: P. minor and P. regia were closely related sister species, P. leucorodia was sister to the minor-regia clade, and P. alba was sister to the minor-regia-leucorodia clade. Relationships of P. flavipes and P. ajaja were less well resolved: these species either formed a clade that was sister to the four-species clade, or were successive sisters to this clade. This phylogeny is consistent with ideas of relatedness derived from spoonbill morphology. Our limited sampling of the Threskiornithinae (ibises), the putative sister group to the spoonbills, indicated that this group is paraphyletic, in agreement with previous molecular data; this suggests that separation of the Threskiornithidae into subfamilies Plataleinae and Threskiornithinae may not be warranted.

Phylogenetic analysis of the Prionini (Coleoptera: Cerambycidae: Prioninae) from China based on mitochondrial ribosomal RNA genes and Cytochrome oxidase I gene

Zootaxa ◽  
2010 ◽  
Vol 2487 (1) ◽  
pp. 1 ◽  
Author(s):  
BO FENG ◽  
LI CHEN ◽  
YAN-LI E ◽  
KAI-DI ZHENG
Keyword(s):  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Phylogenetic Signal ◽  
Mitochondrial Gene ◽  
Single Gene ◽  
Divergence Time ◽  
Mitochondrial Genes ◽  
12S Rrna ◽  
Molecular Systematic ◽  
Close Relationship

This is the first molecular systematic treatment of the Prionini. Here, three mitochondrial genes were partially sequenced from the Chinese Prionini to analyze phylogenetic relationships. Nucleotide compositions of three mitochondrial genes in the Chinese Prionini are biased toward A and T as in other insects. Ratios of transition vs. transversion (Ts/Tv) in 12S rRNA decrease with divergence time. However, ratios in 16S rRNA first increase with divergence time but decrease when divergence time is prolonged. Some nodes have poor bootstrap values or Bayesian posterior probabilities in phylogenetic trees reconstructed from single mitochondrial gene. In addition, some conflicting clades are found among phylogenetic trees based on a different gene. Therefore, a single mitochondrial gene provides limited phylogenetic signal and phylogenetic relationships based on a single gene sequence may be questionable. The Chinese Prionini is a monophyletic group. However, the genus Dorysthenes is paraphyletic. Dorysthenes fossatus should be transferred from Dorysthenes but the true status of D. fossatus is currently unknown. Species of Dorysthenes (excluding D. fossatus) constitute a monophyletic clade and there is close relationship between Dorysthenes paradoxus and Dorysthenes zivetta.

Towards a dated molecular phylogeny of the Tanypodinae (Chironomidae, Diptera)

2017 ◽  
Vol 31 (3) ◽  
pp. 302 ◽  
Author(s):  
M. N. Krosch ◽  
P. S. Cranston ◽  
L. M. Bryant ◽  
F. Strutt ◽  
S. R. McCluen
Keyword(s):  
Molecular Phylogeny ◽  
Mixed Model ◽  
Mitochondrial Protein ◽  
Divergence Time ◽  
Molecular Data ◽  
Ribosomal Gene ◽  
Protein Coding ◽  
Weak Support ◽  
Gene Coi ◽  
Inference Methods

A dated molecular phylogeny is proposed for the Tanypodinae, a diverse subfamily of Chironomidae (Diptera). We used molecular data from fragments of one ribosomal gene (28S), one nuclear protein-coding gene (CAD), and one mitochondrial protein-coding gene (COI), analysed using mixed model Bayesian and maximum likelihood inference methods. All proposed tribes were sampled, namely, Anatopyniini, Clinotanypodini, Coelopyniini, Fittkauimyiini, Macropelopiini, Natarsiini, Pentaneurini, Procladiini and Tanypodini. A multilocus dataset of 1938 characters was compiled from 123 individuals including outgroups. Monophyly was supported for all tribes although some relationships were not robust. Relationships between tribes and some genus groups are highly congruent with a morphology-based estimate. Relationships within tribe Pentaneurini mostly find weak support, yet previously hypothesised groupings and monophyly or lack thereof in well-sampled genera are revealed. The tempo of diversification of the family was deduced by divergence time analysis (BEAST). Origination of a subfamily stem group in the late Jurassic to early Cretaceous was inferred, with all tribes and many genera of Pentaneurini originating and diversifying in the Cretaceous. Some nodes are biogeographically informative. Gene sections supported the backbone, but more extensive sampling is needed to estimate shallower phylogenies and to better understand the tempo and diversification of Tanypodinae.

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.

Molecular phylogeny of the butterfly tribe Baorini Doherty, 1886 (Hesperiidae, Hesperiinae) in China

Zootaxa ◽  
2019 ◽  
Vol 4565 (1) ◽  
pp. 108 ◽  
Author(s):  
WEIBIN JIANG ◽  
HAIYAN HE ◽  
YUANYUAN LI ◽  
YING WANG ◽  
CHEN GE ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Maximum Likelihood ◽  
Species Diversity ◽  
Molecular Phylogeny ◽  
Phylogenetic Relationships ◽  
Mitochondrial Genes ◽  
Nuclear Genes ◽  
Large Group ◽  
The Status

The butterfly tribe Baorini Doherty, 1886 is a large group of skippers. In this study, a total of 8 genera and 41 species of putative members of this tribe, which represent most of the generic diversity and nearly all the species diversity of the group in China, were sequenced for two mitochondrial genes and three nuclear genes (2084 bp). Phylogenetic relationships and subdivision of this tribe were investigated and the status of the genera are discussed. Partitioned maximum likelihood analyses were performed based on the combined dataset. Our results suggest that the data are split into two well-supported clades in the phylogeny tree. This analysis also represents the most complete phylogenetic analysis of the tribe Baorini in China to date, and includes several genera and species that have been previously excluded from published phylogenies of this group. 

Molecular phylogenetics and taxonomic reanalysis of the family Mithracidae MacLeay (Decapoda : Brachyura : Majoidea)

2014 ◽  
Vol 28 (2) ◽  
pp. 145 ◽  
Author(s):  
Amanda M. Windsor ◽  
Darryl L. Felder
Keyword(s):  
Molecular Phylogeny ◽  
Phylogenetic Relationships ◽  
Molecular Phylogenetics ◽  
Morphological Characters ◽  
Mitochondrial Genes ◽  
Hard Substrate ◽  
The Family ◽  
Molecular Dataset

Mithracid crabs comprise a primarily subtidal reef- and rubble-dwelling group inhabiting both tropical and subtropical seas. Despite their relative ubiquity in many hard-substrate environments, there has been little consensus about their phylogenetic relationships or whether their group rank should be that of subfamily or family. We have used a combined molecular dataset of two nuclear (18S, H3) and three mitochondrial (12S, 16S, COI) genes to build a preliminary molecular phylogeny of Majoidea in order to examine the membership of Mithracidae. We then built a second molecular phylogeny based on three mitochondrial genes to assess the internal composition of the family, and conducted comparative morphological examinations of genera and species that resolved in unexpected positions on the phylogram. Four genera are designated under new or resurrected names on the basis of molecular and morphological characters, while memberships of several other existing genera are modified. Following review of molecular and morphological characters, the genera Coelocerus, Cyclocoeloma, Cyphocarcinus, Leptopisa, Micippa, Picrocerodes, Stenocionops and Tiarinia are provisionally excluded from Mithracidae s.s., while Hemus and Pitho are included in it. A key to genera of Mithracidae is provided.

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