Resolving Phylogenetic Relationships within Passeriformes Based on Mitochondrial Genes and Inferring the Evolution of Their Mitogenomes in Terms of Duplications

Abstract Mitochondrial genes are placed on one molecule, which implies that they should carry consistent phylogenetic information. Following this advantage, we present a well-supported phylogeny based on mitochondrial genomes from almost 300 representatives of Passeriformes, the most numerous and differentiated Aves order. The analyses resolved the phylogenetic position of paraphyletic Basal and Transitional Oscines. Passerida occurred divided into two groups, one containing Paroidea and Sylvioidea, whereas the other, Passeroidea and Muscicapoidea. Analyses of mitogenomes showed four types of rearrangements including a duplicated control region (CR) with adjacent genes. Mapping the presence and absence of duplications onto the phylogenetic tree revealed that the duplication was the ancestral state for passerines and was maintained in early diverged lineages. Next, the duplication could be lost and occurred independently at least four times according to the most parsimonious scenario. In some lineages, two CR copies have been inherited from an ancient duplication and highly diverged, whereas in others, the second copy became similar to the first one due to concerted evolution. The second CR copies accumulated over twice as many substitutions as the first ones. However, the second CRs were not completely eliminated and were retained for a long time, which suggests that both regions can fulfill an important role in mitogenomes. Phylogenetic analyses based on CR sequences subjected to the complex evolution can produce tree topologies inconsistent with real evolutionary relationships between species. Passerines with two CRs showed a higher metabolic rate in relation to their body mass.

Download Full-text

The phylogenetic position of the solitary zoanthid genus Sphenopus (Cnidaria: Hexacorallia)

Contributions to Zoology ◽

10.1163/18759866-08101003 ◽

2012 ◽

Vol 81 (1) ◽

pp. 43-54 ◽

Cited By ~ 14

Author(s):

James D. Reimer ◽

Meifang Lin ◽

Takuma Fujii ◽

David J.W. Lane ◽

Bert W. Hoeksema

Keyword(s):

Marine Invertebrates ◽

Phylogenetic Analyses ◽

Solid Substrate ◽

Ancestral State Reconstruction ◽

Phylogenetic Position ◽

Ancestral State ◽

State Reconstruction ◽

Unique Character ◽

The Family ◽

Southern Taiwan

The zoanthid genus Sphenopus (Cnidaria: Anthozoa: Zoantharia), like many other brachycnemic zoanthids, is found in shallow subtropical and tropical waters, but is uniquely unitary (solitary, monostomatous), azooxanthellate, and free-living. With sparse knowledge of its phylogenetic position, this study examines the phylogenetic position of Sphenopus within the family Sphenopidae utilizing specimens from southern Taiwan and Brunei collected in 1999-2011, and furthermore analyzes the evolution of its unique character set via ancestral state reconstruction analyses. Phylogenetic analyses surprisingly show Sphenopus to be phylogenetically positioned within the genus Palythoa, which is colonial (polystomatous), zooxanthellate, and attached to solid substrate. Ancestral state reconstruction strongly indicates that the unique characters of Sphenopus have evolved recently within Palythoa and only in the Sphenopuslineage. These results indicate that zoanthid body plans can evolve with rapidity, as in some other marine invertebrates, and that the traditional definitions of zoanthid genera may need reexamination.

Download Full-text

Description of Tottonophyes enigmatica gen. nov., sp. nov. (Hydrozoa, Siphonophora, Calycophorae), with a reappraisal of the function and homology of nectophoral canals

Zootaxa ◽

10.11646/zootaxa.4415.3.3 ◽

2018 ◽

Vol 4415 (3) ◽

pp. 452 ◽

Cited By ~ 1

Author(s):

P. R. PUGH ◽

C.W. DUNN ◽

S.H.D. HADDOCK

Keyword(s):

New Species ◽

Phylogenetic Analyses ◽

Sister Group ◽

The Other ◽

Phylogenetic Position ◽

Unique Combination ◽

New Family ◽

Molecular Phylogenetic ◽

Distinct Morphology ◽

A New Species

A new species of calycophoran siphonophore, Tottonophyes enigmatica gen. nov, sp. nov., is described. It has a unique combination of traits, some shared with prayomorphs (including two rounded nectophores) and some with clausophyid diphyomorphs (the nectophores are dissimilar, with one slightly larger and slightly to the anterior of the other, and both possess a somatocyst). Molecular phylogenetic analyses indicate that the new species is the sister group to all other diphyomorphs. A new family, Tottonophyidae, is established for it. Its phylogenetic position and distinct morphology help clarify diphyomorph evolution. The function and homology of the nectophoral canals and somatocyst is also re-examined and further clarification is given to their nomenclature.

Download Full-text

Large neotheropods from the Upper Triassic of North America and the early evolution of large theropod body sizes

Journal of Paleontology ◽

10.1017/jpa.2019.13 ◽

2019 ◽

Vol 93 (5) ◽

pp. 1010-1030 ◽

Cited By ~ 3

Author(s):

Christopher T. Griffin

Keyword(s):

Body Size ◽

Phylogenetic Analyses ◽

Large Body ◽

Upper Triassic ◽

Early Evolution ◽

Phylogenetic Position ◽

Ancestral State ◽

Femur Length ◽

Theropod Dinosaurs ◽

Body Sizes

AbstractLarge body sizes among nonavian theropod dinosaurs is a major feature in the evolution of this clade, with theropods reaching greater sizes than any other terrestrial carnivores. However, the early evolution of large body sizes among theropods is obscured by an incomplete fossil record, with the largest Triassic theropods represented by only a few individuals of uncertain ontogenetic stage. Here I describe two neotheropod specimens from the Upper Triassic Bull Canyon Formation of New Mexico and place them in a broader comparative context of early theropod anatomy. These specimens possess morphologies indicative of ontogenetic immaturity (e.g., absence of femoral bone scars, lack of co-ossification between the astragalus and calcaneum), and phylogenetic analyses recover these specimens as early-diverging neotheropods in a polytomy with other early neotheropods at the base of the clade. Ancestral state reconstruction for body size suggests that the ancestral theropod condition was small (~240 mm femur length), but the ancestral neotheropod was larger (~300–340 mm femur length), with coelophysoids experiencing secondary body size reduction, although this is highly dependent on the phylogenetic position of a few key taxa. Theropods evolved large body sizes before the Triassic–Jurassic extinction, as hypothesized in most other ancestral state reconstructions of theropod body sizes, but remained rare relative to smaller theropods until the Jurassic.

Download Full-text

Multilocus sequence analysis and 16S rRNA gene sequencing reveal that Yersinia frederiksenii genospecies 2 is Yersinia massiliensis

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.047175-0 ◽

2013 ◽

Vol 63 (Pt_8) ◽

pp. 3124-3129 ◽

Cited By ~ 4

Author(s):

Roberto A. Souza ◽

Priscilla F. M. Imori ◽

Juliana P. Falcão

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Type Species ◽

Phylogenetic Analyses ◽

16S Rrna Gene Sequencing ◽

The Other ◽

Phylogenetic Position ◽

Rrna Gene ◽

Content Type ◽

Link Type

Since Yersinia frederiksenii was first described in 1980, it has been recognized genotypically as a heterogeneous species, comprising three phenotypically indistinguishable genospecies. In this study, the sequence of the 16S rRNA gene and the concatenated sequences of six housekeeping genes (glnA, gyrB, hsp60, recA, rpoB and sodA) of all the currently known species of the genus Yersinia were used to determine the phylogenetic position of Y. frederiksenii genospecies 2 in the genus Yersinia . The phylogenetic analyses grouped the Y. frederiksenii genospecies 2 strains in a monophyletic group together with representative strains of Yersinia massiliensis . Moreover, the Y. frederiksenii genospecies 2 strains were also grouped apart from the other species of the genus Yersinia and far from the other two genospecies of Y. frederiksenii . All of the observations made in this study support the conclusion that Y. frederiksenii genospecies 2 should be reclassified as Y. massiliensis .

Download Full-text

Mitochondrial genomes and phylogenetic analysis of Central American weakly-electric fishes: Apteronotus rostratus, Brachyhypopomus occidentalis and Sternopygus dariensis

10.1101/353565 ◽

2018 ◽

Author(s):

Celestino Aguilar ◽

Matthew J. Miller ◽

Jose R. Loaiza ◽

Rüdiger Krahe ◽

Luis F. De León

Keyword(s):

Phylogenetic Analyses ◽

Electric Organ ◽

Sequence Divergence ◽

Central American ◽

Phylogenetic Position ◽

Mitochondrial Genomes ◽

South American ◽

South American Species ◽

Neotropical Fishes ◽

Electric Fishes

AbstractElectric fishes are a diverse group of freshwater organisms with the ability to generate electric organ discharges (EODs) that are used for communication and electrolocation. Over 200 species have originated in South America, but of these, only a few have managed to colonize the Central American Isthmus. Here, we assembled two complete and one nearly complete mitochondrial genomes (mitogenomes) for three Central American Gymnotiformes: Sternopygus dariensis, Brachyhypopomus occidentalis and Apteronotus rostratus. We then explored the three species’ phylogenetic position in the context of South American electric fishes. Mitogenomes were organized in the standard fish mitogenome order, and presented sizes of 16,600, 16,540 and 15,940 base pairs (bp) (nearly complete) for S. dariensis, B. occidentalis and A. rostratus, respectively. We uncovered a novel 60 bp intergenic spacer (IGS) located between the COII and tRNALys genes, which appears to be unique to the Apteronotidae. Furthermore, phylogenetic relationships supported the traditional monophyly of Gymnotiformes, with the three species positioned within their respective family. In addition, the genus Apteronotus was placed as the basal taxon of the order. Finally, we found high sequence divergence (13.3%) between our B. occidentalis specimen and a sequence previously reported in GenBank, suggesting that the prior mitogenome of B. occidentalis represents a different South American species that was misidentified. Indeed, phylogenetic analyses using Cytochrome b gene across the genus placed the previously reported individual within B. bennetti. Our study provides novel mitogenome resources that will advance our understanding of the diversity and phylogenetic history of Neotropical fishes.

Download Full-text

Comparative Mitogenomics and Phylogenetic Analyses of Pentatomoidea (Hemiptera: Heteroptera)

Genes ◽

10.3390/genes12091306 ◽

2021 ◽

Vol 12 (9) ◽

pp. 1306

Author(s):

Shiwen Xu ◽

Yunfei Wu ◽

Yingqi Liu ◽

Ping Zhao ◽

Zhuo Chen ◽

...

Keyword(s):

Phylogenetic Relationships ◽

Phylogenetic Analyses ◽

Heterogeneous Mixture ◽

Protein Coding ◽

Coding Regions ◽

The Third ◽

The Family ◽

Long Time ◽

Codon Positions ◽

Tree Topologies

Pentatomoidea is the largest superfamily of Pentatomomorpha; however, the phylogenetic relationships among pentatomoid families have been debated for a long time. In the present study, we gathered the mitogenomes of 55 species from eight common families (Acanthosomatidae, Cydnidae, Dinidoridae, Scutelleridae, Tessaratomidae, Plataspidae, Urostylididae and Pentatomidae), including 20 newly sequenced mitogenomes, and conducted comparative mitogenomic studies with an emphasis on the structures of non-coding regions. Heterogeneity in the base composition, and contrasting evolutionary rates were encountered among the mitogenomes in Pentatomoidea, especially in Urostylididae, which may lead to unstable phylogenetic topologies. When the family Urostylididae is excluded in taxa sampling or the third codon positions of protein coding genes are removed, phylogenetic analyses under site-homogenous models could provide more stable tree topologies. However, the relationships between families remained the same in all PhyloBayes analyses under the site-heterogeneous mixture model CAT + GTR with different datasets and were recovered as (Cydnidae + (((Tessaratomidae + Dinidoridae) + (Plataspidae + Scutelleridae)) + ((Acanthosomatidae + Urostylididae) + Pentatomidae)))). Our study showed that data optimizing strategies after heterogeneity assessments based on denser sampling and the use of site-heterogeneous mixture models are essential for further analysis of the phylogenetic relationships of Pentatomoidea.

Download Full-text

Assessment of mitochondrial genomes for heterobranch gastropod phylogenetics

10.21203/rs.3.rs-30542/v1 ◽

2020 ◽

Author(s):

Rebecca M Varney ◽

Bastian Brenzinger ◽

Manuel António E. Malaquias ◽

Christopher P. Meyer ◽

Michael Schrödl ◽

...

Keyword(s):

Gene Order ◽

Phylogenetic Analyses ◽

Single Gene ◽

Taxonomic Revision ◽

Land Snails ◽

Current Understanding ◽

Evolutionary Relationships ◽

Mitochondrial Genomes ◽

Small Subset ◽

Weak Support

Abstract ● Background: Heterobranchia is a diverse clade of marine, freshwater, and terrestrial gastropod molluscs. It includes such disparate taxa as nudibranchs, sea hares, bubble snails, pulmonate land snails and slugs, and a number of (mostly small-bodied) poorly known snails and slugs collectively referred to as the “lower heterobranchs.” Evolutionary relationships within Heterobranchia have been challenging to resolve and the group has been subject to frequent and significant taxonomic revision. Mitochondrial (mt) genomes can be a useful molecular marker for phylogenetics but, to date, sequences have been available for only a relatively small subset of Heterobranchia.● Results: To assess the utility of mitochondrial genomes for resolving evolutionary relationships within this clade, eleven new mt genomes were sequenced including representatives of several groups of “lower heterobranchs.” Phylogenetic analyses of concatenated matrices of the thirteen protein coding genes found weak support for most higher-level relationships even after several taxa with extremely high rates of evolution were excluded. Bayesian inference analysis with the CAT + GTR model resulted in a reconstruction that is much more consistent with the current understanding of heterobranch phylogeny than maximum likelihood analyses using site-homogeneous models. Interestingly, dramatic gene rearrangements were detected within and between multiple clades. However, a single gene order is conserved across the majority of heterobranch clades.● Conclusions: Mitochondrial genomes provide support for shallow nodes within Heterobranchia, but despite a relatively conserved gene order and recovery of a topology largely consistent with the current understanding of heterobranch phylogeny, mitochondrial genomes appear to be too variable to serve as good phylogenetic markers for resolving deeper splits within this clade.

Download Full-text

Evolutionary position of breviate amoebae and the primary eukaryote divergence

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2008.1358 ◽

2008 ◽

Vol 276 (1657) ◽

pp. 597-604 ◽

Cited By ~ 63

Author(s):

Marianne A. Minge ◽

Jeffrey D Silberman ◽

Russell J.S Orr ◽

Thomas Cavalier-Smith ◽

Kamran Shalchian-Tabrizi ◽

...

Keyword(s):

Sequence Data ◽

Protein Sequences ◽

Mitochondrial Genes ◽

The Other ◽

Ancestral State ◽

Free Living ◽

Molecular Sequence Data ◽

Molecular Sequence ◽

Eukaryote Evolution ◽

Key Questions

Integration of ultrastructural and molecular sequence data has revealed six supergroups of eukaryote organisms (excavates, Rhizaria, chromalveolates, Plantae, Amoebozoa and opisthokonts), and the root of the eukaryote evolutionary tree is suggested to lie between unikonts (Amoebozoa, opisthokonts) and bikonts (the other supergroups). However, some smaller lineages remain of uncertain affinity. One of these unassigned taxa is the anaerobic, free-living, amoeboid flagellate Breviata anathema , which is of key significance as it is unclear whether it is a unikont (i.e. possibly the deepest branching amoebozoan) or a bikont. To establish its evolutionary position, we sequenced thousands of Breviata genes and calculated trees using 78 protein sequences. Our trees and specific substitutions in the 18S RNA sequence indicate that Breviata is related to other Amoebozoa, thereby significantly increasing the cellular diversity of this phylum and establishing Breviata as a deep-branching unikont. We discuss the implications of these results for the ancestral state of Amoebozoa and eukaryotes generally, demonstrating that phylogenomics of phylogenetically ‘nomadic’ species can elucidate key questions in eukaryote evolution. Furthermore, mitochondrial genes among the Breviata ESTs demonstrate that Breviata probably contains a modified anaerobic mitochondrion. With these findings, remnants of mitochondria have been detected in all putatively deep-branching amitochondriate organisms.

Download Full-text

On the phylogenetic position of the Danish strain of the black honeybee (the Læsø bee), Apis mellifera mellifera L. (Hymenoptera: Apidae) inferred from mitochondrial DNA sequences

Insect Systematics & Evolution ◽

10.1163/187631296x00070 ◽

1996 ◽

Vol 27 (3) ◽

pp. 241-250 ◽

Cited By ~ 2

Author(s):

Bo Vest Pedersen

Keyword(s):

Apis Mellifera ◽

Dna Sequences ◽

Direct Sequencing ◽

Phylogenetic Analyses ◽

Pcr Amplification ◽

The Other ◽

Phylogenetic Position ◽

Apis Mellifera Mellifera ◽

Different Strains ◽

I Gene

AbstractA comparison of DNA sequences from one Danish (Laesø) and four Swedish strains of Apis mellifera mellifera (the black honeybee), A. m. ligustica (the Italian honeybee), A. m. carnica, and A. m. anatoliaca was performed. The sequences were produced using PCR amplification and direct sequencing of two mtDNA sequences common to all species. The two segments tested were: 1) a 897 bp region of the mt CO-I gene, and 2) a 434-881 bp region of the last part of the mt CO-I gene, the tRNAleu gene, an intergenic region and a small section in the beginning of the CO-II gene. The comparisons of the 897 bp region of the mt CO-I gene showed that two haplotypes with a difference of 15 bp were observed - one haplotype comprising the black honeybee and one all the other subspecies. The alignments of the CO-I / CO-II regions indicate that the strains of the black honeybee could be divided into two types in the studied region: one with 685 bp comprised the Danish strain (Laesø) and the strain from Stockholm's SkærgÅrd, and the other with 881 bp included Swedish strains from UmeÅ, Västerbotten and Jamtland. All the other subspecies, which in the studied region differed from each other only in a few base substitutions, have 434 bp. The length differences are mainly due to duplications in the investigated region. The study shows that the different subspecies can be identified on the basis of mtDNA. The phylogenetic analyses showed that the black honeybee, which can be further divided into different strains on basis of the number of duplications, seems to stand in an isolated position - originating presumably from a long termed isolation during and after the last glaciation.

Download Full-text

Molecular phylogeny inferred from the mitochondrial genomes of Plecoptera with Oyamia nigribasis (Plecoptera: Perlidae)

Scientific Reports ◽

10.1038/s41598-020-78082-y ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Meng-Yuan Zhao ◽

Qing-Bo Huo ◽

Yu-Zhou Du

Keyword(s):

Ribosomal Rna ◽

Tandem Repeats ◽

Phylogenetic Analyses ◽

The Other ◽

Mitochondrial Genomes ◽

Stem Loop ◽

Protein Coding ◽

Protein Coding Genes ◽

Noncoding Control Region ◽

Rna Genes

AbstractIn this study, the mitochondrial genome of the stonefly, Oyamia nigribasis Banks, 1920 (Plecoptera: Perlidae), was sequenced and compared with the mtDNA genomes of 38 other stoneflies and two Ephemerae. The O. nigribasis mitogenome is a circular 15,923 bp molecule that encodes a large, noncoding control region (CR) and 37 typical mtDNA genes; these include 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), and two ribosomal RNA genes (rRNAs), respectively. Most of the PCGs initiated with ATN and terminated with TAN. The dihydrouridine (DHU) arm of tRNASer (AGN) was missing, whereas the other 21 tRNAs all exhibited the typical cloverleaf secondary structure. Stem-loop (SL) structures and tandem repeats were identified in the CR. Phylogenetic analyses using Bayesian inference and maximum likelihood were undertaken to determine relationships between stoneflies. Results indicated that the Antarctoperlaria, which contains Gripopterygidae, was absolutely separated from Arctoperlaria; this finding agrees with morphology. Finally, the overall relationships could be summarized as follows ((((Notonemouridae + Nemouridae) + Leuctridae) + (Scopuridae + (Capniidae + Taeniopterygidae))) + (((Perlodidae + Chloroperlidae) + Perlidae) + (Pteronarcyidae + (Peltoperlidae + Styloperlidae))) + ((Diamphipnoidae + Eustheniidae) + Gripopterygidae)).

Download Full-text