scholarly journals A phylogenomic tree of fungi: evolutionary relationships among Calonectria ilicicola and 586 fungal mitochondrial genomes

2020 ◽  
Vol 5 (2) ◽  
pp. 1709-1711
Author(s):  
Yunpeng Gai ◽  
Ruqian Pan ◽  
Xujian Peng
Keyword(s):  
Evolutionary Relationships ◽  
Mitochondrial Genomes ◽  
Calonectria Ilicicola

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

2019 ◽  
Vol 11 (10) ◽  
pp. 2824-2849 ◽  
Author(s):  
Paweł Mackiewicz ◽  
Adam Dawid Urantówka ◽  
Aleksandra Kroczak ◽  
Dorota Mackiewicz
Keyword(s):  
Phylogenetic Analyses ◽  
Mitochondrial Genes ◽  
The Other ◽  
Phylogenetic Position ◽  
Evolutionary Relationships ◽  
Mitochondrial Genomes ◽  
Ancestral State ◽  
Phylogenetic Information ◽  
Long Time ◽  
Tree Topologies

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.

scholarly journals Assessment of mitochondrial genomes for heterobranch gastropod phylogenetics

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Rebecca M. Varney ◽  
Bastian Brenzinger ◽  
Manuel António E. Malaquias ◽  
Christopher P. Meyer ◽  
Michael Schrödl ◽  
...  
Keyword(s):  
Single Gene ◽  
Taxonomic Revision ◽  
Land Snails ◽  
Current Understanding ◽  
Evolutionary Relationships ◽  
Mitochondrial Genomes ◽  
Small Subset ◽  
Protein Coding ◽  
Weak Support ◽  
Rates Of Evolution

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”. Maximum likelihood 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 with the CAT + GTR model resulted in a reconstruction that is much more consistent with the current understanding of heterobranch phylogeny. Notably, this analysis recovered Valvatoidea and Orbitestelloidea in a polytomy with a clade including all other heterobranchs, highlighting these taxa as important to understanding early heterobranch evolution. Also, dramatic gene rearrangements were detected within and between multiple clades. However, a single gene order is conserved across the majority of heterobranch clades. Conclusions Analysis of mitochondrial genomes in a Bayesian framework with the site heterogeneous CAT + GTR model resulted in a topology largely consistent with the current understanding of heterobranch phylogeny. However, mitochondrial genomes appear to be too variable to serve as good phylogenetic markers for robustly resolving a number of deeper splits within this clade.

scholarly journals Characterization of four mitochondrial genomes of family Neritidae (Gastropoda: Neritimorpha) and insight into its phylogenetic relationships

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jian-tong Feng ◽  
Li-ping Xia ◽  
Cheng-rui Yan ◽  
Jing Miao ◽  
Ying-ying Ye ◽  
...  
Keyword(s):  
Molecular Clock ◽  
Gene Order ◽  
Phylogenetic Relationships ◽  
Evolutionary Relationships ◽  
Mitochondrial Genomes ◽  
Phylogenetic Resolution ◽  
Relaxed Molecular Clock ◽  
Insight Into ◽  
Complete Mitochondrial Genomes

AbstractNeritidae is one of the most diverse families of Neritimorpha and possesses euryhaline properties. Members of this family usually live on tropical and subtropical coasts and are mainly gregarious. The phylogenetic relationships between several subclasses of Gastropoda have been controversial for many years. With an increase in the number of described species of Neritidae, the knowledge of the evolutionary relationships in this family has improved. In the present study, we sequenced four complete mitochondrial genomes from two genera (Clithon and Nerita) and compared them with available complete mitochondrial genomes of Neritidae. Gene order exhibited a highly conserved pattern among three genera in the Neritidae family. Our results improved the phylogenetic resolution within Neritidae, and more comprehensive taxonomic sampling of subclass Neritimorpha was proposed. Furthermore, we reconstructed the divergence among the main lineages of 19 Neritimorpha taxa under an uncorrelated relaxed molecular clock.

scholarly journals Assessment of mitochondrial genomes for heterobranch gastropod phylogenetics

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.

scholarly journals Ten Complete Mitochondrial Genomes of Gymnocharacini (Stethaprioninae, Characiformes). Insights Into Evolutionary Relationships and a Repetitive Element in the Control Region (D-loop)

2021 ◽  
Vol 9 ◽  
Author(s):  
Rubens Pasa ◽  
Fabiano Bezerra Menegídio ◽  
Igor Henrique Rodrigues-Oliveira ◽  
Iuri Batista da Silva ◽  
Matheus Lewi Cruz Bonaccorsi de Campos ◽  
...  
Keyword(s):  
Control Region ◽  
Repetitive Element ◽  
Evolutionary Relationships ◽  
Mitochondrial Genomes ◽  
D Loop ◽  
Complete Mitochondrial Genomes

scholarly journals Assessment of mitochondrial genomes for heterobranch gastropod phylogenetics

2020 ◽  
Author(s):  
Rebecca M Varney ◽  
Bastian Brenzinger ◽  
Manuel António E. Malaquias ◽  
Christopher P. Meyer ◽  
Michael Schrödl ◽  
...  
Keyword(s):  
Single Gene ◽  
Taxonomic Revision ◽  
Land Snails ◽  
Current Understanding ◽  
Evolutionary Relationships ◽  
Mitochondrial Genomes ◽  
Small Subset ◽  
Protein Coding ◽  
Weak Support ◽  
Rates Of Evolution

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.” Maximum likelihood 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 with the CAT+GTR model resulted in a reconstruction that is much more consistent with the current understanding of heterobranch phylogeny. Notably, this analysis recovered Valvatoidea and Orbitestelloidea in a polytomy with a clade including all other heterobranchs, highlighting these taxa as important to understanding early heterobranch evolution. Also, dramatic gene rearrangements were detected within and between multiple clades. However, a single gene order is conserved across the majority of heterobranch clades.Conclusions Analysis of mitochondrial genomes in a Bayesian framework with the site heterogeneous CAT+GTR model resulted in a topology largely consistent with the current understanding of heterobranch phylogeny. However, mitochondrial genomes appear to be too variable to serve as good phylogenetic markers for robustly resolving a number of deeper splits within this clade.

scholarly journals Assessment of mitochondrial genomes for heterobranch gastropod phylogenetics

2020 ◽  
Author(s):  
Rebecca M Varney ◽  
Bastian Brenzinger ◽  
Manuel António E. Malaquias ◽  
Christopher P. Meyer ◽  
Michael Schrödl ◽  
...  
Keyword(s):  
Single Gene ◽  
Taxonomic Revision ◽  
Land Snails ◽  
Current Understanding ◽  
Evolutionary Relationships ◽  
Mitochondrial Genomes ◽  
Small Subset ◽  
Protein Coding ◽  
Weak Support ◽  
Rates Of Evolution

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.” Maximum likelihood 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. Notably, this analysis recovered Valvatoidea and Orbitestelloidea in a polytomy sister to all other heterobranchs, highlighting these taxa as important to understanding early heterobranch evolution. Also, dramatic gene rearrangements were detected within and between multiple clades. However, a single gene order is conserved across the majority of heterobranch clades.Conclusions Analysis of mitochondrial genomes in a Bayesian framework with the site heterogeneous CAT+GTR model resulted in a topology largely consistent with the current understanding of heterobranch phylogeny. However, mitochondrial genomes appear to be too variable to serve as good phylogenetic markers for robustly resolving a number of deeper splits within this clade.

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