How old are dragonflies and damselflies? Odonata (Insecta) transcriptomics resolve familial relationships

SummaryDragonflies and damselflies, representing the insect order Odonata, are among the earliest flying insects with living (extant) representatives. However, unravelling details of their long evolutionary history, such as egg laying (oviposition) strategies, is impeded by unresolved phylogenetic relationships, an issue particularly prevalent in damselfly families and fossil lineages. Here we present the first transcriptome-based phylogenetic reconstruction of Odonata, analyzing 2,980 protein-coding genes in 105 species representing nearly all of the order’s families (except Austropetaliidae and Neopetaliidae). All damselfly families and most dragonfly families are recovered as monophyletic groups. Our Molecular clock estimates suggest that crown-Zygoptera (damselflies) and -Anisoptera (dragonflies) both arose during the late Triassic. Several of the observed long inner branches in our topology are indicative of the extinction of once flourishing lineages. We also find that exophytic egg laying behaviour with a reduced ovipositor evolved in certain dragonflies during the late Jurassic / early Cretaceous. Lastly, we find that certain fossils have an unexpected deterring impact in divergence dating analysis.

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Comparative Analyses of the Chloroplast Genomes of Patchouli Plants and Their Relatives in Pogostemon (Lamiaceae)

Plants ◽

10.3390/plants9111497 ◽

2020 ◽

Vol 9 (11) ◽

pp. 1497

Author(s):

Cai-Yun Zhang ◽

Tong-Jian Liu ◽

Xiao-Lu Mo ◽

Hui-Run Huang ◽

Gang Yao ◽

...

Keyword(s):

Nucleotide Diversity ◽

Phylogenetic Analyses ◽

Phylogenetic Reconstruction ◽

Gc Content ◽

Protein Coding ◽

Protein Coding Genes ◽

Great Economic Importance ◽

Chloroplast Genomes ◽

Interspecific Divergence ◽

Variation Range

Pogostemon Desf., the largest genus of the tribe Pogostemoneae (Lamiaceae), consists of ca. 80 species distributed mainly from South and Southeast Asia to China. The genus contains many patchouli plants, which are of great economic importance but taxonomically difficult. Therefore, it is necessary to characterize more chloroplast (cp) genomes for infrageneric phylogeny analyses and species identification of Pogostemon, especially for patchouli plants. In this study, we newly generated four cp genomes for three patchouli plants (i.e., Pogostemon plectranthoides Desf., P. septentrionalis C. Y. Wu et Y. C. Huang, and two cultivars of P. cablin (Blanoco) Benth.). Comparison of all samples (including online available cp genomes of P. yatabeanus (Makino) Press and P. stellatus (Lour.) Kuntze) suggested that Pogostemon cp genomes are highly conserved in terms of genome size and gene content, with a typical quadripartite circle structure. Interspecific divergence of cp genomes has been maintained at a relatively low level, though seven divergence hotspot regions were identified by stepwise window analysis. The nucleotide diversity (Pi) value was correlated significantly with gap proportion (indels), but significantly negative with GC content. Our phylogenetic analyses based on 80 protein-coding genes yielded high-resolution backbone topologies for the Lamiaceae and Pogostemon. For the overall mean substitution rates, the synonymous (dS) and nonsynonymous (dN) substitution rate values of protein-coding genes varied approximately threefold, while the dN values among different functional gene groups showed a wider variation range. Overall, the cp genomes of Pogostemon will be useful for phylogenetic reconstruction, species delimitation and identification in the future.

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Comprehensive phylogenetic reconstruction of relationships in Octocorallia (Cnidaria: Anthozoa) from the Atlantic ocean using mtMutS and nad2 genes tree reconstructions

Biogeosciences Discussions ◽

10.5194/bgd-9-16977-2012 ◽

2012 ◽

Vol 9 (12) ◽

pp. 16977-16998

Author(s):

K. J. Morris ◽

S. Herrera ◽

C. Gubili ◽

P. A. Tyler ◽

A. Rogers ◽

...

Keyword(s):

Atlantic Ocean ◽

Phylogenetic Relationships ◽

Mitochondrial Protein ◽

Phylogenetic Reconstruction ◽

Protein Coding ◽

Protein Coding Genes ◽

The Third ◽

Ecological Importance

Abstract. Despite being an abundant group of significant ecological importance the phylogenetic relationships of the Octocorallia remain poorly understood and very much understudied. We used 1132 bp of two mitochondrial protein-coding genes, nad2 and mtMutS (previously referred to as msh1), to construct a phylogeny for 161 octocoral specimens from the Atlantic, including both Isididae and non-Isididae species. We found that four clades were supported using a concatenated alignment. Two of these (A and B) were in general agreement with the of Holaxonia–Alcyoniina and Anthomastus–Corallium clades identified by previous work. The third and fourth clades represent a split of the Calcaxonia–Pennatulacea clade resulting in a clade containing the Pennatulacea and a small number of Isididae specimens and a second clade containing the remaining Calcaxonia. When individual genes were considered nad2 largely agreed with previous work with MtMutS also producing a fourth clade corresponding to a split of Isididae species from the Calcaxonia–Pennatulacea clade. It is expected these difference are a consequence of the inclusion of Isisdae species that have undergone a gene inversion in the mtMutS gene causing their separation in the MtMutS only tree. The fourth clade in the concatenated tree is also suspected to be a result of this gene inversion, as there were very few Isidiae species included in previous work tree and thus this separation would not be clearly resolved. A~larger phylogeny including both Isididae and non Isididae species is required to further resolve these clades.

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Balbiani ring DNA: Sequence comparisons and evolutionary history of a family of hierarchically repetitive protein-coding genes

Journal of Molecular Evolution ◽

10.1007/bf02104734 ◽

1984 ◽

Vol 20 (3-4) ◽

pp. 281-295 ◽

Cited By ~ 36

Author(s):

James Pustell ◽

Fotis C. Kafatos ◽

Ulrich Wobus ◽

Helmut Bäumlein

Keyword(s):

Dna Sequence ◽

Evolutionary History ◽

Balbiani Ring ◽

Sequence Comparisons ◽

Protein Coding ◽

Protein Coding Genes ◽

History Of ◽

Repetitive Protein

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Complete Mitochondrial DNA Genome of Nine Species of Sharks and Rays and Their Phylogenetic Placement among Modern Elasmobranchs

Genes ◽

10.3390/genes12030324 ◽

2021 ◽

Vol 12 (3) ◽

pp. 324

Author(s):

Vasiliki Kousteni ◽

Sofia Mazzoleni ◽

Katerina Vasileiadou ◽

Michail Rovatsos

Keyword(s):

Mitochondrial Dna ◽

Evolutionary History ◽

Complete Sequence ◽

Whole Genome ◽

Protein Coding ◽

Protein Coding Genes ◽

Phylogenetic Placement ◽

Statistical Support ◽

History Of ◽

High Statistical Support

Chondrichthyes occupy a key position in the phylogeny of vertebrates. The complete sequence of the mitochondrial genome (mitogenome) of four species of sharks and five species of rays was obtained by whole genome sequencing (DNA-seq) in the Illumina HiSeq2500 platform. The arrangement and features of the genes in the assembled mitogenomes were identical to those found in vertebrates. Both Maximum Likelihood (ML) and Bayesian Inference (BI) analyses were used to reconstruct the phylogenetic relationships among 172 species (including 163 mitogenomes retrieved from GenBank) based on the concatenated dataset of 13 individual protein coding genes. Both ML and BI analyses did not support the “Hypnosqualea” hypothesis and confirmed the monophyly of sharks and rays. The broad notion in shark phylogeny, namely the division of sharks into Galeomorphii and Squalomorphii and the monophyly of the eight shark orders, was also supported. The phylogenetic placement of all nine species sequenced in this study produced high statistical support values. The present study expands our knowledge on the systematics, genetic differentiation, and conservation genetics of the species studied, and contributes to our understanding of the evolutionary history of Chondrichthyes.

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