A comprehensive phylogenomic study unveils evolutionary patterns and challenges in the mitochondrial genomes of Carcharhiniformes: A focus on Triakidae.

The complex evolutionary patterns in the mitochondrial genome (mitogenome) of the most species-rich shark order, the Carcharhiniformes (ground sharks) has led to challenges in the phylogenomic reconstruction of the families and genera belonging to the order, particularly the family Triakidae (houndsharks). The current state of Triakidae phylogeny remains controversial, with arguments for both monophyly and paraphyly within the family. We hypothesize that this variability is triggered by the selection of different a priori partitioning schemes to account for site and gene heterogeneity within the mitogenome. Here we used an extensive statistical framework to select the a priori partitioning scheme for inference of the mitochondrial phylogenomic relationships within Carcharhiniformes, tested site heterogeneous CAT + GTR + G4 models and incorporated the multi-species coalescent model (MSCM) into our analyses to account for the influence of gene tree discordance on species tree inference. We included five newly assembled houndshark mitogenomes to increase resolution of Triakidae. During the assembly procedure, we uncovered a 714 bp-duplication in the mitogenome of Galeorhinus galeus. Phylogenetic reconstruction confirmed monophyly within Triakidae and the existence of two distinct clades of the expanded Mustelus genus. The latter alludes to potential evolutionary reversal of reproductive mode from placental to aplacental, suggesting that reproductive mode has played a role in the trajectory of adaptive divergence. These new sequences have the potential to contribute to population genomic investigations, species phylogeography delineation, environmental DNA metabarcoding databases and, ultimately, improved conservation strategies for these ecologically and economically important species.

Comparative mitogenomics of Brachiopods reveals conservatism in articulate species and unusualness in inarticulate species.

BACKGROUND: Brachiopods are a phylum of marine invertebrates with over 10,000 fossil species. Today, there are fewer than 500 extant species assigned to the class Articulata or Inarticulata and for which knowledge of evolutionary genetics and genomics is still poor. Until now, complete mitogenome sequences of two inarticulate species and four articulate species were available. METHODS AND RESULTS: The complete mitogenome of the inarticulate brachiopod species Lingula reevii (20,778 bp) was obtained by using next generation sequencing. It contains 12 protein-coding genes (the annotation of atp8 is unsure), two ribosomal RNA genes, 26 transfer RNA genes, and one supernumerary ORF that is also conserved in the inarticulate species Lingula anatina. It is hypothesized that this ORF could represent a Lingula-specific mtORFan gene (without obvious homology to other genes). Comparative mitogenomics indicate the mitochondrial gene order of L. reevii is unique among brachiopods, and that compared to articulate species, inarticulate species exhibit massive mitogenome rearrangements, deviant ATP8 protein sequences and supernumerary ORFs, possibly representing species- or lineage-specific mtORFan genes. CONCLUSION: The results of this study enrich genetics knowledge of extant brachiopods, which may eventually help to test hypotheses about their decline.

Taxonomic Status and Phylogenetic Relationship of the Charadriidae Family Based on Complete Mitogenomes.

Background: The Charadriiformes provide a good source for researching evolution owing to their diverse distribution, behavior, morphology, and ecology. However, in the Charadrii, family-level relationships remain understudied, and the monophyly of Charadriidae is also a subject of controversy. Methods: In the present study, we generated complete mitogenomes for two species, Charadrius leschenaultii and Charadrius mongolus, which were found to be 16,905 bp and 16,844 bp in length, respectively. Among the 13 protein codon genes, we observed variation in the rate of non-synonymous substitution rates, with the slowest rate found in COI and the fastest rate observed in ATP8. The Ka/Ks ratio for all Charadriidae species was significantly lower than one, which inferred that the protein-coding genes underwent purifying selection. Results: Phylogenetic analysis based on the genes of Cyt b, 12S and ND2 revealed that the genus Pluvialis is the sister group of three families (Haematopodidae, Ibidorhynchidae, Recurvirostridae). However, the phylogenetic analysis based on complete mitogenomes indicated that the genus Pluvialis is within the Charadriidae family. Conclusion: This study highlights the importance of carefully selecting the number of genes used to obtain accurate estimates of the species tree. It also suggests that relying on partial mtDNA genes with fast-evolving rates may lead to misleading results when resolving the Pluvialis sister group. Future research should focus on sequencing more mitogenomes at different taxonomic levels to gain a better understanding of the features and phylogenetic relationships within the Charadriiformes order.

Ion Torrent data for the genome assembly and phylogenomic placement of mitochondrial genomes with a focus on houndsharks (Chondrichthyes: Triakidae).

Here, we present, for the first time, the Ion TorrentⓇ next-generation sequencing (NGS) data for five houndsharks (Chondrichthyes: Triakidae), which include Galeorhinus galeus (number of bases pairs (bp) 17,487; GenBank accession number ON652874), Mustelus asterias (16,708; ON652873), Mustelus mosis (16,755; ON075077), Mustelus palumbes (16,708; ON075076), and Triakis megalopterus (16,746; ON075075). All assembled mitogenomes encode 13 protein-coding genes (PCGs), two ribosomal (r)RNA genes, and 22 transfer (t)RNA genes (tRNALeu and tRNASer are duplicated), except for G. galeus which contains 23 tRNA genes where tRNAThr is duplicated. The data presented in this paper can assist other researchers in further elucidating the diversification of triakid species and the phylogenetic relationships within Carcharhiniformes (groundsharks) as mitogenomes accumulate in public repositories.

The complete mitochondrial genome of the rodent flea Nosopsyllus laeviceps: genome description, comparative analysis, and phylogenetic implications.

BACKGROUND: Fleas are one of the most common and pervasive ectoparasites worldwide, comprising at least 2500 valid species. They are vectors of several disease-causing agents, such as Yersinia pestis. Despite their significance, however, the molecular genetics, biology, and phylogenetics of fleas remain poorly understood. METHODS: We sequenced, assembled, and annotated the complete mitochondrial (mt) genome of the rodent flea Nosopsyllus laeviceps using next-generation sequencing technology. Then we combined the new mitogenome generated here with mt genomic data available for 23 other flea species to perform comparative mitogenomics, nucleotide diversity, and evolutionary rate analysis. Subsequently, the phylogenetic relationship within the order Siphonaptera was explored using the Bayesian inference (BI) and maximum likelihood (ML) methods based on concentrated data for 13 mt protein-coding genes. RESULTS: The complete mt genome of the rodent flea N. laeviceps was 16,533 base pairs (bp) in a circular DNA molecule, containing 37 typical genes (13 protein-coding genes, 22 transfer RNA [tRNA] genes, and two ribosomal RNA [rRNA] genes) with one large non-coding region (NCR). Comparative analysis among the order Siphonaptera showed a stable gene order with no gene arrangement, and high AT content (76.71-83.21%) with an apparent negative AT and GC skew except in three fleas Aviostivalius klossi bispiniformis, Leptopsylla segnis, and Neopsylla specialis. Moreover, we found robust evidence that the cytochrome c oxidase subunit 1 (cox1) gene was the most conserved protein-coding gene (Pi = 0.15, non-synonymous/synonymous [Ka/Ks] ratio = 0.13) of fleas. Phylogenomic analysis conducted using two methods revealed different topologies, but both results strongly indicated that (i) the families Ceratophyllidae and Leptopsyllidae were paraphyletic and were the closest to each other, and (ii) the family Ctenophthalmidae was paraphyletic. CONCLUSIONS: In this study, we obtained a high-quality mt genome of the rodent flea N. laeviceps and performed comparative mitogenomics and phylogeny of the order Siphonaptera using the mt database. The results will enrich the mt genome data for fleas, lay a foundation for the phylogenetic analysis of fleas, and promote the evolutionary analysis of Siphonaptera.