The complete mitogenome of the fairy shrimp Streptocephalus cafer (Lovén, 1847) (Crustacea: Branchiopoda: Anostraca) from an ephemeral pond in Botswana, southern Africa

Mitogenomic phylogeny and divergence time estimation of Artemia Leach, 1819 (Branchiopoda: Anostraca) with emphasis on parthenogenetic lineages

The brine shrimp Artemia, a crustacean adapted to the extreme conditions of hypersaline environments, comprises nine regionally distributed sexual species scattered (island-like) over heterogeneous environments and asexual (parthenogenetic) lineages with different ploidies. Such sexual and asexual interaction within the genus raises questions regarding the origin and time of divergence of both sexual species and asexual lineages, including the persistence of the latter over time, a problem not yet clarified using single mitochondrial and nuclear markers. Based on the complete mitochondrial genome of all species and parthenogenetic lineages, this article first describes the mitogenomic characteristics (nucleotide compositions, genome mapping, codon usage, and tRNA secondary structure) of sexual species and asexual types and, secondly, it provides a comprehensive updated phylogenetic analysis. Molecular dating and geographical evidence suggest that the ancestral Artemia taxon originated in ca. 33.97 Mya during the Paleogene Period. The mitogenomic comparisons suggest that the common ancestor of diploid and triploid parthenogenetic lineages (ca. 0.07 Mya) originated from a historical ancestor (ca. 0.61 Mya) in the Late Pleistocene. Additionally, the common ancestor of tetraploid and pentaploid parthenogenetic lineages (ca. 0.05 Mya) diverged from a historical maternal ancestor with A. sinica (ca. 0.96 Mya) in the early Pleistocene. The parthenogenetic lineages do not share a direct ancestor with any sexual species. The Asian clade ancestor diverged more recently (ca. 14.27 Mya, Middle Miocene). The mitogenomic characteristics, maternal phylogenetic tree, and especially divergence time prove that A. monica and A. franciscana are two biological species.

Daphnia sp. (Branchiopoda: Cladocera) Mitochondrial Genome Gene Rearrangement and Phylogenetic Position Within Branchiopoda

In high-altitude (4500 m) freshwater lakes, Daphnia is the apex species and the dominant zooplankton. It frequently dwells in the same lake as the Gammarid. Branchiopoda, a class of Arthropoda, Crustacea, is a relatively primitive group in the subphylum Crustacea, which originated in the Cambrian period of the Paleozoic. The complete mitogenome sequence of Daphnia sp. (Branchiopoda: Cladocera) was sequenced and annotated in this study and deposited in GenBank. The sequence structure of this species was studied by comparing the original sequences with BLAST. In addition, we have also researched the mechanisms of their mitochondrial gene rearrangement by establishing a model. We have used the Bayesian inference [BI] and maximum likelihood [ML] methods to proceed with phylogenetic analysis inference, which generates identical phylogenetic topology that reveals the phylogenetic state of Daphnia. The complete mitogenome of Daphnia sp. shows that it was 15,254 bp in length and included two control regions (CRs) and 37 genes (13 protein-coding genes, 22 tRNAs and two ribosomal RNAs [16S and 12S]). In addition to tRNA-Ser (GCT), other tRNAs have a typical cloverleaf secondary structure. Meanwhile, the mitogenome of Daphnia sp. was clearly rearranged when compared to the mitogenome of typical Daphnia. In a word, we report a newly sequenced mitogenome of Daphnia sp. with a unique rearrangement phenomenon. These results will be helpful for further phylogenetic research and provide a foundation for future studies on the characteristics of the mitochondrial gene arrangement process in Daphnia.

The complete mitochondrial genome of water flea Ceriodaphnia dubia (Crustacea: Cladocera) NIES strain

Water flea Ceriodaphnia dubia has been widely used for risk assessments of chemicals and environmental contamination. In this study, the complete mitochondrial genome (mitogenome) of this species NIES strain was determined using short-read high throughput and long-read sequencing technologies. The mitogenome of C. dubia was 15,170 bp in length and consisted of 13 protein-coding genes (PCGs), 2 ribosomal RNAs (rRNAs), and 22 transfer RNAs (tRNAs). The gene order was identical to the pattern conserved across crustaceans. The complete mitogenome of the NIES strain will serve as genetical reference in ecological risk assessments in Japan, as well as resources for future phylogenetical studies using cladocerans.

The complete mitochondrial genome of the Arctic fairy shrimp Branchinectapaludosa (Müller, 1788) (Anostraca, Branchinectidae) from Sirius Passet, North Greenland

Here we report the complete mitochondrial genome of the Arctic fairy shrimp, Branchinectapaludosa (Müller, 1788) (Anostraca, Branchinectidae), which was collected in the High Arctic of North Greenland. A complete 16,059 bp mitochondrion of B.paludosa was sequenced and assembled with the Illumina next generation sequencing platform. The B.paludosa mitogenome contains 13 PCGs, 22 tRNAs and 2 rRNA genes that are commonly observed in most metazoans and shows the conserved gene arrangement pattern of Anostraca. Our results of the phylogenomic analysis are consistent with the previous phylogenetic relationship, based on nuclear 18S ribosomal DNA. The B.paludosa mitogenome will be useful for understanding the geographical distribution and phylogenetic relationship of anostracans.

Comparative Mitogenomic Analyses and New Insights into the Phylogeny of Thamnocephalidae (Branchiopoda: Anostraca)

Thamnocephalidae, a family of Anostraca which is widely distributed on all continents of the world except Antarctica, currently consists of six genera and approximately 63 recognized species. The relationships among genera in Thamnocephalidae and the monophyly of Thamnocephalidae, determined using morphological characteristics or gene markers, remain controversial. In order to address the relationships within Thamnocephalidae, we sequenced Branchinella kugenumaensis mitogenomes and conducted a comparative analysis to reveal the divergence across mitogenomes of B. kugenumaensis. Using newly obtained mitogenomes together with available Anostracan genomic sequences, we present the most complete phylogenomic understanding of Anostraca to date. We observed high divergence across mitogenomes of B. kugenumaensis. Meanwhile, phylogenetic analyses based on both amino acids and nucleotides of the protein-coding genes (PCG) provide significant support for a non-monophyletic Thamnocephalidae within Anostraca, with Asian Branchinella more closely related to Streptocephalidae than Australian Branchinella. The phylogenetic relationships within Anostraca were recovered as follows: Branchinectidae + Chirocephalidae as the basal group of Anostraca and halophilic Artemiidae as a sister to the clade Thamnocephalidae + Streptocephalidae. Both Bayesian inference (BI)- and maximum likelihood (ML)-based analyses produced identical topologies.

Complete mitochondrial genomes of three fairy shrimps from snowmelt pools in Japan

Background

Fairy shrimps belong to order Anostraca, class Branchiopoda, subphylum Crustacea, and phylum Arthropoda. Three fairy shrimp species (Eubranchipus uchidai, E. asanumai, and E. hatanakai) that inhabit snowmelt pools are currently known in Japan. Whole mitochondrial genomes are useful genetic information for conducting phylogenetic analyses. Mitochondrial genome sequences for Branchiopoda members are gradually being collated.

Results

Six whole mitochondrial genomes from the three Eubranchipus species are presented here. Eubranchipus species share the anostracan pattern of gene arrangement in their mitochondrial genomes. The mitochondrial genomes of the Eubranchipus species have a higher GC content than those of other anostracans. Accelerated substitution rates in the lineage of Eubranchipus species were observed.

Conclusion

This study is the first to obtain whole mitochondrial genomes for Far Eastern Eubranchipus species. We show that the nucleotide sequences of cytochrome oxidase subunit I and the 16S ribosomal RNA of E. asanumai presented in a previous study were nuclear mitochondrial DNA segments. Higher GC contents and accelerated substitution rates are specific characteristics of the mitochondrial genomes of Far Eastern Eubranchipus. The results will be useful for further investigations of the evolution of Anostraca as well as Branchiopoda.

Thermal limits and preferences of large branchiopods (Branchiopoda: Anostraca and Spinicaudata) from temporary wetland arid zone systems

Large branchiopods are specialist crustaceans adapted for life in temporary, thermally dynamic wetland ecosystems. Certain large branchiopod species are, however, restricted to specific temporary wetland types, exemplified by their physico-chemical and hydroperiod characteristics. Here, we contrasted the thermal preference and critical thermal maxima (CT_max) and minima (CT_min) of southern African anostracans and spinicaudatans found exclusively in either temporary rock-pool or pan wetland types. We hypothesized that environment of origin would be a good predictor of thermal preference and critical thermal limits. To test this, Branchiopodopsis tridens (Anostraca) and Leptestheria brevirostris (Spinicaudata) were collected from rock-pool habitats, while Streptocephalus cafer (Anostraca) and a Gondwanalimnadia sp. (Spinicaudata) were collected from pan habitats. In contrast to our hypothesis, taxonomic relatedness was a better predictor of CT_max and temperature preference than environment of origin. Spinicaudatans were significantly more tolerant of high temperatures than anostracans, with L. brevirostris and Gondwanalimnadia sp. median CT_max values of 45.1 °C and 44.1 °C, respectively, followed by S. cafer (42.8 °C) and B. tridens (41.4 °C). Neither environment or taxonomic relatedness were good predictors of CT_min trends, with B. tridens (0.9 °C) and Gondwanalimnadia sp. (2.1 °C) having the lowest median CT_min values, followed by L. brevirostris (3.4 °C) and S. cafer (3.6 °C). On the contrary, temperature preferences differed according to taxa, with spinicaudatans significantly preferring higher temperatures than anostracans. Leptestheria brevirostris and Gondwanalimnadia sp. both spent most time at temperatures 30-32 °C, S. cafer at 18-20 °C and B. tridens at 21-23 °C. Constrained thermal traits reported here suggest that the studied anostracans might be more susceptible to projected climatic warming than the spinicaudatans, irrespective of habitat type, however, these taxa may also compensate through phenotypic plasticity.