The complete mitogenome of Leptestheria brevirostris Barnard, 1924, a rock pool clam shrimp (Branchiopoda: Spinicaudata) from Central District, Botswana.
Ontology highlight
ABSTRACT:
SUBMITTER: Emami-Khoyi A
PROVIDER: S-EPMC7894449 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Clam shrimps (Spinicaudata) are a widespread and diverse crustacean group that frequent temporary aquatic habitats, but few complete mitochondrial genomes have been published for this group. Here, we report the mitogenome of an undescribed Gondwanalimnadia species from Botswana. Raw sequences were assembled into a single circular genome with a total length of 15,663 bp. Thirteen protein-coding genes, 22 tRNAs, and 2 rRNAs were identified using the MITOS pipeline. The mitogenome's GC content is 33.52%. Phylogenetic analysis using protein-coding genes confirmed that Gondwanalimnadia sp. is closely related to another member of the Limnadiidae, Limnadia lenticularis.
| S-EPMC7510826 | biostudies-literature
Project description:Spinicaudata (spiny clam shrimp) is a taxon of Branchiopoda occurring since the Devonian and today it occurs nearly globally in temporary water bodies. We present the most species-rich phylogenetic analyses of this taxon based on four molecular loci: COI, 16S rRNA, EF1α and 28S rRNA. Our results support previous findings that Cyzicidae sensu lato is paraphyletic. To render Cyzicidae monophyletic we establish a fourth extant spinicaudatan family to accommodate Eocyzicus. Within Cyzicidae, none of the genera Cyzicus, Caenestheria or Caenestheriella are monophyletic, and the morphological characters used to define these genera (condyle length and rostrum shape) are not associated with well-delimited clades within Cyzicidae. There is insufficient resolution to elucidate the relationships within Leptestheriidae. However, there is sufficient evidence to show that the leptestheriid genera Eoleptestheria and Leptestheria are non-monophyletic, and there is no support for the genus Leptestheriella. Molecular clock analyses suggest that the wide geographic distribution of many spinicaudatan taxa across multiple continents is largely based on vicariance associated with the break-up of Pangea and Gondwana. Trans-oceanic dispersal has occurred in some taxa (e.g., Eulimnadia and within Leptestheriidae) but has been relatively rare. Our results highlight the need to revise the taxonomy of Cyzicidae and Leptestheriidae and provide evidence that the global spinicaudatan diversity may be underestimated due to the presence of numerous cryptic species. We establish Eocyzicidae fam. nov. to accommodate the genus Eocyzicus. Consequently, Cyzicidae comprises only two genera -Cyzicus and Ozestheria. Ozestheria occurs also in Africa and Asia and Ozestheria pilosa new comb. is assigned to this genus.
| S-EPMC7746975 | biostudies-literature
Project description:Fairy shrimps (Anostraca) constitute an important component of seasonally aquatic habitats, but few complete mitochondrial genomes have been published for this group. Here, we report the mitogenome of a common southern African species, Streptocephalus cafer, from Botswana (accession number: MN720104). Low-coverage shotgun sequencing recovered two contigs 15653 bp and 1347 bp in length that are separated by a repetitive region of unknown length within the non-coding control region. The mitogenome's GC content is 31.80%. Phylogenetic analysis using protein-coding genes confirms the sister taxon relationship of S. cafer with the only other congener whose mitogenome has been reconstructed to date, the Asian S. sirindhornae.
| S-EPMC7748636 | biostudies-literature
Project description:Eulimnadia and Paralimnadia are both strongly supported, monophyletic limnadiid lineages based on molecular studies. However, defining the two taxa morphologically relies on the presence/absence of a subcercopodal spiniform projection; otherwise there is considerable overlap and confusion in morphological characters between the two taxa. The most discriminatory of these characters are examined here and applied to Australasian species. As a result, five Eulimnadia species are transferred to Paralimnadia. These characters are then applied to world Eulimnadia species and other limnadiid genera which share key features with Eulimnadia.
| S-EPMC7736776 | biostudies-literature
Project description:It is still a challenge to reconstruct the deep phylogenetic relationships within spinicaudatans, and there are several different competing hypotheses regarding the interrelationships among Eocyzicidae, Cyzicidae s. s., Leptestheriidae, and Limnadiidae of the Suborder Spinicaudata. In order to explore the source of the inconsistencies, we focus on the sequence variation and the structure model of two rRNA genes based on extensive taxa sampling. The comparative sequence analysis revealed heterogeneity across species and the existence of conserved motifs in all spinicaudatan species. The level of intraspecific heterogeneity differed among species, which suggested that some species might have undergone a relaxed concerted evolution with respect to the 28S rRNA gene. The Bayesian analyses were performed on nuclear (28S rRNA, EF1α) and mitochondrial (16S rRNA, COI) genes. Further, we investigated compositional heterogeneity between lineages and assessed the potential for phylogenetic noise compared to signal in the combined data set. Reducing the non-phylogenetic signals and application of optimal rRNA model recovered a topology congruent with inference from the transcriptome data, whereby Limnadiidae was placed as a sister group to Leptestheriidae + Eocyzicidae with high support (topology I). Tests of alternative hypotheses provided implicit support for four competing topologies, and topology I was the best.
| S-EPMC8625258 | biostudies-literature
Project description:Clam shrimps are freshwater branchiopod crustaceans which often present complicated breeding systems including asexual reproduction (parthenogenesis) and mixed mating systems (in androdioecious species both selfing and outcrossing occurs due to the co-presence of hermaphrodites and males). Reproductive patterns of Spinicaudata, which contains most clam shrimp species, have received much attention. Another group of clam shrimps, Laevicaudata, which holds a key position in branchiopod phylogeny, has practically not been studied. As a part of the mating process, males clasp to the carapace margin of the females with a pair (or two pairs) of anterior trunk limbs modified as claspers. Previous studies have shown that clasper morphology is important in a phylogenetic context, and that some parts of the claspers in Spinicaudata and Laevicaudata may have undergone a remarkable parallel evolution. Here we have used video microscopy to study aspects of the mating behaviour, egg extrusion, and fertilization in Lynceus brachyurus (Laevicaudata). It is shown that fertilization is likely to be external and that the peculiar tri-lobed lateral lamellae of female's hind body assist in guiding the egg mass to the exopodal egg carriers where they are collected by their distal setation. The functional morphology of the male claspers was studied in detail by close-up video recordings. The movable "finger" of the clasper bends around the female's carapace edge and serves to hold the female during mating. The larger palp grasps around the female carapace margin in a way very similar to the movable "finger", possibly indirectly providing sensory input on the "finger" position. A brief comparative study of the claspers of a spinicaudatan clam shrimp showed both similarities and differences to the laevicaudatan claspers. The presence of two pairs of claspers in Spinicaudata seems to give males a better hold of the female which may play a role during extended mate guarding.
| S-EPMC3879279 | biostudies-literature
Project description:Temporary water bodies are important freshwater habitats in the arid zone of Australia. They harbor a distinct fauna and provide important feeding and breeding grounds for water birds. This paper assesses, on the basis of haplotype networks, analyses of molecular variation and relaxed molecular clock divergence time estimates, the phylogeographic history, and population structure of four common temporary water species of the Australian endemic clam shrimp taxon Limnadopsis in eastern and central Australia (an area of >1,350,000 km(2)). Mitochondrial cytochrome c oxidase subunit I sequences of 413 individuals and a subset of 63 nuclear internal transcribed spacer 2 sequences were analyzed. Genetic differentiation was observed between populations inhabiting southeastern and central Australia and those inhabiting the northern Lake Eyre Basin and Western Australia. However, over large parts of the study area and across river drainage systems in southeastern and central Australia (the Murray-Darling Basin, Bulloo River, and southern Lake Eyre Basin), no evidence of population subdivision was observed in any of the four Limnadopsis species. This indicates recent gene flow across an area of ∼800,000 km(2). This finding contrasts with patterns observed in other Australian arid zone taxa, particularly freshwater species, whose populations are often structured according to drainage systems. The lack of genetic differentiation within the area in question may be linked to the huge number of highly nomadic water birds that potentially disperse the resting eggs of Limnadopsis among temporary water bodies. Genetically undifferentiated populations on a large geographic scale contrast starkly with findings for many other large branchiopods in other parts of the world, where pronounced genetic structure is often observed even in populations inhabiting pools separated by a few kilometers. Due to its divergent genetic lineages (up to 5.6% uncorrected p-distance) and the relaxed molecular clock divergence time estimates obtained, Limnadopsis parvispinus is assumed to have inhabited the Murray-Darling Basin continuously since the mid-Pliocene (∼4 million years ago). This means that suitable temporary water bodies would have existed in this area throughout the wet-dry cycles of the Pleistocene.
| S-EPMC3434933 | biostudies-literature
Project description:A survey of the large branchiopod fauna of the Eastern Cape Karoo region of South Africa was undertaken to provide baseline biodiversity information in light of impending shale gas development activities in the region. Twenty-two waterbodies, including nine dams and thirteen natural depression wetlands, were sampled during November 2014 and April 2015. A total of 13 species belonging to four orders were collected, comprising five anostracans, one notostracan, six spinicaudatans and one laevicaudatan. Cyzicus australis was most common, occurring in 46% of the waterbodies. Species co-occurred in 87% of the waterbodies, with a maximum number of six species recorded from the same waterbody. Our new distribution records for Lynceus truncatus, Streptocephalus spinicaudatus and Streptocephalus indistinctus represent substantial expansions of the previously known ranges for these species. Tarkastad is now the westernmost record for Streptocephalus spinicaudatus, while Jansenville now constitutes the southernmost record for Streptocephalus indistinctus. Large branchiopod distribution data from previous Eastern Cape records were combined with our current data, demonstrating that a total of 23 large branchiopod species have been recorded from the region to date. As the Karoo is one of the few major shale basins in the world where the natural baseline is still largely intact, this survey forms a basis for future reference and surface water quality monitoring during the process of shale gas exploration/extraction.
| S-EPMC5102048 | biostudies-literature
Project description:The class Branchiopoda, whose origin dates back to Cambrian, includes ~ 1200 species which mainly occupy freshwater habitats. The phylogeny and systematics of the class have been debated for long time, until recent phylogenomic analyses allowed to better clarify the relationships among major clades. Based on these data, the clade Anostraca (fairy and brine shrimps) is sister to all other branchiopods, and the Notostraca (tadpole shrimps) results as sister group to Diplostraca, which includes Laevicaudata + Spinicaudata (clam shrimps) and Cladoceromorpha (water fleas + Cyclestherida). In the present analysis, thanks to an increased taxon sampling, a complex picture emerges. Most of the analyzed mitogenomes show the Pancrustacea gene order while in several other taxa they are found rearranged. These rearrangements, though, occur unevenly among taxa, most of them being found in Cladocera, and their taxonomic distribution does not agree with the phylogeny. Our data also seems to suggest the possibility of potentially homoplastic, alternative gene order within Daphniidae.
| S-EPMC8942981 | biostudies-literature
Project description:We examined the potential utility of museum specimens as a source for genetic analysis of fairy shrimp. Because of loss of their vernal pool habitat, some fairy shrimp (including Branchinectasandiegonensis and Branchinectalynchi) are listed as threatened or endangered in Southern California by the United States Fish and Wildlife Service. Management of those species requires extensive population genetics studies and the resolution of important genetic complexity (e.g. possible hybridization between endangered and non-endangered species). Regulations mandating deposition of specimens of listed species have resulted in thousands of specimens accessioned into the Natural History Museum of Los Angeles County that have been preserved in a variety of solutions. We subsampled those specimens, as well as other Anostraca with known collection and preservation histories, to test their potential for genetic analysis by attempting DNA extraction and amplification for mt16SrDNA. Fixation and preservation in not denatured ethanol had a far greater sequencing success rate than other (and unknown) fixatives and preservatives. To maximize scientific value we recommend field preservation in 95% not denatured ethanol (or, if pure ethanol is unavailable, high-proof drinking spirits, e.g. Everclear™, or 151 proof white rum), followed by storage in 95% not denatured ethanol.
| S-EPMC4283361 | biostudies-literature