Mesozoic fossils (>145 Mya) suggest the antiquity of the subgenera of Daphnia and their coevolution with chaoborid predators

Dietary exposure of the water flea Daphnia galeata to microcystin-LR

Harmful substances like the cyanotoxin microcystin-leucine-arginine (MC-LR) are commonly found in eutrophic freshwater environments, posing risks to aquatic organisms. The water flea, Daphnia, is a well-established model organism for environmental toxicology research. Nevertheless, there is currently insufficient research on the genes that respond to MC-LR in Daphnia galeata. This study aimed to gain insights into the notable genes that react significantly to MC-LR. In this study, we generated an extensive RNA-Seq sequences isolated from the D. galeata HK strain, Han River in Korea. This strain was nourished with a diet of the green microalga Chlorella vulgaris and treated with pure MC-LR at a concentration of 36 ug/L. The transcriptome profile in response to the MC-LR treatment was obtained and 336 differentially expressed genes were subjected to Gene Ontology (GO) and euKaryotic Orthologous Groups of proteins analyses. GO enrichment analysis showed that chemical stimulus, amino sugar metabolic and catabolic process, oxidative stress, and detoxification were highly enriched, in reverse, proteolysis and fucosylation were underpresented. Detoxification process related genes such as peroxidase-like, chorion, and thyroid peroxidase-like were enriched for eliminating or neutralizing MC_LR from an organism's body. Furthermore, functional protein classification revealed an upregulation of lipid and inorganic ion transport processes, while amino acid and carbohydrate transport processes were found to be downregulated. These findings offer insights into how organisms respond to ecotoxic stimuli, providing valuable information for understanding adaptation or defense pathways.

New species of Kuqaia from the Lower Jurassic of Sweden indicates a possible water flea (Crustacea: Branchiopoda) affinity

The enigmatic acid-resistant mesofossil genus Kuqaia is emended, a new species (Kuqaia scanicus) is instituted, and three established species are described from the Lower Jurassic (lower Pliensbachian) of the Kävlinge BH-928 core, in southern Sweden. Kuqaia has a distribution across the middle northern latitudes of Pangaea and is restricted to Lower to lower Middle Jurassic strata. Morphological characters support Kuqaia being the ephippia (resting egg/embryo cases) of Cladocera (Crustacea: Branchiopoda), and a probable early stem-group taxon of the Daphnia lineage. The paleoecology of the small planktonic crustaceans indicate purely fresh-water environments, such as lakes or ponds, all occurrences being in continental deposits, and the Kuqaia specimens possibly represent dry-season resting eggs. Chemical analyses of these and similar fossils, and of extant invertebrate eggs and egg cases are recommended to improve resolution of the biological affiliations of such mesofossil groups.

Possible mediation of Cladocera species by a researcher's chest wader

Mediation of aquatic species has become an increasing problem for the last few decades. With the increasing commercial import, species' direct or indirect spread can gain more space. There are several ways for them to land in their new home and spread through the country. Most of the aquatic species are spread by waterways, boats, vehicles, or even with the help of humans. Cladocerans have a good dispersal ability, thanks to their small size, additionally they possess good adaptation, and mechanisms to develop resting eggs. Benthic or littoral species can be mediated much more easily due to their living space, and with the help of human activities (e.g., scientists, anglers and people working in water bodies) they have a higher chance to colonize new habitats. Our goal was to explore if Cladocera species might be mediated by a scientist chest wader, while sampling in similar-sized, close-to-each other lakes, with different utilization. Most of the species were found in abandoned fishing lakes, followed by oxbow lakes (protected), and ultimately in intensively fished lakes. NMDS showed that samples from lakes with the same utilization are similar to each other. Differently utilized lakes can have various Cladocera species, even though they are closely related to each other. Based on the results, scientists can mediate species on their chest wader from lake to lake and may deteriorate the results. We recommend a necessary chest wader cleaning after every sampling process, especially when samples are taken from differently utilized lakes.

Genome Assembly of a Relict Arabian Species of Daphnia O. F. Müller (Crustacea: Cladocera) Adapted to the Desert Life

The water flea Daphnia O.F. Müller 1776 (Crustacea: Cladocera) is an important model of recent evolutionary biology. Here, we report a complete genome of Daphnia (Ctenodaphnia) arabica (Crustacea: Cladocera), recently described species endemic to deserts of the United Arab Emirates. In this study, genome analysis of D. arabica was carried out to investigate its genomic differences, complexity as well as its historical origins within the subgenus Daphnia (Ctenodaphnia). Hybrid genome assembly of D. arabica resulted in ~116 Mb of the assembled genome, with an N50 of ~1.13 Mb (BUSCO score of 99.2%). From the assembled genome, in total protein coding, 5374 tRNA and 643 rRNA genes were annotated. We found that the D. arabica complete genome differed from those of other Daphnia species deposited in the NCBI database but was close to that of D. cf. similoides. However, its divergence time estimate sets D. arabica in the Mesozoic, and our demographic analysis showed a great reduction in its genetic diversity compared to other Daphnia species. Interestingly, the population expansion in its diversity occurred during the megadrought climate around 100 Ka ago, reflecting the adaptive feature of the species to arid and drought-affected environments. Moreover, the PFAM comparative analysis highlights the presence of the important domain SOSS complex subunit C in D. arabica, which is missing in all other studied species of Daphnia. This complex consists of a few subunits (A, B, C) working together to maintain the genome stability (i.e., promoting the reparation of DNA under stress). We propose that this domain could play a role in maintaining the fitness and survival of this species in the desert environment. The present study will pave the way for future research to identify the genes that were gained or lost in this species and identify which of these were key factors to its adaptation to the harsh desert environment.

Multiple Recent Colonizations of the Australian Region by the Chydorus sphaericus Group (Crustacea: Cladocera)

Biotic introductions are an ongoing disruption for many ecosystems. For passively dispersed freshwater zooplankton, transcontinental introductions have been common but are poorly studied in the southern hemisphere. Here we assess the hypothesis of recent introduction for populations of the Chydorus sphaericus group (Crustacea: Cladocera) in Australia. We analyzed 254 sequences (63 original sequences) from the cytochrome oxidase I region of mitochondrial DNA of Chydorus sp., which included global representation. Three Australian populations were connected with separate clades in the northern hemisphere, suggesting multiple colonization events for Australia. The timescale of the divergences was consistent with recent (Quaternary) dispersal. As Australian populations are exposed to migrating birds from the northern hemisphere, both avian and anthropogenic sources are candidates for dispersal vectors. We concluded that recent cross-hemisphere dispersal in the Chydorus sphaericus group is more common than previously believed.

Mitogenomics of Cladocera (Branchiopoda): Marked gene order rearrangements and independent predation roots

Cladocera (Crustacea: Branchiopoda) is a key group of invertebrates. Despite a long history of phylogenetic research, relationships within this group remain disputed. We here provide new insights based on 15 new mitochondrial genomes obtained from high-throughput sequencing (HTS) and 40 mitogenomes extracted from published HTS datasets. Together with 25 mitogenomes from GenBank, we generated a matrix of 80 mitogenomes, 44 of them belonging to Cladocera. We also obtained a matrix with 168 nuclear orthologous genes to further assess the phylogenetic result from mitogenomes based on published data and one new HTS data ofLeptodora. Maximum likelihood and Bayesian phylogenetic analyses recovered all Branchiopoda orders as monophyletic and supported a sister-group relationship between Anomopoda and Onychopoda, making the taxon Gymnomera paraphyletic and supporting an independent origin of predatory Haplopoda and Onychopoda. The nuclear phylogeny and topological tests also support Gymnomera as paraphyletic, and the nuclear phylogeny strongly supports a sister-group relationship between Ctenopoda and Haplopoda. We provide a fossil-calibrated time tree, congruent with a Carboniferous origin for Cladocera and a subsequent diversification of the crown group of Anomopoda, Onychopoda, and Ctenopoda, at least in the Triassic. Despite their long evolutionary history, non-Cladoceran Branchiopoda exhibited high mitogenome structural stability. On the other hand, 21 out of 24 gene rearrangements occurred within the relatively younger Cladocera. We found the differential base compositional skewness patterns between Daphnia s.s. and Ctenodaphnia, which might be related to the divergence between these taxa. We also provide evidence to support the recent finding that Spinicaudata possesses mitogenomes with inversed compositional skewness without gene rearrangement. Such a pattern has only been reported in Spinicaudata.

Bosminopsis deitersi (Crustacea: Cladocera) as an ancient species group: a revision

Water fleas (Crustacea: Cladocera) of the Family Bosminidae have been studied since the founding of paleolimnology and freshwater ecology. However, one species, Bosminopsis deitersi, stands out for its exceptional multicontinental range and broad ecological requirements. Here we use an integrated morphological and multilocus genetic approach to address the species problem in B. deitersi. We analyzed 32 populations of B. deitersi s. lat. Two nuclear and two mitochondrial loci were used to carry out the bGMYC, mPTP and STACEY algorithms for species delimitation. Detailed morphological study was also carried out across continents. The evidence indicated a widely distributed cryptic species in the Old World (Bosminopsis zernowi) that is genetically divergent from B. deitersi s.str. We revised the taxonomy and redescribed the species in this complex. Our sampling indicated that B. zernowi had weak genetic differentiation across its range. A molecular clock and biogeographic analysis with fossil calibrations suggested a Mesozoic origin for the Bosminopsis deitersi group. Our evidence rejects the single species hypothesis for B. deitersi and is consistent with an ancient species group (potentially Mesozoic) that shows marked morphological conservation. The family Bosminidae, then, has examples of both rapid morphological evolution (Holocene Bosmina), and morphological stasis (Bosminopsis).

Speciation in Daphnia

The microcrustacean Daphnia is arguably one of the most studied zooplankton species, having a well understood ecology, life history, and a relatively well studied evolutionary history. Despite this wealth of knowledge, species boundaries within closely related species in this genus often remain elusive and the major evolutionary forces driving the diversity of daphniids remain controversial. This genus contains more than 80 species with multiple cryptic species complexes, with many closely related species able to hybridize. Here, we review speciation research in Daphnia within the framework of current speciation theory. We evaluate the role of geography, ecology, and biology in restricting gene flow and promoting diversification. Of the 253 speciation studies on Daphnia, the majority of studies examine geographic barriers (55%). While evidence shows that geographic barriers play a role in species divergence, ecological barriers are also probably prominent in Daphnia speciation. We assess the contribution of ecological and nonecological reproductive isolating barriers between closely related species of Daphnia and found that none of the reproductive isolating barriers are restricting gene flow completely. Research on reproductive isolating barriers has disproportionally focused on two species complexes, the Daphnia pulex and Daphnia longispina species complexes. Finally, we identify areas of research that remain relatively unexplored and discuss future research directions that build our understanding of speciation in daphniids.

Pleistocene Branchiopods (Cladocera, Anostraca) from Transbaikalian Siberia Demonstrate Morphological and Ecological Stasis

Pleistocene water bodies have been studied using the paleolimnological approach, which traces environmental changes using particular subfossils as ecological proxies, rather than analysis of the paleocommunities themselves. Within a given taphocoenosis, the presence and quantity of animals are related to environmental conditions rather than to community types where relationships between taxa are stabilized during their long-term co-occurrence and are (at least partially) more important than the particular environmental conditions at the time of deposition, which may have experienced significant seasonal and inter-seasonal variations. Here, we analyze Branchiopoda (Crustacea) of two paleolocalities in the Transbaikalian Region of Russia: Urtuy (MIS3) and Nozhiy (older than 1.5 million years). Cladocerans Daphnia (Ctenodaphnia) magna, D. (C.) similis, D. (Daphnia) pulex, Ceriodaphnia pulchella-reticulata, C. laticaudata, Simocephalus sp., Moina cf. brachiata, M. macropopa clade, Chydorus cf. sphaericus, Capmtocercus sp. and anostracans Branchinecta cf. paludosa, and Streptocephalus (Streptocephalus) sp. are found in two localities. With the exception of the last taxon, which now occurs in the southern Holarctic, all other taxa inhabit the Transbaikalian Region. Within Eurasia, the steppe zone has the greatest diversity of large branchiopods and a high diversity of some cladocerans, such as subgenus Daphnia (Ctenodaphnia) and Moina sp. Here we demonstrated that the branchiopod community in shallow steppe water bodies has been unchanged since at least the Pleistocene, demonstrating long-term morphological and ecological stasis.

A new species group from the Daphnia curvirostris species complex (Cladocera: Anomopoda) from the eastern Palaearctic: taxonomy, phylogeny and phylogeography

The eastern Palaearctic is a centre of diversity for freshwater cladocerans (Crustacea), but little is known about the evolution and taxonomy of this diversity. Daphnia curvirostris is a Holarctic species complex that has most of its diversity in the eastern Palaearctic. We examined the phylogeography, rates of evolution and taxonomic status for each clade of the D. curvirostris complex using morphological and genetic evidence from four genes. The cybertaxonomical and morphological evidence supported an eastern Palaearctic clade, with at least four species (described here as the Daphnia korovchinskyi sp. nov. group) having diagnostic morphological characters. We also detected convergent morphological characters in the D. curvirostris complex that provided information about species boundaries. Two of the new species (Daphnia koreana sp. nov. and Daphnia ishidai sp. nov.) are known from single ponds and are threatened by human activity. Divergence time estimates suggested an ancient origin (12–28 Mya) for the D. korovchinskyi group, but these estimates are complicated by the small number of calibration points.

Genetic control of male production in Daphnia pulex

Daphnia normally reproduce by cyclical parthenogenesis, with offspring sex being determined by environmental cues. However, some females have lost the ability to produce males. Our results demonstrate that this loss of male-producing ability is controlled by a dominant allele at a single locus. We identified the locus by comparing whole-genome sequences of 67 nonmale-producing (NMP) and 100 male-producing (MP) clones from 5 Daphnia pulex populations, revealing 132 NMP-linked SNPs and 59 NMP-linked indels within a single 1.1-Mb nonrecombining region on chromosome I. These markers include 7 nonsynonymous mutations, all of which are located within one unannotated protein-coding gene (gene 8960). Within this single gene, all of the marker-linked NMP haplotypes from different populations form a monophyletic clade, suggesting a single origin of the NMP phenotype, with the NMP haplotype originating by introgression from a sister species, Daphnia pulicaria Methyl farnesoate (MF) is the innate juvenile hormone in daphnids, which induces the production of males and whose inhibition results in female-only production. Gene 8960 is sensitive to treatment by MF in MP clones, but such responsiveness is greatly reduced in NMP clones. Thus, we hypothesize that gene 8960 is located downstream of the MF-signaling pathway in D. pulex, with the NMP phenotype being caused by expression change of gene 8960.

Evolution of Gene Expression during a Transition from Environmental to Genetic Sex Determination

Genetic sex determination (GSD) can evolve from environmental sex determination (ESD) via an intermediate state in which both coexist in the same population. Such mixed populations are found in the crustacean Daphnia magna, where non-male producers (NMP, genetically determined females) coexist with male producers (MP), in which male production is environmentally inducible and can also artificially be triggered by exposure to juvenile hormone. This makes Daphnia magna a rare model species for the study of evolutionary transitions from ESD to GSD. Although the chromosomal location of the NMP-determining mutation has been mapped, the actual genes and pathways involved in the evolution of GSD from ESD remain unknown. Here, we present a transcriptomic analysis of MP and NMP females under control (female producing) and under hormone exposure conditions. We found ∼100 differentially expressed genes between MP and NMP under control conditions. Genes in the NMP-determining chromosome region were especially likely to show such constitutive expression differences. Hormone exposure led to expression changes of an additional ∼100 (MP) to ∼600 (NMP) genes, with an almost systematic upregulation of those genes in NMP. These observations suggest that the NMP phenotype is not determined by a simple "loss-of-function" mutation. Rather, homeostasis of female offspring production under hormone exposure appears to be an active state, tightly regulated by complex mechanisms involving many genes. In a broader view, this illustrates that the evolution of GSD, while potentially initiated by a single mutation, likely leads to secondary integration involving many genes and pathways.

Phylogeography of Daphnia magna Straus (Crustacea: Cladocera) in Northern Eurasia: Evidence for a deep longitudinal split between mitochondrial lineages

Species with a large geographic distributions present a challenge for phylogeographic studies due to logistic difficulties of obtaining adequate sampling. For instance, in most species with a Holarctic distribution, the majority of studies has concentrated on the European or North American part of the distribution, with the Eastern Palearctic region being notably understudied. Here, we study the phylogeography of the freshwater cladoceran Daphnia magna Straus, 1820 (Crustacea: Cladocera), based on partial mitochondrial COI sequences and using specimens from populations spread longitudinally from westernmost Europe to easternmost Asia, with many samples from previously strongly understudied regions in Siberia and Eastern Asia. The results confirm the previously suspected deep split between Eastern and Western mitochondrial haplotype super-clades. We find a narrow contact zone between these two super-clades in the eastern part of Western Siberia, with proven co-occurrence in a single lake in the Novosibirsk region. However, at present there is no evidence suggesting that the two mitochondrial super-clades represent cryptic species. Rather, they may be explained by secondary contact after expansion from different refugia. Interestingly, Central Siberia has previously been found to be an important contact zone also in other cladoceran species, and may thus be a crucial area for understanding the Eurasian phylogeography of freshwater invertebrates. Together, our study provides an unprecedented complete, while still not global, picture of the phylogeography of this important model species.

The sea cucumber genome provides insights into morphological evolution and visceral regeneration

Apart from sharing common ancestry with chordates, sea cucumbers exhibit a unique morphology and exceptional regenerative capacity. Here we present the complete genome sequence of an economically important sea cucumber, A. japonicus, generated using Illumina and PacBio platforms, to achieve an assembly of approximately 805 Mb (contig N50 of 190 Kb and scaffold N50 of 486 Kb), with 30,350 protein-coding genes and high continuity. We used this resource to explore key genetic mechanisms behind the unique biological characters of sea cucumbers. Phylogenetic and comparative genomic analyses revealed the presence of marker genes associated with notochord and gill slits, suggesting that these chordate features were present in ancestral echinoderms. The unique shape and weak mineralization of the sea cucumber adult body were also preliminarily explained by the contraction of biomineralization genes. Genome, transcriptome, and proteome analyses of organ regrowth after induced evisceration provided insight into the molecular underpinnings of visceral regeneration, including a specific tandem-duplicated prostatic secretory protein of 94 amino acids (PSP94)-like gene family and a significantly expanded fibrinogen-related protein (FREP) gene family. This high-quality genome resource will provide a useful framework for future research into biological processes and evolution in deuterostomes, including remarkable regenerative abilities that could have medical applications. Moreover, the multiomics data will be of prime value for commercial sea cucumber breeding programs.

Echinoderms, ubiquitous in the marine environment, are important from evolutionary, ecological, and socioeconomic perspectives. Together with chordates and hemichordates, they form the deuterostome clade, making them a crucial node in the study of chordate ancestry. Within echinoderms, class Holothuroidea is unique; its members (the sea cucumbers) display remarkable regenerative abilities and play key roles as sediment bioturbators and symbiotic hosts, and many are prized in the seafood and pharmaceutical industries. The sea cucumber genome therefore has the potential to significantly contribute to our understanding of important evolutionary and biological processes and help enhance aquaculture programs. Here we present a high-quality genome sequence for the economically important species Apostichopus japonicus. Through comparative analyses, we identified 763 echinoderm-specific gene families enriched in genes encoding membrane proteins, ion channels, and signal transduction proteins. Marker genes associated with the notochord and gill slits were also found, providing valuable insight into the origin of chordates. The reduced number and low expression levels of biomineralization genes reflect the skeletal degeneration seen in sea cucumbers. Importantly, 2 gene families appeared to be expanded in A. japonicus and may play crucial roles in its heightened regenerative potential. Together, findings from the sea cucumber genome provide important and novel insights into echinoderm and deuterostome biology.

Transition from Environmental to Partial Genetic Sex Determination in Daphnia through the Evolution of a Female-Determining Incipient W Chromosome

Sex chromosomes can evolve during the evolution of genetic sex determination (GSD) from environmental sex determination (ESD). Despite theoretical attention, early mechanisms involved in the transition from ESD to GSD have yet to be studied in nature. No mixed ESD-GSD animal species have been reported, except for some species of Daphnia, small freshwater crustaceans in which sex is usually determined solely by the environment, but in which a dominant female sex-determining locus is present in some populations. This locus follows Mendelian single-locus inheritance, but has otherwise not been characterized genetically. We now show that the sex-determining genomic region maps to the same low-recombining peri-centromeric region of linkage group 3 (LG3) in three highly divergent populations of D. magna, and spans 3.6 Mb. Despite low levels of recombination, the associated region contains signs of historical recombination, suggesting a role for selection acting on several genes thereby maintaining linkage disequilibrium among the 36 associated SNPs. The region carries numerous genes involved in sex differentiation in other taxa, including transformer2 and sox9. Taken together, the region determining the genetic females shows characteristics of a sex-related supergene, suggesting that LG3 is potentially an incipient W chromosome despite the lack of significant additional restriction of recombination between Z and W. The occurrence of the female-determining locus in a pre-existing low recombining region illustrates one possible form of recombination suppression in sex chromosomes. D. magna is a promising model for studying the evolutionary transitions from ESD to GSD and early sex chromosome evolution.

Ancient and Recent Duplications Support Functional Diversity of Daphnia Opsins

Daphnia pulex has the largest known family of opsins, genes critical for photoreception and vision in animals. This diversity may be functionally redundant, arising from recent processes, or ancient duplications may have been preserved due to distinct functions and independent contributions to fitness. We analyzed opsins in D. pulex and its distant congener Daphnia magna. We identified 48 opsins in the D. pulex genome and 32 in D. magna. We inferred the complement of opsins in the last common ancestor of all Daphnia and evaluated the history of opsin duplication and loss. We further analyzed sequence variation to assess possible functional diversification among Daphnia opsins. Much of the opsin expansion occurred before the D. pulex-D. magna split more than 145 Mya, and both Daphnia lineages preserved most ancient opsins. More recent expansion occurred in pteropsins and long-wavelength visual opsins in both species, particularly D. pulex. Recent duplications were not random: the same ancestral genes duplicated independently in each modern species. Most ancient and some recent duplications involved differentiation at residues known to influence spectral tuning of visual opsins. Arthropsins show evidence of gene conversion between tandemly arrayed paralogs in functionally important domains. Intron-exon gene structure was generally conserved within clades inferred from sequences, although pteropsins showed substantial intron size variation. Overall, our analyses support the hypotheses that diverse opsins are maintained due to diverse functional roles in photoreception and vision, that functional diversification is both ancient and recent, and that multiple evolutionary processes have influenced different types of opsins.

Phylogeography of the Chydorus sphaericus Group (Cladocera: Chydoridae) in the Northern Palearctic

The biodiversity and the biogeography are still poorly understood for freshwater invertebrates. The crustacean Chydorus sphaericus-brevilabris complex (Cladocera: Chydoridae) is composed of species that are important components of Holarctic freshwater food webs. Recent morphological and genetic study of the complex has indicated a substantial species diversity in the northern hemisphere. However, we know little of the geographic boundaries of these novel lineages. Moreover, a large section of the Palearctic remains unexamined at the genetic level. Here we attempt to address the biodiversity knowledge gap for the Chydorus sphaericus group in the central Palearctic and assess its diversity and biogeographic boundaries. We sequenced nuclear (ITS-2) and mitochondrial (COI) gene regions of Chydorus specimens across the Palearctic and compared them with already available Holarctic sequences. We detected six main clades in the C. sphaericus group in the Palearctic, of which two of the groups are novel. Three of the more divergent clades are geographically widespread. The central portion of Eurasia (the Yenisey River basin) appears to be a narrow zone of secondary contact for phylogroups that expanded from European and Beringian refugia. As such, the previously unsampled central Palearctic represents an important region for understanding the evolutionary consequences of Pleistocene climatic oscillations on the Chydorus sphaericus group.

DNA Barcoding Reveals High Cryptic Diversity in the North Eurasian Moina Species (Crustacea: Cladocera)

Species of the genus Moina Baird (Cladocera: Moinidae) often dominate freshwater crustacean communities in temporary water bodies. Several species of Moina are used as food for fish larvae in aquaculture, as bioindicators in toxicological studies, and as common subjects for physiological studies. The aim of this paper is to estimate biodiversity of Moina in northern Eurasia using the standard DNA barcoding approach based on the cytochrome c oxidase subunit I (COI) gene. We analysed 160 newly obtained and 157 existing COI sequences, and found evidence for 21 phylogroups of Moina, some of which were detected here for the first time. Our study confirmed the opinion that the actual species diversity of cladocerans is several times higher than is presently accepted. Our results also indicated that Moina has the second richest species diversity among the cladoceran genera (with only Daphnia O. F. Mueller having a greater diversity of species). Our study strongly supports division of Moina into two faunistic groups: European-Western Siberian and Eastern Siberian-Far Eastern, with a transitional zone at the Yenisey River basin (Eastern Siberia). Here, we refrain from taxonomic descriptions of new species, as this requires a thorough morphological and taxonomic study for each putative taxon.

Distribution of the DNA transposon family, Pokey in the Daphnia pulex species complex

BACKGROUND

The Pokey family of DNA transposons consists of two putatively autonomous groups, PokeyA and PokeyB, and two groups of Miniature Inverted-repeat Transposable Elements (MITEs), mPok1 and mPok2. This TE family is unusual as it inserts into a specific site in ribosomal (r)DNA, as well as other locations in Daphnia genomes. The goals of this study were to determine the distribution of the Pokey family in lineages of the Daphnia pulex species complex, and to test the hypothesis that unusally high PokeyA number in some isolates of Daphnia pulicaria is the result of recent transposition. To do this, we estimated the haploid number of Pokey, mPok, and rRNA genes in 45 isolates from five Daphnia lineages using quantitative PCR. We also cloned and sequenced partial copies of PokeyA from four isolates of D. pulicaria.

RESULTS

Haploid PokeyA and PokeyB number is generally less than 20 and tends to be higher outside rDNA in four lineages. Conversely, the number of both groups is much higher outside rDNA (~120) in D. arenata, and PokeyB is also somewhat higher inside rDNA. mPok1 was only detected in D. arenata. mPok2 occurs both outside (~30) and inside rDNA (~6) in D. arenata, but was rare (≤2) outside rDNA in the other four lineages. There is no correlation between Pokey and rRNA gene number (mean = 240 across lineages) in any lineage. Variation among cloned partial PokeyA sequences is significantly higher in isolates with high number compared to isolates with an average number.

CONCLUSIONS

The high Pokey number outside rDNA in D. arenata and inside rDNA in some D. pulicaria isolates is consistent with a recent increase in transposition rate. The D. pulicaria increase may have been triggered by insertion of PokeyA into a region of transcriptionally active rDNA. The expansion in D. arenata (thought to be of hybrid origin) may be a consequence of release from epigenetic repression following hybridization. Previous work found D. obtusa to be very different from the D. pulex complex; mean PokeyA is higher in rDNA (~75), rDNA array size is nearly twice as large (415), and the two are positively correlated. The predominance of Pokey in only one location could be explained by purifying selection against ectopic recombination between elements inside and outside rDNA.

Position of the dentifera-group in the Coronatella-branch and its relocation to a new genus: Magnospina gen. n. (Crustacea, Chydoridae, Aloninae)

Magnospina gen. n. was created to relocate species of the dentifera-group from Alona sensu lato (Crustacea: Cladocera) and include Magnospina dentifera comb. n. and Magnospina siamensis comb. n. The synapomorphies of the Magnospina gen. n. are (1) basal spines longer than 2/3 of the postabdominal claw, (2) presence of 1-4 large denticles, broad at their bases, protruding downwards, without setules between them. Morphological traits such as habitus, rostrum and postabdomen shape, armature of IDL setae, number of setae on the exopod of limb III are also important in the distinction between Magnospina gen. n. and other genera from the Coronatella-branch. The morphology of Magnospina dentifera comb. n. male confirms the closer relationship with the clade composed by the elgans-group from Alona sensu lato, Ovalona and Leberis, but the external morphology, morphology of the postabdominal claw, basal spine and setae 2-3 of IDL support their separation from any of the group cited. It is concluded that the Coronatella-lineage of Aloninae is composed of the genera Coronatella, Anthalona, Karualona, Bergamina, Extremalona, Ovalona, Celsinotum, Leberis and Magnospina gen. n. The elegans-group from Alona sensu lato also belongs to Coronatella-lineage, but still need formal allocation.

Comparative paleovirological analysis of crustaceans identifies multiple widespread viral groups

Background

The discovery of many fragments of viral genomes integrated in the genome of their eukaryotic host (endogenous viral elements; EVEs) has recently opened new avenues to further our understanding of viral evolution and of host-virus interactions. Here, we report the results of a comprehensive screen for EVEs in crustaceans. Following up on the recent discovery of EVEs in the terrestrial isopod, Armadillidium vulgare, we scanned the genomes of six crustacean species: a terrestrial isopod (Armadillidium nasatum), two water fleas (Daphnia pulex and D. pulicaria), two copepods (the salmon louse, Lepeophtheirus salmonis and Eurytemora affinis), and a freshwater amphipod (Hyalella azteca).

Results

In total, we found 210 EVEs representing 14 different lineages belonging to five different viral groups that are present in two to five species: Bunyaviridae (−ssRNA), Circoviridae (ssDNA), Mononegavirales (−ssRNA), Parvoviridae (ssDNA) and Totiviridae (dsRNA). The identification of shared orthologous insertions between A. nasatum and A. vulgare indicates that EVEs have been maintained over several millions of years, although we did not find any evidence supporting exaptation. Overall, the different degrees of EVE degradation (from none to >10 nonsense mutations) suggest that endogenization has been recurrent during the evolution of the various crustacean taxa. Our study is the first to report EVEs in D. pulicaria, E. affinis and H. azteca, many of which are likely to result from recent endogenization of currently circulating viruses.

Conclusions

In conclusion, we have unearthed a large diversity of EVEs from crustacean genomes, and shown that four of the five viral groups we uncovered (Bunyaviridae, Circoviridae, Mononegavirales, Parvoviridae) were and may still be present in three to four highly divergent crustacean taxa. In addition, the discovery of recent EVEs offers an interesting opportunity to characterize new exogenous viruses currently circulating in economically or ecologically important copepod species.

Electronic supplementary material

The online version of this article (doi:10.1186/s13100-015-0047-3) contains supplementary material, which is available to authorized users.

Confirmation through genetic analysis of the existence of many local phyloclades of the genus Simocephalus (Crustacea, Cladocera) in China

Previously, a series of Simocephalus taxa (Cladocera: Daphniidae) from China were described. Most were proposed to be junior synonyms in the last revision of the genus. Using original material from China and data from GenBank, we investigate the biodiversity and phylogeny of Simocephalus using sequences of the cytochrome c oxidase subunit I (COI) and the nuclear 18S genes. In both cases, neighbor-joining, maximum likelihood and Bayesian inference analyses led to highly congruent tree topologies. The grouping of the deeper clades agrees with the inter-generic classification of Orlova-Bienkowskaja (2001). Only the populations of S. serrulatus from Eurasia and North America seem to be closely related, and there are no other shared species between the two continents. Our study unambiguously confirms the existence of many lineages from the subgenera of Simocephalus (Echinocaudus) and Simocephalus s.str. in China, but their morphology needs to be reexamined by taking a wider range of characters (e.g., of female thoracic limbs and adult males) into consideration.

Formation and structure of the ephippium (resting egg case) in relation to molting and egg laying in the water flea Daphnia pulex De Geer (Cladocera: Daphniidae)

Resting eggs produced by daphnid species in response to environmental deterioration play an important role in colonizing new habitats or in re-establishing extinct populations. Females lay resting eggs into the space within the dorsal part of their carapace and form an egg case called the ephippium to protect them. Previous studies mainly reported the morphology of the completely formed ephippium and/or the forming ephippium of an uncertain stage. To understand ephippium formation and to clarify key transitions in the formation of resting eggs, we examined the structure and formation of the ephippium in the water flea Daphnia pulex De Geer (Cladocera: Daphniidae) by stereomicroscopy, histology, and scanning electron microscopy. The females used in this study produced resting eggs by obligate parthenogenesis. We divided ephippium formation into four stages based on two molts and a single ovulation, as follows. Stage I begins 13 min after molting in adult females that do not ovulate. In Stage II, immediately after the first molt, a protuberance appears beneath the neck region and the carapace begins to thicken. In Stage III, the resting eggs ovulate and the carapace in the area of the forming ephippium becomes much thicker than the normal carapace and accumulates dark pigmentation. In Stage IV, following the second molt, the female sheds the ephippium with the enclosed resting eggs and forms a new carapace. These stages will provide a useful reference for future studies on resting egg formation.

Selectively maintained paleoviruses in Holarctic water fleas reveal an ancient origin for phleboviruses

The ecological model, Daphnia pulex (Cladocera: Daphniidae), is broadly distributed in Holarctic freshwater habitats and has been the subject of multidisciplinary study for over half a century, but never has a natural RNA virus infection been reported in daphnids. Here we report on a group of paleoviruses related to RNA dependent RNA polymerase in the genome of D. pulex. Phylogenetic analysis suggests that these paleoviruses are derived from a viral lineage within the genus Phlebovirus. Comparison of the genomic sequences flanking individual paleoviruses reveal that some are orthologous viral insertions having been present in the common ancestor of the D. pulex species complex, which is millions of years old. Still, we detected some sites that have the signature of purifying selection. In contrast, other paleoviruses in this group seem to be unique to specific host lineages and even contain undisrupted open reading frames, suggesting either more recent acquisition, or selective maintenance.

Multiple global radiations in tadpole shrimps challenge the concept of 'living fossils'

'Living fossils', a phrase first coined by Darwin, are defined as species with limited recent diversification and high morphological stasis over long periods of evolutionary time. Morphological stasis, however, can potentially lead to diversification rates being underestimated. Notostraca, or tadpole shrimps, is an ancient, globally distributed order of branchiopod crustaceans regarded as 'living fossils' because their rich fossil record dates back to the early Devonian and their morphology is highly conserved. Recent phylogenetic reconstructions have shown a strong biogeographic signal, suggesting diversification due to continental breakup, and widespread cryptic speciation. However, morphological conservatism makes it difficult to place fossil taxa in a phylogenetic context. Here we reveal for the first time the timing and tempo of tadpole shrimp diversification by inferring a robust multilocus phylogeny of Branchiopoda and applying Bayesian divergence dating techniques using reliable fossil calibrations external to Notostraca. Our results suggest at least two bouts of global radiation in Notostraca, one of them recent, so questioning the validity of the 'living fossils' concept in groups where cryptic speciation is widespread.

Cyclestheria hislopi (Crustacea: Branchiopoda): a group of morphologically cryptic species with origins in the Cretaceous

Cyclestheria hislopi is thought to be the only extant species of Cyclestherida. It is the sister taxon of all Cladocera and displays morphological characteristics intermediate of Spinicaudata and Cladocera. Using one mitochondrial (COI) and two nuclear (EF1α and 28S rRNA) markers, we tested the hypothesis that C. hislopi represents a single circumtropic species. South American (French Guiana), Asian (India, Indonesia, Singapore) and several Australian populations were included in our investigation. Phylogenetic and genetic distance analyses revealed remarkable intercontinental genetic differentiation (uncorrected p-distances COI>13%, EF1α>3% and 28S>4%). Each continent was found to have at least one distinct Cyclestheria species, with Australia boasting four distinct main lineages which may be attributed to two to three species. The divergence of these species (constituting crown group Cyclestherida) was, on the basis of phylogenetic analyses of COI and EF1α combined with molecular clock estimates using several fossil branchiopod calibration points or a COI substitution rate of 1.4% per million years, dated to the Cretaceous. This was when the South American lineage split from the Asian-Australian lineage, with the latter diverging further in the Paleogene. Today's circumtropic distribution of Cyclestheria may be best explained by a combination of Gondwana vicariance and later dispersal across Asia and Australia when the tectonic plates of the two continents drew closer in the early Miocene. The lack of morphological differentiation that has taken place in this taxon over such a long evolutionary period contrasts with the high level of differentiation and diversification observed in its sister taxon the Cladocera. Further insights into the evolution of Cyclestheria may help us to understand the evolutionary success of the Cladocera.