Whole-Genome Phylogenetic Reconstruction as a Powerful Tool to Reveal Homoplasy and Ancient Rapid Radiation in Waterflea Evolution.

Although phylogeny estimation is notoriously difficult in radiations that occurred several hundred million years ago, phylogenomic approaches offer new ways to examine relationships among ancient lineages and evaluate hypotheses that are key to evolutionary biology. Here, we reconstruct the deep-rooted relationships of one of the oldest living arthropod clades, the branchiopod crustaceans, using a kaleidoscopic approach. We use concatenation and coalescent tree-building methods to analyze a large multigene data set at the nucleotide and amino acid level and examine gene tree versus species tree discordance. We unequivocally resolve long-debated relationships among extant orders of the Cladocera, the waterfleas, an ecologically relevant zooplankton group in global aquatic and marine ecosystems that is famous for its model systems in ecology and evolution. To build the data set, we assembled eight de novo genomes of key taxa including representatives of all extant cladoceran orders and suborders. Our phylogenetic analysis focused on a BUSCO-based set of 823 conserved single-copy orthologs shared among 23 representative taxa spanning all living branchiopod orders, including 11 cladoceran families. Our analysis supports the monophyly of the Cladocera and reveals remarkable homoplasy in their body plans. We found large phylogenetic distances between lineages with similar ecological specializations, indicating independent evolution in major body plans, such as in the pelagic predatory orders Haplopoda and Onychopoda (the "Gymnomera"). In addition, we assessed rapid cladogenesis by estimating relative timings of divergence in major lineages using reliable fossil-calibrated priors on eight nodes in the branchiopod tree, suggesting a Paleozoic origin around 325 Ma for the cladoceran ancestor and an ancient rapid radiation around 252 Ma at the Perm/Triassic boundary. These findings raise new questions about the roles of homoplasy and rapid radiation in the diversification of the cladocerans and help examine trait evolution from a genomic perspective in a functionally well understood, ancient arthropod group. [Cladocera; Daphnia; evolution; homoplasy; molecular clock; phylogenomics; systematics; waterfleas.].

Phylogenetic relationships and cryptic species in the genus Sthenoteuthis (Cephalopoda: Ommastrephidae) in the South China Sea.

Large squids of the genus Sthenoteuthis are commercially relevant species that include two truly oceanic squids. They are large nektonic predators being widely distributed throughout tropical and subtropical waters of the Atlantic and Indo-Pacific Ocean. The present study investigates different morphs varying in size at maturity, and assesses the genetic divergence in Sthenotheutis in relation to geographic patterns in the South China Sea. We obtained sequences using a mitochondrial (cytochrome c oxidase subunit I) and a nuclear (Histone H3) gene marker from 111 individuals in 23 locations of the South China Sea. In combination with sequences available in public databases, we performed tests on DNA taxonomy, mostly based on molecular phylogenies. Our results suggest that the genus Sthenoteuthis includes at least three species. The Indo-Pacific purpleback squid Sthenoteuthis oualaniensis contains at least two genetically distinct lineages that can be considered separate species, a dwarf species and a medium-sized species, separated by both the mitochondrial marker and the more conserved nuclear marker. We also assessed whether the few cases of mitonuclear discordance could be the result of genetic introgression and past hybridization or incongruence lineage sorting. The medium-sized species is more widely distributed and dominant in the South China Sea than the dwarf species. The medium-sized species inhabits the whole South China Sea, whereas the dwarf species is restricted to the equatorial waters of the South China Sea. The medium-sized species has two further genetic clades, one distributed in the East Pacific Ocean and the other in the South China Sea. This high level of genetic differentiation is in agreement with the discriminant analysis on the morphological measurements, clearly separating the dwarf and medium-sized species, indicating the presence of a complex of pseudo-cryptic species in S. oualaniensis, clearly identifiable by differences in DNA sequences and in body size, and statistically differentiated in their body measurements.

A fossil-calibrated phylogenomic analysis of Daphnia and the Daphniidae.

In the post-genomic era, much of phylogenetic analyses still relies on mitochondrial DNA, either alone or in combination with few nuclear genes. Although this approach often makes it possible to construct well-supported trees, it is limited because mtDNA describes the history of a single locus, and nuclear phylogenies based on a few loci may be biased, leading to inaccurate tree topologies and biased estimations of species divergence time. In this study, we perform a phylogenomic analysis of the Daphniidae family (Crustacea: Branchiopoda: Anomopoda) including some of the most frequently studied model organisms (Daphnia magna and D. pulex) whose phylogenetic relationships have been based primarily on an assessment of a few mtDNA genes. Using high-throughput sequencing, we were able to assemble 38 whole mitochondrial genomes and draft nuclear genomes for 18 species, including at least one species for each known genus of the family Daphniidae. Here we present phylogenies based on 636 nuclear single-copy genes shared among all sampled taxa and based on whole mtDNA genomes. The phylogenies we obtained were highly supported and showed some discrepancies between nuclear and mtDNA based trees at deeper nodes. We also identified a new candidate sister lineage of Daphnia magna. Our time-calibrated genomic trees, which we constructed using both fossil records and substitution rates, yielded very different estimates of branching event times compared to those based on mtDNA. By providing multi-locus, fossil-calibrated trees of the Daphniidae, our study contributes to an improved phylogenetic framework for ecological and evolutionary studies that use water fleas as a model system.

Male meiosis in Crustacea: synapsis, recombination, epigenetics and fertility in Daphnia magna.

We present the first detailed cytological study of male meiosis in Daphnia (Crustacea: Branchiopoda: Cladocera)-an aquatic microcrustacean with a cyclical parthenogenetic life cycle. Using immunostaining of the testes in Daphnia magna for baseline knowledge, we characterized the different stages of meiotic division and spermiogenesis in relation to the distribution of proteins involved in synapsis, early recombination events and sister chromatid cohesion. We also studied post-translational histone modifications in male spermatocytes, in relation to the dynamic chromatin progression of meiosis. Finally, we applied a DNA fragmentation test to measure sperm quality of D. magna, with respect to levels of inbreeding. As a proxy for fertility, this technique may be used to assess the reproductive health of a sentinel species of aquatic ecosystems. Daphnia proves to be a model species for comparative studies of meiosis that is poised to improve our understanding of the cytological basis of sexual and asexual reproduction.

An annotated checklist of the Cladocera (Crustacea: Branchiopoda) from India.

Based on a revision of available literature on the Indian Cladocera (Crustacea: Branchiopoda), we present an updated checklist, with taxonomical updates and comments for all taxa recorded since the start of research of this group in the country since 1860. We have listed a total of 137 valid taxa, of which most records belong to species groups that need revision worldwide. The situation in Indian Cladocera taxonomy is, at present, insufficient for realistic conclusions on biodiversity, ecology and biogeography. We list suggestions for an improvement of the current situation.

Seed Viability and Potential Germination Rate of Nine Endemic Boswellia Taxa (Burseraceae) from Socotra Island (Yemen).

The endemic Boswellia species (Burseraceae) on Socotra Island (Yemen) are of great local significance due to their various local ethnobotanical uses. However, despite the fact that these trees are endangered, little is known about their biology. We tested seed germination rates in controlled experiments (trials of 21 days) for two subsequent years and for nine endemic taxa of Boswellia occurring on Socotra Island. For this, seeds were collected island-wide from a wide range of localities and for several populations per species. We observed differences in germination among Boswellia species, among species and localities and among both years, which indicates that the development of seeds is strongly affected by external ecological factors. Although we noted a large variation in seed germination (relatively high in Boswellia socotrana), and half of the species showed relatively low mean daily germination, our study indicated that all endangered endemic Frankincense Tree taxa of Socotra harbor the potential for in situ conservation through recruitment, given that known impacts can be reduced in local replantation areas (e.g., grazing).

The most latent cladoceran in the Holarctic revealed-sinking Unapertura Sarmaja-Korjonen, Hakojärvi amp; Korhola, 2000 into the genus Rhynchotalona Norman, 1903 (Branchiopoda: Cladocera: Chydoridae).

The morphology of one of the smallest chydorid cladocerans in the world, Unapertura latens Sarmaja-Korjonen, Hakojärvi Korhola, 2000 (Branchiopoda: Cladocera: Anomopoda) is studied herein. External features and postabdomen of the adult parthenogenetic female are discussed in detail for the first time, based on an intact specimen from northern Finland. Originally described on Quaternary fossil remains, we investigate the validity of the monotypic genus Unapertura and its position within the Aloninae subfamily, in particular in relation to Rhynchotalona Norman, 1903. As a result, we rename the taxon as Rhynchotalona latens comb. nov., based on morphology. The species, a glacial relict, seems one of the rarest cladocerans in contemporary waters in Finland, yet intact specimens are clearly overlooked and recent remains in surface sediments suggest an Arctic-Alpine distribution in oligotrophic habitats in the Holarctic.

A new stygobiotic Stenasellus Dollfus, 1897 (Asellota: Stenasellidae) from Socotra Island, Yemen.

We describe a new species of Stenasellus Dollfus, 1897 (Isopoda: Asellota: Stenasellidae) from stagnant freshwater habitats in a cave on Socotra Island, Yemen. S. taitii n. sp. is the first endemic stenasellid found in Socotra, showing relatively closer morphological affinities to species from the Middle East (Oman, Iran) than from the African mainland, corresponding to the known paleogeographical connection of the archipelago to Southern Arabia. With notes on the protection of Socotran groundwaters.

A new case of false "wide" distribution for tropical cladocerans: the genus Notoalona Rajapaksa amp; Fernando, 1987 (Crustacea: Cladocera) in the Old World.

Members of the genus Notoalona Rajapaksa Fernando, 1987 (Cladocera: Chydoridae: Aloninae) are small-sized chydorids, inhabiting tropical water bodies around the World. Based on morphological features two species, N. globulosa (Daday, 1898) and N. pseudomacronyx Van Damme, Maiphae Sa-Ardrit, 2013, were revealed in tropical Asia, but the status of African populations has remained unclear for a long time. Some authors identified African specimens as N. globulosa, others considered them as potentially new species awaiting description. Here we reexamined morphology of Notoalona populations from tropical Asia (Thailand, Laos) and Africa (Ethiopia, Kenya, Sudan and Madagascar). Although parthenogenetic females from Asia and Africa are basically similar, a single stable difference was found. In N. globulosa, the length of the basal spine and claw base are almost equal to each other, while in all investigated African specimens the basal spine is two times longer than base of postabdominal claw. This feature allows us to identify African populations as N. pseudomacronyx. Length of the setules in the basal group near the postabdominal basal spine, which was previously discussed in the literature as a specific feature for African populations, in fact, is overly variable and cannot be considered as diagnostic characteristic for the description of African populations as a separate taxon. Thus, the distribution range of N. pseudomacronyx is hereby expanded from South Africa to South East Asia, while N. globulosa s.l. occupies water bodies from tropical Asia to Australia. The same distribution patterns, when sibling species occur together in tropical Asia, have been shown for some other cladocerans as well. No doubt, the Asian tropics may be a particularly interesting area for future investigations on co-occurrence of sibling cladocerans, their ecology, behavior, genetics and potential hybridization.

First record of the Neotropical cladoceran Diaphanosoma fluviatile in the Great Lakes basin.

The ctenopod Diaphanosoma fluviatile has been reported primarily from the Neotropical region and occasionally from the southern United States. D. fluviatile was collected in the Great Lakes basin (the Maumee River, Western Lake Erie, and Lake Michigan) in 2015 and 2018, far north from its previously known distribution. The occurrence of this southern species in the Maumee River and Great Lakes may be the result of an anthropogenic introduction, although a natural range expansion cannot be excluded. This report documents the northernmost record of D. fluviatile in the Nearctic region, extending the known distribution of the species to 42°N, which is a notable increase of 11 degrees latitude. Our detection of D. fluviatile is the first record of this southern species from the Laurentian Great Lakes drainage.

A record of Notostraca on Socotra Island and the importance of local conservation of the habitat.

The first record of Triops Schrank, 1803 (Crustacea: Branchiopoda: Notostraca: Triopsidae) from Socotra Island is presented herein. Besides Madagascar and the current note, the genus is unknown from Indian Ocean islands. A brief morphological exploration indicates that the Socotran Triops cf. granarius (Lucas, 1864) (trachyaspis form) belongs to an African clade within this widespread Old World species complex and not to T. granarius s.str. from East Asia. Detailed morphological and molecular revision of the poorly studied Middle Eastern and Northern African populations in comparison to East Asian populations are needed to understand this group and the phylogenetic position and status of the Socotran tadpole shrimp. Found in a single locality (the archeological site Eriosh) in the rapidly changing coastal plains on Socotra, together with other large branchiopods (endemic Anostraca and unidentified Spinicaudata), the insular Triops population and the regionally neglected temporary lake habitat deserve a special protection status from a biodiversity conservation perspective. Triops cf. granarius is hereby suggested as a local flagship species for the conservation of temporary pool habitats on the island.