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.

A redescription of the Mediterranean endemic cladoceran Daphnia chevreuxi Richard, 1896 (Cladocera: Daphniidae).

The Mediterranean area is a biodiversity and endemism hotspot. Circum-Mediterranean taxa are known among different hydrobionts, including the water fleas. Some Mediterranean endemic cladoceran taxa have been described or redescribed according to modern taxonomical standards, but accurate drawings are missing for others. Here we redescribe the Mediterranean endemic Daphnia chevreuxi Richard, 1896 (Crustacea: Cladocera) and briefly review available data on its distribution and ecology. The species is confirmed to be a typical inhabitant of the temporary ponds of the central Mediterranean area, whereas its populations from the eastern Balkans and the Middle East should be studied in order to check for their actual identity. We conclude that the Mediterranean area is an example of a well-studied region as Cladocera are concerned, but the study of other regions is necessary in order to understand better the cladoceran diversity and distribution patterns in Eurasia.

Ceriodaphnia smirnovi (Crustacea: Cladocera), a new species from the Mediterranean Region, and a phylogenetic analysis of the commonest species.

Species of the genus Ceriodaphnia Dana, 1853 (Crustacea: Cladocera: Daphniidae) are present in the plankton of many freshwater bodies all around the World. However, the taxonomy of the genus is still poorly developed. Most species have been described in the nineteenth century and data on their morphology and distribution should be revised according to current standards. Currently, due to lack of reliable morphological and genetic data, almost all nominal species of Ceriodaphnia are considered as species groups rather than separate biological species, complicating the detection and description of new species of the genus. Here, we redescribe the morphology of Ceriodaphnia quadrangula (O.F. Müller, 1785) based on material close to the type locality in Denmark, and describe a new species of Ceriodaphnia from the Mediterranean region. Also, we provide a phylogenetic analysis using existing and novel sequences of mitochondrial DNA of the commonest species of the genus. Ceriodaphnia smirnovi sp. nov. can be easily distinguished from C. quadrangula via presence of the head pore and the structure of the second thoracic limb, the postabdomen and the ephippium. From other species of Ceriodaphnia known to date C. smirnovi sp. nov. can also be separated on ephippium structure and some other fine morphological features. Although distribution range of C. smirnovi sp. nov. must be clarified in the future based on analysis of more sampling points, most likely, it is restricted to the Mediterranean region. The phylogenetic analyses showed high divergence among 16 different clades (mean clade separation of 13±2.3 % (mean ± SD) and 20.7±2.1% for 16S and COI respectively). These clades belonged to 11 described species and 5 undescribed. The high intraspecific variability of some species indicates the possible existence of more undescribed species within present species groups.

A new species of Flavalona Sinev amp; Dumont, 2016 (Crustacea: Branchiopoda) from Bale Mountains, Ethiopia.

Here we describe a new species of Flavalona Sinev Dumont, 2016 (Cladocera: Chydoridae) based on material from Bale Mountains, Ethiopia. F. darkovi sp. nov. clearly differs from other species of Flavalona known to date by fine ornamentation of valves, proportions of head pores, proximal exopod spine and seta on the middle exopod segment of antenna II. This species may be considered as endemic taxon of high mountain water bodies of Bale Mountains at an altitude of about 4000 m.a.s.l. Investigated species of the genus Flavalona in Africa demonstrate strong local mountain endemism accompanied by morphological differences between closest taxa, but the real diversity of this group in Africa is underestimated yet, and further studies are urgently need. Since the high mountain water ecosystems in Africa are especially vulnerable to increasing anthropogenic impact and global climate warming, it is necessary to speed up the studies of high mountain invertebrates and develop special measures for protection of such ecosystems.

Unexpected mitochondrial lineage diversity within the genus Alonella Sars, 1862 (Crustacea: Cladocera) across the Northern Hemisphere.

Representatives of the genus Alonella Sars (Crustacea: Cladocera: Chydorinae) belong to the smallest known water fleas. Although species of Alonella are widely distributed and often abundant in acidic and mountain water bodies, their diversity is poorly studied. Morphological and genetic approaches have been complicated by the minute size of these microcrustaceans. As a result, taxonomists have avoided revising these species. Here, we present genetic data on Alonella species diversity across the Northern Hemisphere with particular attention to the A. excisa species complex. We analyzed 82 16S rRNA sequences (all newly obtained), and 78 COI sequences (39 were newly obtained). The results revealed at least twelve divergent phylogenetic lineages, possible cryptic species, of Alonella, with different distribution patterns. As expected, the potential species diversity of this genus is significantly higher than traditionally accepted. The A. excisa complex is represented by nine divergent clades in the Northern Hemisphere, some of them have relatively broad distribution ranges and others are more locally distributed. Our results provide a genetic background for subsequent morphological analyses, formal descriptions of Alonella species and detailed phylogeographical studies.

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).

Position of Moina wierzejskii Richard, 1895 (Crustacea: Cladocera) within the genus Moina Baird, 1850 in the light of new morphological data.

The family Moinidae (Crustacea: Cladocera) is intensively studied recently. Last genetic investigations revealed a huge diversity of species in the genus Moina Baird, 1850, comparable with the number of species in the genus Daphnia O.F. Müller, 1776. However, unlike daphniids, the taxonomy of moinids is understudied. Along with new still undescribed species, there are many inadequately described and illegitimately forgotten taxa within Moinidae. Moinids of tropical and subtropical regions remain especially poorly studied, and their features are ignored in recent intergeneric systems. Here we redescribe the morphology of M. wierzejskii Richard, 1895, a peculiar Moina from the New World, and discuss its position within the genus Moina s.l. In the taxonomic scheme, designed for European moinids, M. wierzejskii takes an intermediate position between subgenera Exomoina Hudec, 2010 and Moina s.str. Similarly to European species belonging to M. (Exomoina), females of M. wierzejskii have a modified Ilyocryptus-like labrum and an ephippium with two resting eggs. However, the males have no exopod on the thoracic limb I which suggests that this species is closer to the subgenus Moina s.str. The lack of exopod on male thoracic limb I was also marked in another species of the genus from the New World, M. hutchinsoni Brehm, 1937. To date such unusual combination of morphological features is unknown for any moinids from the Old World and Australia. We hope that our observations will stimulate deep phylogenetic studies of peculiar moinids inhabiting the New World.

Partial revision of the neustonic genus Scapholeberis Schoedler, 1858 (Crustacea: Cladocera): decoding of the barcoding results.

Water fleas (Crustacea: Cladocera) are among the most intensively studied freshwater invertebrates. However, ecologically important daphniids that live on the surface layer (neuston) remain taxonomically confused. Here we attempt to reconcile genetic and morphological information for the neustonic genus Scapholeberis Schoedler, 1858 (Cladocera: Daphniidae) and present the first revision of the Scapholeberis kingii species group. We analyzed new and existing mitochondrial DNA sequences (сytochrome C oxidase subunit I gene region) together with morphology for all but one of the known species of the neustonic daphniids. Morphological comparisons of available populations, belonging to the Scapholeberis kingii species group from several Australian, Asian and African localities, revealed, that they are almost identical according to parthenogenetic females. However, Australian populations can be reliably distinguished from Asian ones based on the morphology of gamogenetic females. Mitochondrial DNA data analyses revealed divergent lineages (>17% for the DNA barcoding COI region) for the three different species (Australia, Asia and Africa). Based on this set of data, we redescribed S. kingii Sars, 1888 from Australia, its terra typica, and described a new species, S. smirnovi sp.nov. from the Russian Far East, Korea and Japan. The status of populations from Ethiopia and the Republic of South Africa remained unclear, because in the African material and the putative type material, we found only parthenogenetic females. Our results provide an integrative revision of the S. kingii species group and improve the taxonomic scaffold used for barcoding and genomics for the remaining species groups in the daphniid genus Scapholeberis.

Crustacean remains from the Yuka mammoth raise questions about non-analogue freshwater communities in the Beringian region during the Pleistocene.

Frozen permafrost Pleistocene mammal carcasses with soft tissue remains are subject to intensive study and help elucidate the palaeoenvironment where these animals lived. Here we present an inventory of the freshwater fauna and flora found in a sediment sample from the mummified Woolly Mammoth carcass found in August 2010, from the Oyogos Yar coast near the Kondratievo River in the Laptev Sea region, Sakha (Yakutia) Republic, NE Russia. Our study demonstrates that the waterbody where the carcass was buried could be characterized as a shallow pond or lake inhabited mainly by taxa which are present in this area today, but additionally by some branchiopod crustacean taxa currently absent or unusual in the region although they exist in the arid zone of Eurasia (steppes and semi-deserts). These findings suggest that some "non-analogue" crustacean communities co-existed with the "Mammoth fauna". Our findings raise questions about the nature of the waterbodies that existed in Beringia during the MIS3 climatic optimum when the mammoth was alive.

A redescription of Moina australiensis Sars, 1896 (Cladocera: Moinidae) with short notes on Australian moinids.

Australia harbors numerous peculiar organisms, but microscopic aquatic invertebrates remain scarcely studied here. Cladocera (Crustacea: Branchiopoda) is considered as one of the most important models for freshwater biogeography, but the lack of adequate species identifications devalues large-scale biogeographical conclusions. In this paper we redescribe morphology of rare and poorly known Moina australiensis Sars, 1896 based on material from its terra typica. Among Australian moinids, M. australiensis is similar to M. tenuicornis Sars, 1896. These two taxa reliably differ from each other in (1) proportions of the antenna I and (2) armature of the inner margin of valve. M. australiensis has a relatively short antenna I and setulae near ventral setae on inner side of the valve grouped into bunches. M. tenuicornis has an elongated antenna I and setulae on described region forming a uniform, continuous row. Presumably, distribution ranges of both species are restricted to Australia. Also, according to literature data, M. baylyi Forró, 1985, M. flexuosa Sars, 1896 and M. propinqua Sars, 1885 may be considered as peculiar Australian taxa. At the same time, M. micrura Kurz, 1875, M. aff. weismanni Ishikawa, 1896 and Moinodaphnia macleayi (King, 1853) have significantly broader distribution ranges. In fact, distribution ranges of all these taxa should be re-evaluated in the future based on careful identification of species in the original samples. In this sense, newly conducted morphological redescriptions of some rare and poorly known taxa are only first steps to evaluation of moinid biodiversity in Australia and in the global scale.

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.

A new species of Moina Baird, 1850 (Cladocera: Moinidae) from Thailand.

A new species of Moina Baird, 1850 (Cladocera: Moinidae) is described based on material collected from Thailand (South-East Asia). In tropical Asia, Moina siamensis sp. nov. could be confused easily with M. weismanni Ishikawa, 1896, because of morphological similarities in parthenogenetic females and males of both species. The outstanding difference between these two taxa concerns the structure of the ephippium in gamogenetic females, which is highly visible under light and scanning electron microscopes. The mature ephippium of M. weismanni is strongly tuberous, with distinct borders between cells, whereas the ephippium of M. siamensis sp. nov. is significantly less tuberous, with prominent longitudinal lines in its central region. Since gamogenetic females only appear sporadically in moinid populations, distribution ranges of M. siamensis sp. nov., M. weismanni and sibling taxa must be clarified precisely using genetic markers in the future. Preliminary investigations of the ephippium structure may be useful for estimating the differences between populations, thus revealing much diversity within Moinidae.

A record of Disparalona hamata (Birge, 1879) (Cladocera: Chydoridae) in phytotelmata of Tillandsia aguascalentensis Gardner, 1984 (Poales: Bromeliaceae).

Bromeliads (Bromeliaceae) are an extremely diverse family of the angiosperms widely distributed in the tropical and subtropical regions of the Americas and West Africa. They often serve as phytotelmata, accumulating rainwater between leaves. Such water reservoirs can be inhabited by diverse organisms. But to date not much attention is paid to inventory of these organisms, with careful identification of each taxon. We found a microcrustacean Disparalona hamata (Birge, 1879) (Crustacea: Cladocera) in the bromeliad Tillandsia aguascalentensis Gardner, 1984 in Mexico. Investigated population included parthenogenetic females, gamogenetic females and males. Hereby the population apparently can pass the full life cycle under conditions of phytotelmata. Along with ecological observations, we provide additional taxonomic notes on the genus Disparalona Fryer, 1968 itself. Recently a series of morphological revisions was conducted for this genus. It was subdivided into two subgenera: Disparalona s.str. and Mixopleuroxus Hudec, 2010. But, in fact, the second taxon is a junior synonym of Leptorhynchus Daday, 1905. In this regard here we provide an updated list of taxonomic synonyms for the subgenus Leptorhynchus.

Identification of Ceriodaphnia Dana, 1853 (Crustacea: Cladocera) taxa from European Russia based on ephippial morphology.

Over the last decades significant progress was achieved in the investigations of water fleas (Crustacea: Cladocera). Their morphology, taxonomy and biogeography can be considered as well-studied, but still there are genera almost ignored by taxonomists. The genus Ceriodaphnia Dana, 1853 (Cladocera: Daphniidae) belongs to such problematic groups. From previous publications, it is obvious that different taxa from the genus have a very different morphology of their ephippia. Here, we study ephippium morphology in six common taxa from central-northern European Russia (Ceriodaphnia megops Sars, 1862; C. laticaudata P.E. Müller, 1867; C. rotunda (Straus, 1820) sensu Sars, 1862; C. quadrangula (O.F. Müller, 1785); C. pulchella Sars, 1862; C. reticulata (Jurine, 1820)) using light and scanning electron microscopy. A key to their identification based on ephippium morphology is proposed. This could be the starting point for revisions based on morphological characters with special emphasis on ephippia. Also, we propose that Ceriodaphnia taxa at least from the Holocene subfossil samples could be identified to the species group level according to structure of their ephippia. This approach to identification of Ceriodaphnia remains in sediments could improve palaeoecological reconstructions. However a global revision of the genus is still needed.

A new case of West-East differentiation of the freshwater fauna in Northern Eurasia: the Pleuroxus trigonellus species group (Crustacea: Cladocera: Chydoridae).

Cladocerans (Crustacea: Branchiopoda) of Northern Eurasia traditionally belong to the most intensively studied groups of freshwater microcrustaceans. However, despite a significant progress in our knowledge of different aspects on their biology, some intriguing questions remain unresolved. The hypothesis of cladoceran faunas differentiation between the western and eastern parts of Northern Eurasia agrees with the continental endemism concept. But to date few cladoceran species groups have been investigated through the whole North Eurasian range. Our current work contributes to the confirmation of this hypothesis through a revision of the poorly studied Pleuroxus trigonellus species group. Based on material from Europe, we redescibed morphology of Pleuroxus trigonellus (O.F. Müller, 1776) s.str. and found that its distribution range is potentially restricted to the western portion of Northern Eurasia. At the same time, morphologically similar populations from the eastern portion of Eurasia belong to a new species, Pleuroxus yakutensis sp. nov. These two species are basically similar in general morphology of parthenogenetic and gamogenetic females, but have clear differences in the male morphology. Additionally we offer an identification key for discrimination of the P. trigonellus group from P. uncinatus (Baird, 1850) according to morphological features of the males.

A revision of the genus Leberis Smirnov, 1989 (Cladocera: Chydoridae) in the Old World and Australia.

A comparison between populations of the diaphanus-group of Leberis Smirnov, 1989 from Australia and India confirmed that Australian L. diaphanus (King, 1853) and Indian L. punctatus (Daday, 1898) are separate species. Morphology of parthenogenetic females of L. punctatus is redescribed for the first time. Some fine details of morphology are re-examined in other species of Leberis, taxonomically significant features and their variability are studied. In the Old World L. punctatus could be confused with L. diaphanus, but the former differs from the latter mainly in the details of thoracic limbs I and IV. Both species have relatively broad distribution ranges: L. punctatus inhabits South Asia, Africa and penetrates Southeast Asia, L. diaphanus is a widespread taxon in the water bodies of Australia, Southeast Asia and South China. Diversity of the genus in the Old World is underestimated yet, and further investigations are desirable.

A new species of Acroperus Baird, 1843 (Cladocera: Chydoridae) from Africa.

A new species of Acroperus Baird, 1843 (Cladocera: Chydoridae) is described based on the material from Lake Tana, Ethiopia and two water bodies in Eastern Cape, Republic of South Africa. In Africa, Acroperus africanus sp. nov. had a chance to be confused by previous authors with Palearctic A. harpae (Baird, 1834) and A. angustatus Sars, 1863, but it could be easily distinguished from the latter by: (1) smaller seta on the proximal segment of antenna II endopod; (2) larger values of seta 3/seta 2 length ratio on the limb I, as well as some additional features. Diversity of the genus in Africa is underestimated yet, and further investigations of taxon distribution and ecology are necessary.