Spring and autumn fauna of Cladocera (Crustacea: Branchiopoda) in the center of East Asia plain: Hunan and Hubei Provinces of China

Cladoceran (Crustacea: Branchiopoda) fauna of Hunan and Hubei provinces of China was studied in April 2014 and October 2018. 49 species of Cladocera were found, Anthalona sanoamuangae Sinev & Kotov, 2012 was recorded for China for the first time. Eight species were newly recorded for central China, taxonomic status of four species was clarified. Among the observed species, 19 taxa are predominantly Boreal, 13 species are recorded predominantly in south part of temperate zone and subtropics, and 17 species are mainly tropical. Significant difference was revealed between the spring and autumn fauna: Boreal species were the most frequent in spring, whereas subtropical and tropical species became more common in autumn. Species diversity and composition of the cladoceran fauna in the center of East Asia plain is discussed.

Microcrustaceans (Cladocera and Copepoda) of the Boreal/Tropical Transition Zone in the Russian Far East: A Case Study of Species Associations in Three Large Lakes

The Far East of Russia is a region where boreal and tropical faunas mix; it is also a zone of cladoceran endemism. The present study aimed to compare a set of microcrustacean (Cladocera and Copepoda) associations in three large lakes of the Russian Far East: Khanka, Bolon, and Chukchagir. The associations of the microcrustaceans were identified based on the function of the discrete hypergeometric distribution. Many of the 108 taxa found here were unaffiliated with an association. Interestingly, the portion of taxa involved and “not involved” in species associations differed among geographic faunistic complexes. The rate of endemism was significantly higher among the taxa incorporated into the associations as compared to the “not involved” taxa. In all the lakes, there were large clusters of phytophilous species characteristic of the macrophyte zone (and its margins) and clusters characteristic of pelagic and sublittoral plankton. We found that in the three lakes, the microcrustaceans formed a set of functionally similar associations, but the taxonomic composition of each functional association was specific to each lake. We hypothesize that the composition of functional clusters reflects the history of colonization for each water body. That is, the founder effects and subsequent “monopolization” of habitats have affected species associations.

Population genetic differentiation of Daphnia sinensis in a lasting high-phosphorus Chinese lake, Lake Chaohu

Ecological shifts (e.g., eutrophication) can affect the genetic differentiation of zooplankton populations in lakes. However, the role of environmental change in a lasting high-phosphorus lake driving the genetic differentiation of zooplankton population structure over time is poorly understood. In this paper, the changes of the genetic diversity and differentiation of Daphnia sinensis population were studied by using the mitochondrial COI gene and microsatellite markers on modern groups (from January to June 2016) and historic groups (obtained from resting eggs in the sediments) in Lake Chaohu. Based on the microsatellite markers, six modern groups were clustered into two clusters (the WG cluster and SG cluster) during the seasonal dynamics, whereas the genetic differentiation of the five historic groups showed a wave-like pattern and had evolved into four clusters. Moreover, the haplotype network showed that six modern groups had one origin center whereas five historic groups had two origin centers based on the mitochondrial COI gene marker. Fu’s Fs neutral test and Tajima’s test indicated that the five historic groups deviated from neutral evolution and showed a bottleneck effect in the history process. Water temperature and total dissolved phosphorus were obviously associated with the seasonal genetic differentiation of D. sinensis, whereas nitrogen content of the sediments was significantly related to the long-term microevolution of D. sinensis in the high-phosphorus environment. Therefore, the changing pattern of D. sinensis population genetic structure was one of the environmental selections probably combined with co-evolutionary, where rapid-increasing nitrogen level had a large impact on D. sinensis population genetic structure in lasting high phosphorus environment in Lake Chaohu.

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.

Daphnia japonica sp. nov. (Crustacea: Cladocera) an eastern Palearctic montane species with mitochondrial discordance

The Daphnia longispina complex (Crustacea: Cladocera) contains several keystone freshwater species such as D. longispina O.F. Müller (D. rosea Sars is a junior synonym), D. galeata Sars, D. cucullata Sars, and D. dentifera Forbes. The complex is common throughout the Holarctic, but there are several geographic regions where local forms have been assigned to European species names based on a superficial morphological resemblance. Here we examine the species status of a form that was previously assigned to D. rosea from a montane bog pond on Honshu, Japan. We used two nuclear non-coding loci (nDNA), mitochondrial sequences (the ND2 protein-coding region) and morphology for evidence. The mitochondrial gene evidence supported the existence of a divergent lineage that is more closely related to D. galeata than to D. dentifera. However, morphology and the nuclear DNA data indicated a lineage that is most closely related to D. dentifera. As our evidence supported the existence of a cohesive divergent lineage, we described a new species, Daphnia japonica sp. nov. Recognition of local and subalpine diversity in this group is critical as ongoing anthropogenic disturbance has been associated with introductions, local extirpations, and hybridization.

Mitochondrial Lineage Diversity and Phylogeography of Daphnia (Daphnia) (Crustacea: Cladocera) in North-East Russia

The variability of the 12S gene fragment of the mtDNA for taxa belonging to subgenus Daphnia (Daphnia) O.F. Müller, 1776 (Crustacea: Cladocera) in NE Russia is studied, and their phylogenetic analysis performed. We identified (based both on morphological and molecular data) nine species belonging to four species complexes, namely: (A) D. longispina s.l.: (1) D. longispina O.F. Müller, 1776; (2) D. dentifera Forbes, 1893; (3) D. galeata Sars, 1864; (4) D. umbra Taylor, Hebert et Colbourne, 1996; (B) D. cristata s.l.: (5) D. cristata Sars, 1862; (6) D. longiremis Sars, 1862; (C) D. curvirostris s.l.: (7) D. curvirostris Eylmann, 1887; (D) D. pulex s.l.: (8) D. pulex Leydig, 1860; (9) D. middendorffiana Fischer, 1851. Rare arcto-mountainous taxon D. umbra was found in the mountains of the Sakha (Yakutia) Republic for the first time. Species diversity in NE Asia is relatively low, and the most revealed taxa are trans-Beringian. We also performed a phylogeographic analysis of D. dentifera and D. pulex s.l., the two most common species in NE Russia. Our new data allow us to assume that the daphniids of NE Asia have undergone various evolutionary scenarios during the Pleistocene period: survival is within some local refugia, and re-colonization from these areas and from North America through the Beringian land bridge, etc. We agree with previous authors who revealed that the patterns in the studied species groups are relatively recent (of Late Pleistocene or even Holocene age), although the main phylogenetic daphniid lineages (mainly congruent with the biological species) are very old. Our results provide convincing evidence for the hypothesis that NE Russia is a very important source of modern haplotypic diversity for the cladocerans.

Sea–land transition drove terrestrial amphipod diversification in East Asia, with a description of a new species

Sea–land transition caused by marine incursion and regression is hypothesized to be a major driving force in terrestrial biodiversity, providing opportunities for marine ancestors to colonize terrestrial habitats and driving vicariant speciation in distinct geographical regions. Here, we test this hypothesis in East Asia using amphipods of the Morinoia japonica complex. We constructed a dataset from 269 individuals covering all known ranges of this species complex. Phylogenetic and biogeographic analyses revealed that sea–land transition during the Miocene drove the coastal ancestor to invade terrestrial habitats in East Asia and subsequently split into eight biogeographic lineages in eastern China, Korea, Japan and some Pacific islands. Stepping-stone dispersal resulted in a relatively wide distribution of M. japonica, and long-term geographical isolation led to the diversification of the M. japonica complex. Species delimitation analysis suggests that this complex contains eight species. We describe the geographical group from eastern China as a new species, Morinoia aosen sp. nov., based on genetic and morphological comparisons with other geographical groups. Type specimens are deposited in the Institute of Zoology, Chinese Academy of Sciences (IZCAS) in Beijing, China.

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.

New Sets of Primers for DNA Identification of Non-Indigenous Fish Species in the Volga-Kama Basin (European Russia)

Adequate species’ identification is critical for the detection and monitoring of biological invasions. In this study, we proposed and assessed the efficiency of newly created primer sets for the genetic identification of non-indigenous species (NIS) of fishes in the Volga basin based on: (a) a “long” fragment of cytochrome c oxidase subunit one of the mitochondrial gene (COI) (0.7 kb), used in “classical” DNA barcoding; (b) a short 3’-fragment (0.3 kb) of COI, suitable for use in high-throughput sequencing systems (i.e., for dietary analysis); (c) fragment of 16S mitochondrial rRNA, including those designed to fill the library of reference sequences for work on the metabarcoding of communities and eDNA studies; (d) a fragment of 18S nuclear rRNA, including two hypervariable regions V1-V2, valuable for animal phylogeny. All four sets of primers demonstrated a high amplification efficiency and high specificity for freshwater fish. Also, we proposed the protocols for the cost-effective isolation of total DNA and purification of the PCR product without the use of commercial kits. We propose an algorithm to carry out extremely cheap studies on the assessment of biological diversity without expensive equipment. We also present original data on the genetic polymorphism of all mass NIS fish species in the Volga-Kama region. The high efficiency of DNA identification based on our primers is shown relative to the traditional monitoring of biological invasions.

Genetic Signature of a Past Anthropogenic Transportation of a Far-Eastern Endemic Cladoceran (Crustacea: Daphniidae) to the Volga Basin

Most studies of water flea (Crustacea: Cladocera) invasions are concentrated on a few taxa with an obvious harmful influence on native ecosystems, while our knowledge of cases of anthropogenic introduction with not-so-obvious consequences, in most other taxa, is poor. We found in the Volga basin (European Russia) a population that contained D. curvirostris Eylmann, 1887 and its hybrids with D. korovchinskyi Kotov et al. 2021. The latter taxon is endemic to the Far East and it has appeared in the Volga basin as a result of past human-mediated transportation. The population from Bakhilovo is represented by two strongly different groups of the COI haplotypes belonging, respectively, to (1) D. curvirostris and (2) D. korovchinskyi. We detected SNPs in the position 60 of the HSP-90ex3 locus and in the 195 positions of 28S rRNA locus, which differentiate two species. Part of the specimens from Bakhilovo belonged to D. curvirostris s.str., demonstrating homozygote SNP sites in two loci, but two specimens had heterozygote SNP sites in both nuclear loci. They belong to D. curvirostris x korovchinskyi hybrids. Most morphological traits of the females were characteristic of D. curvirostris. We found in some specimens some characters which could suggest their hybrid status, but this opinion is a hypothesis only, which needs to be checked on more ample material. The exact hybrid system in this pond is not known. Moreover, we have no evidences of sexual reproduction of the hybrids; they could reproduce by parthenogenesis only as is known for hybrids of the D. pulex group, or continuously crossing with parents like some members of D. longispina group. However, poor parental D. korovchinskyi was not detected in the pond either morphologically or genetically. The exact vector of its past anthropogenic transportation to the Volga is unknown. Most probably, just ephippia of D. korovchinskyi were translocated replaced from the Khabarovsk Territory to the Samara Area somehow. This is the first report on hybrids within the D. curvirostris species complex. Here, we demonstrated that accurate studies with deep resolution increase the number of revealed cryptic invasions. We expect that the number of revealed cases of cryptic interspecific invasions will grow rapidly.

Crustaceans in the Meiobenthos and Plankton of the Thermokarst Lakes and Polygonal Ponds in the Lena River Delta (Northern Yakutia, Russia): Species Composition and Factors Regulating Assemblage Structures

Information about invertebrates in the low-flow water bodies of northeastern Siberia is far from complete. In particular, little is known about crustaceans—one of the main components of meiobenthic and zooplanktonic communities. An open question is which environmental factors significantly affect the crustaceans in different taxonomic and ecological groups? Based on the data collected on the zooplankton and meiobenthos in the tundra ponds in the southern part of the Lena River Delta, analysis of the crustacean taxocene structure was performed. In total, 59 crustacean species and taxa were found. Five of these are new for the region. The species richness was higher in the large thermokarst lakes than in the small water bodies, and the abundance was higher in small polygonal ponds than in the other water bodies. Variations in the Cladocera assemblages were mainly affected by the annual differences in the water temperature; non-harpacticoid copepods were generally determined by hydrochemical factors; and for Harpacticoida, the macrophyte composition was significant. Three types of the crustacean assemblages characteristic of different stages of tundra lake development were distinguished. The hypothesis that the formation of crustacean taxocenes in the Lena River Delta is mainly determined by two types of ecological filters, temperature and local features of the water body, was confirmed.

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).

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.