Daphnia diversity on the Tibetan Plateau measured by DNA taxonomy

Distinct multitrophic biodiversity composition and community organization in a freshwater lake and a hypersaline lake on the Tibetan Plateau

Alpine lakes play pivotal roles in plateau hydrological processes but are highly sensitive to climate change, yet we lack comprehensive knowledge of their multitrophic biodiversity patterns. Here, we compared the biodiversity characteristics of diverse taxonomic groups across water depths and in surface sediments from a freshwater lake and a hypersaline lake on the northwestern Tibetan Plateau. Using multi-marker environmental DNA metabarcoding, we detected 134 cyanobacteria, 443 diatom, 1,519 invertebrate, and 28 vertebrate taxa. Each group had a substantially different community composition in the two lakes, and differences were also found between water and sediments within each lake. Cooccurrence network analysis revealed higher network complexity, lower modularity, and fewer negative cohesions in the hypersaline lake, suggesting that high salinity may destabilize ecological networks. Our results provide the first holistic view of Tibetan lake biodiversity under contrasting salinity levels and reveal structural differences in the ecological networks that may impact ecosystem resilience.

Application of Moina mongolica and Daphniopsis tibetana in marine ecotoxicology studies in China: A review

Moina mongolica and Daphniopsis tibetana are typical saline Cladocera in China that are characterized by a wide salinity range, rapid reproduction, and high-density culture. In this paper, the characteristics and life history of M. mongolica and D. tibetana are reviewed. The application of these two species of Cladocera to ecotoxicology in recent years is also summarized from the aspects of environmental factors and environmental pollutants, including ultraviolet B radiation, temperature, salinity, alkalinity, pH, heavy metals, harmful red tide, pesticides, and persistent organic pollutants. Additionally, the toxicity sensitivity of saline Cladocera in different reproductive statuses and inter-generational embryos is discussed. Finally, the need to enhance knowledge of the molecular genomics, population dynamics, and strategies for protection of saline Cladocera, along with the need for establishment of estuarine and marine environmental monitoring standards are discussed. Overall, this review highlights the potential for using these Cladocera species as indicator organisms for estuarine and marine ecotoxicology studies.

Analysis of the complete mitogenome of Daphnia galeata from the Han River, South Korea: structure comparison and control region evolution

Daphnia galeata is an important plankton in aquatic ecosystems. As a widely distributed species, D. galeata has been found throughout the Holarctic region. Understanding the genetic diversity and evolution of D. galeata requires the accumulation of genetic information from different locations. Even though the mitochondrial genome (mitogenome) sequence of D. galeata has already been reported, little is known about the evolution of its mitochondrial control region. In this study, D. galeata samples were collected from the Han River on the Korean Peninsula and its partial nd2 gene was sequenced for haplotype network analysis. This analysis showed that four clades of D. galeata were present in the Holarctic region. Moreover, the D. galeata examined in this study belonged to clade D and was specific to South Korea. The mitogenome of D. galeata from the Han River showed similar gene content and structure compared to sequences reported from Japan. Furthermore, the structure of control region of the Han River was similar to those of Japanese clones and differed substantially from European clone. Finally, a phylogenetic analysis based on the amino acid sequences of 13 protein-coding genes (PCGs) indicated that D. galeata from the Han River formed a cluster with clones collected from Lakes Kasumigaura, Shirakaba, and Kizaki in Japan. The differences in control region structure and stem and loop structure reflect the different evolutionary directions of the mitogenomes from Asian and European clones. These findings improve our understanding of the mitogenome structure and genetic diversity of D. galeata.

The first DNA barcode library of Chironomidae from the Tibetan Plateau with an evaluation of the status of the public databases

The main aim of this study was to curate a COI barcode library of Chironomidae from the Tibetan Plateau (TP) as an essential supplement to the public database. Another aim is to evaluate the current status of the public database of Chironomidae in aspects of taxonomic coverage, geographic representation, barcode quality, and efficiency for molecular identification, the Tibetan Plateau, China. In this study, 512 individuals of Chironomidae from the TP were identified based on morphological taxonomy and barcode analysis. The metadata of public records of Chironomidae were downloaded from the BOLD, and the quality of the public barcodes was ranked using the BAGS program. The reliability of the public library for molecular identification was evaluated with the newly curated library using the BLAST method. The newly curated library comprised 159 barcode species of 54 genera, of which 58.4% of species were likely new to science. There were great gaps in the taxonomic coverage and geographic representation in the public database, and only 29.18% of barcodes were identified at the species level. The quality of the public database was of concern, with only 20% of species being determined as concordant between BINs and morphological species. The accuracy of molecular identification using the public database was poor, and about 50% of matched barcodes could be correctly identified at the species level at the identity threshold of 97%. Based on these data, some recommendations are included here for improving barcoding studies on Chironomidae. The species richness of Chironomidae from the TP is much higher than ever recorded. Barcodes from more taxonomic groups and geographic regions are urgently needed to fill the great gap in the current public database of Chironomidae. Users should take caution when public databases are adopted as reference libraries for the taxonomic assignment.

Integrative approach for validation of six important fish species inhabiting River Poonch of north-west Himalayan region (India)

Traditionally, species of fish are identified based on morphological characteristics. Although these taxonomic descriptions are essential, there are cases where the morphological characters distinguishing these species show marginal differences. For instance, in the Poonch River in the Himalayas, there are 21 species, out of which some are morphologically similar, and the taxonomic distinction between these species is unclear. Therefore, in this study, we used sequences from two mitochondrial genes, Cytochrome b (Cyt b) and a larger ribosomal subunit (16S rRNA), as well as the morphological analysis to address any taxonomic ambiguities among the six fish species. Maximum Likelihood results revealed that all the species were clustered according to their families and genera. The phenotypic analysis also supported this statement, as all the species of different genera like Schizothorax, Tor, Garra, Traqilabeo, and Glyptothorax are grouped in their particular cluster, it shows that species of a separate class share a mutual morphological characteristic. While genetic analyses of these species suggest nucleotide diversity (p) and haplotype diversity, with Hd values as 0.644 for Cyt b and 0.899 for 16S rRNA, confirming the rich genetic diversity in the river. Overall, we recommend that the integrative approach in delimiting the fish species is more effective than the individual one and can be used to rapidly diagnose a species and understand the evolutionary relationship between the species.

Past climate cooling promoted global dispersal of amphipods from Tian Shan montane lakes to circumboreal lakes

Climate changes have substantial impacts on the geographic distribution of montane lakes and evolutionary dynamics of cold-adapted species. Past climate cooling is hypothesized to have promoted the dispersal of cold-adapted species via montane lakes, while future climate warming is thought to constrain their distributions. We test this hypothesis by using phylogeographic analysis and niche modeling of the Holarctic crustacean Gammarus lacustris with global sampling comprised of 567 sequenced individuals and 3180 occurrence records. We found that the species arose in Tian Shan in Central Asia and dispersed into montane lakes along the Alps, Himalayas, Tibet, East Asia, and the North American Rocky Mountain ranges, with accelerated diversification rates outside Tian Shan. Climatically suitable regions for geographic lineages of G. lacustris were larger during cooling periods (LGM), but smaller during warming periods (Mid-Holocene). In the future (2070) scenario, potential distributions in the Himalayas, North Tibet, South Tibet and North America are predicted to expand, whereas ranges in East Asia, Europe and Tian Shan will decline. Our results suggest that Mid-Miocene-to-Pleistocene continuous cooling promoted multiple independent dispersal events out of Tian Shan due to increased availability of montane lakes via "budding" of lineages. Montane lakes are conduits through which cold-adapted amphipods globally dispersed, dominating circumboreal lakes. However, future climate warming is likely to force organisms to shift upward in altitude and northward in latitude, leading to a future change in local populations. These findings highlight the importance of conservation of montane lakes, especially in the context of climate change.

Phylogenetic analysis of eight species of Anomopoda based on transcriptomic and mitochondrial DNA sequences

Anomopoda is the widespread planktonic microcrustacean, which plays a crucial role in aquatic ecosystem. There are few studies about the evolutionary relationships among various Anomopoda basing on molecular data. In the present study, phylogenetic analysis of eight Anomopoda was carried out. Firstly, the culture system was developed to breed cladocerans. By using this system, eight species (Daphnia magna, D. pulex, D. sinensis, Ceriodaphnia reticulata, Moina micrura, Scapholeberis kingi, Simocephalus vetulus and Eurycercus lamellatus) were purified and cultured stably in the laboratory. Then, transcriptomic sequences and partial mitochondrial DNA sequences were both used to reconstruct the phylogenetic tree among 8 species. Transcriptomic sequences were sequenced on Illumina Hiseq 2500 platform. After assembly and annotation, transcriptomic sequences were spliced together and aligned for phylogenetic analysis. Basing on the orthologous genes derived from transcriptomic sequences, the phylogenetic analysis showed that 4 genera of Daphniidae were clustered into one group, and among the 4 genera, Ceriodaphnia was closer to Daphnia than Simocephalus, while Scapholeberis was farthest from other species. In addition, Eurycercidae was closer to Daphniidae than Moinidae. The phylogenetic trees based on both 12S rRNA and 16S rRNA sequences were similar with that based on transcriptomic sequences. Meanwhile, the phylogenetic tree based on 16S rRNA sequences was more suitable than that based on 12S rRNA sequences. These results suggested that the phylogenetic analysis basing on the transcriptomic sequences was available in cladocerans, which will help us to effectively understand the phylogenetic relationships among various cladocerans.

Evaluation of the Egg Bank of Two Small Himalayan Lakes

High mountain lakes are biodiversity treasures. They host endemic taxa, adapted to live in extreme environments. Among adaptations, production of diapausing eggs allows for overcoming the cold season. These diapausing eggs can rest in the sediments, providing a biotic reservoir known as an egg bank. Here, we estimated changes in abundance of the egg bank in two lakes in the Khumbu Region of the Himalayas, during the last ca. 1100 and 500 years, respectively, by analyzing two sediment cores. We tested viability of the diapausing eggs extracted from different layers of the sediment cores under laboratory conditions. We found that only diapausing eggs of the Monogont rotifer Hexarthra bulgarica nepalensis were able to hatch, thus suggesting that a permanent egg bank is lacking for the other taxa of the lakes, not least for the two Daphnia species described from these sites. Our results confirm previous studies suggesting that in high mountain lakes, the production of diapausing is mainly devoted to seasonal recruitment, therefore leading to a nonpermanent egg bank. The different ability of different taxa to leave viable diapausing eggs in the sediments of high mountain lakes therefore poses serious constraints to capability of buffering risk of biodiversity loss in these extremely fragile environments.

Genetic diversity and differentiation of Daphnia galeata in the middle and lower reaches of the Yangtze River, China

Mitochondrial 16S rDNA and CO I gene were used as molecular markers for the analysis of the genetic diversity and differentiation of Daphnia galeata populations in nine water bodies in the middle and lower reaches of the Yangtze River. In the combined 16S rDNA and CO I gene sequences, 54 variable sites and 44 haplotypes were observed among 219 individuals belonging to nine D. galeata populations. Average haplotype diversity and nucleotide diversity were, respectively, 0.72% and 0.56%. The F-statistics (F ST) value of the D. galeata populations was 0.149. According to the results of the neutral test, D. galeata in the middle and lower reaches of the Yangtze River had experienced a bottleneck effect in the history. Molecular variance analysis indicated that the genetic differentiation of the D. galeata populations mainly occurred within populations (85.09%). Greater genetic differentiations of D. galeata among individuals within populations appeared in the populations from the Huaihe River basin, whereas smaller genetic differentiations occurred in the populations from the middle reaches of the Yangtze River. Strong gene flows were all observed between Group I (four populations from the middle reaches of the Yangtze River) and Group ΙΙ (three populations from the middle and lower reaches of the Yangtze River), and Group ΙΙΙ (two populations from the Huaihe River basin). The effective migration rates (M) were 851.49 from Group I to Group ΙΙ and 685.96 from Group I to Group ΙΙΙ, respectively. However, no significant relationship was observed between the genetic differentiation and geographical distance of the nine populations (r = .137, p > .05). Results suggested that the genetic differentiation of D. galeata in the water bodies in the middle and lower reaches of the Yangtze River resulted mainly from geographical isolation.

Unexpected endemism in the Daphnia longispina complex (Crustacea: Cladocera) in Southern Siberia

The biological significance of regional cladoceran morphotypes in the montane regions of the central Palearctic remains poorly understood. In the Holarctic Daphnia longispina complex (Cladocera: Daphniidae), several variants, lineages and species have been proposed as endemic for Southern Siberia. Daphnia turbinata Sars, for example, named after its unusual head shape, is known only from Southern Siberia. Here we sequence DNA of Daphnia from three mitochondrial genes (12S rRNA, 16S rRNA, and NADH dehydrogenase subunit 2, ND2) from 57 localities in Russia and Mongolia (the majority being from Southern Siberia) and place them in evolutionary context with existing data. Our aim was to examine regional endemism of the Daphnia longispina complex in Southern Siberian; to improve the phylogenetic understanding with improved taxonomic and regional sampling, and to better understand the influence of Pleistocene glaciation on the biogeography of these lineages. At least three lineages showed genetic evidence for endemism in Southern Siberia. There was strong support for D. turbinata as a sister lineage to to D. longispina/D. dentifera. Another endemic, Siberian D. cf. longispina, is a sister group to the longispina group in general. Within D. longispina s. str. there was an endemic Siberian clade with a western range boundary near the Yenisei River Basin. Gene flow estimates among populations (based on F_ST values) were very low for clades of D. longispina on a regional (the original 12S dataset), and on a pan-Eurasian (the extended 12S dataset) scale. Negative values of Fu’s F_S and Tajima’s D tests prevailed for the species examined with significant values found for two D. longispina clades, D. dentifera, D. galeata and D. cristata. Our results support the notion that Southern Siberia is an important biogeographic region for cladocerans as it contained unexpected diversity of endemics (such as D. turbinata, D. cf. longispina and lineages of D. umbra and D. longsipina s.str.) and from being the geographic meeting place of expanding postglacial lineages from eastern and western refugia.

Diversity of the Bosmina (Cladocera: Bosminidae) in China, revealed by analysis of two genetic markers (mtDNA 16S and a nuclear ITS)

BACKGROUND

China is an important biogeographical zone in which the genetic legacies of the Tertiary and Quaternary periods are abundant, and the contemporary geography environment plays an important role in species distribution. Therefore, many biogeographical studies have focused on the organisms of the region, especially zooplankton, which is essential in the formation of biogeographical principles. Moreover, the generality of endemism also reinforces the need for detailed regional studies of zooplankton. Bosmina, a group of cosmopolitan zooplankton, is difficult to identify by morphology, and no genetic data are available to date to assess this species complex in China. In this study, 48 waterbodies were sampled covering a large geographical and ecological range in China, the goal of this research is to explore the species distribution of Bosmina across China and to reveal the genetic information of this species complex, based on two genetic markers (a mtDNA 16S and a nuclear ITS). The diversity of taxa in the Bosmina across China was investigated using molecular tools for the first time.

RESULTS

Two main species were detected in 35 waterbodies: an endemic east Asia B. fatalis, and the B. longirostris that has a Holarctic distribution. B. fatalis had lower genetic polymorphism and population differentiation than B. longirostris. B. fatalis was preponderant in central and eastern China, whereas B. longirostris was dominated in western China. The third lineage (B. hagmanni) was only detected in a reservoir (CJR) of eastern China (Guangdong province). Bosmina had limited distribution on the Tibetan plateau.

CONCLUSIONS

This study revealed that the biogeography of Bosmina appear to be affected by historical events (Pleistocene glaciations) and contemporary environment (such as altitude, eutrophication and isolated habitat).