Genetic diversity and phylogeography of Daphnia similoides sinensis located in the middle and lower reaches of the Yangtze River

Conserved DNA sequence analysis reveals the phylogeography and evolutionary events of Akebia trifoliata in the region across the eastern edge of the Tibetan Plateau and subtropical China

BACKGROUND

The eastern edge of the Qinghai‒Tibet Plateau (QTP) and subtropical China have various regions where plant species originate and thrive, but these regions have been the focus of very few integrative studies. Here, we elucidated the phylogeographic structure of a continuous and widespread Akebia trifoliata population across these two regions.

RESULTS

Sixty-one populations consisting of 391 genotypes were examined to assess population diversity and structure via network distribution analysis, maximum likelihood phylogenetic tree reconstruction, divergence time estimation, demographic history inference, and ancestral area reconstruction of both conserved internal transcribed spacer (ITS) and chloroplast (rps16) DNA sequences. The results showed that the ITS region was more variable than the rps16 region and could be suitable for studying intraspecific phylogeography. The A. trifoliata population displayed high genetic diversity, genetic differentiation and obvious phylogeographical structure, possibly originating on the eastern QTP, expanding during the last glacial-interglacial cycle, diverging in the early Pleistocene and middle Pleistocene, and extensively migrating thereafter. The migration route from west to east along rivers could be largely responsible for the long-distance dispersal of this species, while three main refuges (Qinba Mountains, Nanling Mountains and Yunnan-Guizhou Plateau) with multiple ice shelters facilitated its wide distribution.

CONCLUSIONS

Our results suggested that the from west to east long migration accompanying with the minor short reciprocal migration in the south-north direction, and the three main refuges (the Qinba Mountains, Nanling Mountains and Yunnan-Guizhou Plateau) contributed to the extant geographical distribution of A. trifoliata. In addition, this finding also strongly reduced the discrepancy between glacial contraction and postglacial expansion and the in situ survival hypothesis by simultaneously considering the existence of many similar climate-related ecological niches and migration influences.

β-cyclocitral, a novel AChE inhibitor, contributes to the defense of Microcystis aeruginosa against Daphnia grazing

β-cyclocitral is one of the major compounds in cyanobacterial volatile organic compound (VOCs) and can poison other aquatic organisms. To investigate the effect of β-cyclocitral on cyanobacterial-grazer interactions, Daphnia sinensis was fed Microcystis aeruginosa and exposed to β-cyclocitral. Our present study demonstrated that M. aeruginosa could significantly inhibit D. sinensis grazing. And the grazing inhibition by Microcystis aeruginosa results from the suppression of feeding rate, heart rate, thoracic limb activity and swimming speed of D. sinensis. In addition, M. aeruginosa could also induce intestinal peristalsis and emptying in D. sinensis. Interestingly, our present study found that the exposure to β-cyclocitral could mimic a range of phenotypes induced by M. aeruginosa in D. sinensis. These results suggested that M. aeruginosa could release β-cyclocitral to inhibit Daphnia grazing. To further examine the toxic mechanism of β-cyclocitral in Daphnia, several in vivo and in vitro experiments displayed that β-cyclocitral was a novel inhibitor of acetylcholinesterase (AChE). It could induce the accumulation of acetylcholine (ACh) by inhibiting AchE activity in D. sinensis. High level of endogenous Ach could inhibit feeding rate and induce intestinal peristalsis and emptying in D. sinensis.

Phylogeography and Genetic Structure of the Bush Cricket Decma fissa (Orthoptera, Tettigoniidae) in Southern China

Decma fissa is the most widely distributed species of the genus Decma occuring in southern China. This study presents the first phylogeographic work of D. fissa based on COI, Cytb and ITS sequence. We examined genetic diversity with ITS and mitochondrial sequence respectively, and phylogenetic work was based on the mitochondrial data. A high-level genetic diversity was revealed based on mitochondrial data but a low-level diversity was shown with ITS sequence. For the mitochondrial data, divergence time analysis displayed five lineages. Based on the Mantel test, geographic and genetic distances among D. fissa populations revealed a significant positive correlation. Bayesian skyline plot (BSP) analyses implied that none of three major lineages of D. fissa was seemingly affected by the last glacial maximum (LGM, 0.015-0.025 Mya). Ecological niche modeling was used to predict the distribution of D. fissa in four periods (LGM, Mid-Holocene, current and 2070) in China. Analysis of the ancestral area reconstruction indicated that D. fissa occurred in the South China area.

Comparative transcriptome analysis revealed genes involved in the sexual size dimorphisms and expressed sequence tag-Simple Sequence Repeat loci validation in Odorrana graminea

Sexual size dimorphism (SSD) is widespread among animals and is characterized by differences in body size between sexes. Previous studies suggested SSD might reflect the adaptations of particular sexes to their specific reproductive or ecological roles. The large green cascade frogs (Odorrana graminea) exhibit obvious SSD that females are nearly twice the body size of males. However, the molecular mechanisms underlying SSD of O. graminea are still unknown. In the present study, we first obtained nearly 5 Gb of the transcriptome data through Illumina sequencing, and the de novo transcriptome assembly produced 189,868 unigenes of O. graminea. A total of 774 significantly sex-differentially expressed genes (DEGs) were identified. Of which, 436 DEGs showed significantly higher expression levels in females than those in males, whereas 338 DEGs showed significantly lower expression in females than those in males. We also found 10 sex-differentially expressed genes related to energy metabolism between sexes of O. graminea, and these DEGs were related to the estrogen signaling pathway, oxidative phosphorylation, fatty acid biosynthesis, gastric acid secretion, and nitrogen metabolism. We found that the differences in energy metabolism and steroid hormone synthesis might be the main driving force leading to the sexual growth dimorphism of O. graminea. In addition, a total of 63,269 potential EST-SSR loci and 4,669 EST-SSR loci were detected and validated in different populations of O. graminea and other species within Odorrana. The assembled transcriptome will facilitate functional genomic studies of O. graminea and the developed EST-SSR markers will contribute to the population genetics of the species within Odorrana. The sex-differentially expressed genes involved in energy metabolism might provide insights into the genetic mechanisms underlying the SSD of O. graminea.

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.

The use of various statistical methods for authenticity and detection of adulteration in fish and seafood

Various methodologies including genetic analyses, morphometrics, proteomics, lipidomics, metabolomics, etc. are now used or being developed to authenticate fish and seafood. Such techniques usually lead to the generation of enormous amounts of data. The analysis and interpretation of this information can be particularly challenging. Statistical techniques are therefore commonly used to assist in analyzing these data, visualizing trends and differences and extracting conclusions. This review article aims at presenting and discussing statistical methods used in studies on fish and seafood authenticity and adulteration, allowing researchers to consider their options based on previous successes/failures but also offering some recommendations about the future of such techniques. Techniques such as PCA, AMOVA and FST statistics, that allow the differentiation of genetic groups, or techniques such as MANOVA that allow large data sets of morphometric characteristics or elemental differences to be analyzed are discussed. Furthermore, methods such as cluster analysis, DFA, CVA, CDA and heatmaps/Circos plots that allow samples to be differentiated based on their geographical origin are also reviewed and their advantages and disadvantages as found in past studies are given. Finally, mathematical simulations and modeling are presented in a detailed review of studies using them, together with their advantages and limitations.

Phylogeography and genetic diversity of the widespread katydid Ducetia japonica (Thunberg, 1815) across China

Habitat fragmentation can lower migration rates and genetic connectivity among remaining populations of native species. Ducetia japonica is one of the most widespread katydids in China, but little is known about its genetic structure and phylogeographic distribution. We combined the five-prime region of cytochrome c oxidase subunit I (COI-5P), 11 newly developed microsatellite loci coupled with an ecological niche model (ENM) to examine the genetic diversity and population structure of D. japonica in China and beyond to Laos and Singapore. Both Bayesian inference (BI) and haplotype network methods revealed six mitochondrial COI-5P lineages. The distribution of COI-5P haplotypes may not demonstrate significant phylogeographic structure (N ST > G ST, p > .05). The STRUCTURE analysis based on microsatellite data also revealed six genetic clusters, but discordant with those obtained from COI-5P haplotypes. For both COI-5P and microsatellite data, Mantel tests revealed a significant positive correlation between geographic and genetic distances in mainland China. Bayesian skyline plot (BSP) analyses indicated that the population size of D. japonica's three major mitochondrial COI-5P lineages were seemingly not affected by last glacial maximum (LGM, 0.015-0.025 Mya). The ecological niche models showed that the current distribution of D. japonica was similar to the species' distribution during the LGM period and only slightly extended in northern China. Further phylogeographic studies based on more extensive sampling are needed to identify specific locations of glacial refugia in northern China.

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.