Shaoping Liu

Changes in abundance of larvae of the four domestic Chinese carps in the middle reach of the Yangtze River, China, before and after closing of the Three Gorges Dam

The four domestic Chinese carps, i.e. grass carp (Ctenopharyngodon idella), black carp (Mylopharyngodon piceus), silver carp (Hypophthalmichthys molitrix) and bighead carp (Hypophthalmichthys nobilis), cast their drifting eggs in the running water of the Yangtze River. In 1997 ~ 2005, a systematic study on the dynamics of the abundance the larvae of the four domestic Chinese carps was performed in the middle reach of the Yangtze River, close to Sanzhou city. It was calculated that in breeding seasons from early May to late June every year the abundance of fry drifting through the section of Sanzhou was 3.59 billion in 1997, 2.75 billion in 1998, 2.15 billion in 1999, 2.85 billion in 2000, 1.90 billion in 2001, 1.90 billion in 2002, 406 million in 2003, 339 million in 2004 and 105 million in 2005 respectively. Several environmental parameters related to the dynamics of larval abundance were also examined simultaneously. The construction of the Three Gorges Dam near Yichang between the upper and middle reaches of the Yangtze River has apparently had a drastic influence on the abundance of fish larvae.

Relationship between meteorological conditions and natural reproduction behavior of the four famous Chinese carps

Known as the four famous carps in China, black carp (Mylopharyngodon piceus), grass carp (Ctenopharyngodon idella), silver carp (Hypophthalmichthys molitrix) and bighead carp (Hypophthalmichthys nobilis) are commercially important fish species with a high production in China. To reveal the relationships between meteorological conditions and the natural spawning behavior of these fishes, we considered six meteorological factors (including wind, rainfall, temperature, air pressure, sunshine hours and humidity) and the weather conditions in 80 spawning events. The results showed that the spawning activities were more likely to be activated in consecutive rainy days or days when weather changed drastically, while the spawning activities showed no tendency for the weather type except consecutive rainy days. Our analyses also showed that the average rainfall in the initial spawning days is higher than that in the spawning time windows (the time from the earliest spawning activity to the latest spawning activity), while other meteorological elements remained at more or less the same values in both time periods; spawning activity tended to happen in days when the average air pressure was going down or the average temperature going up, while the other meteorological elements showed no consistent tendency.

Genetic diversity and differentiation between populations of Glyptothorax zanaensis in the middle and lower reaches of the Nujiang River

The development of hydroelectricity in the Nujiang River would have adverse impacts on the populations of Glyptothorax zanaensis. In order to assess the genetic diversity and differentiation of this species, we sequenced the cytochrome b gene of the mitochondria in 102 individuals of the fish collected from 6 sampling sites (Gongshan, Gudeng and Lushui in the Nujiang Prefectural District and Daojie, Mengnuo and Mucheng in the Baoshan Municipal District). A total of 87 variation sites were detected in the fragment of 1 137 bp in length, with which the 102 samples were defined as 36 haplotypes. The haplotype diversity (h) and the nucleotide diversity (pi) of total samples were 0.851+/-0.028 and 0.01356+/-0.0008, respectively. Therefore, the genetic diversity of G. zanaensis was relatively low. However, the genetic diversity of the Nujiang population was significantly higher than that of the Baoshan population. The pairwise Fst value between the populations (0.475-0.846) was higher than that within the population (0.002-0.108), which implied that the Fst value was positively related to geographic distance. Analysis of molecular variance (AMOVA) showed that the genetic differentiation between the populations and within the populations were 53.65% and 46.35%, respectively. The fixation index (Fst value) was 0.5365, indicating that there existed significant differentiation between the Nujiang population and the Baoshan population. The phylogentic tree and networks of the haplotypes of G. zanaensis showed that there were two separate lineages: the Nujiang lineage and the Baoshan lineage. Each lineage represents at least one separated management unit, or belongs to an evolutionary significant unit. It was suggested that in the construction of hydroelectric projects the measures for protecting G. zanaensis should be adopted in fully considering the populations of G. zanaensis and the status quo of their population structure to avoid the occurrence of gene exchange among populations.

Mitochondrial DNA diversity of Glyptothorax zanaensis (Wu et al., 1981) populations in Nu River, China

The hillstream fish, Glyptothorax zanaensis (Wu et al., Oceanol Limnol Sin 12:74–79, 1981) is a freshwater teleost species belonging to the order Siluriformes, endemic to Nu River and Lancang River basin. Because wild stocks of G. zanaensis have declined substantially in recent years, owing to overexploitation, pollution, illegal fishing practices and the development of hydroelectricity in the Nu River, the populations of G. zanaensis have markedly declined in recent years. We studied the mitochondrial DNA cyt b gene to assess the genetic diversity of G. zanaensis in seven tributaries of the Nu River. Seventy variable sites defined 15 haplotypes in 153 individuals. Haplotype diversity and nucleotide diversity were 0.542 ± 0.014 and 0.011 ± 0.007, respectively. The Sunzu River site had the highest haplotype diversity (Hd, 0.893 ± 0.014) and nucleotide diversity ( Pi, 0.010 ± 0.012). Genetic diversity was low in the Dong River, Fengwei River and Mengtong River. Pairwise FST values ranged from 0.00 to 1.00. Significant FST values were found for Sunzu River sampled sites paired with all other populations and Mengtong river sampled site paired with the others. Furthermore, the Nanpeng River sampled site was significantly differentiated from the Luoming River, Dong River and Fengwei River sampled sites. Such knowledge is essential for developing appropriate policies for the rational management of G. zanaensis.

The mitochondrial genome of Gnathopogon imberbis (Cypriniformes, Cyprinidae)

Abstract In the present study, the complete mitogenome sequence of Gnathopogon imberbis is determined using PCR amplification and DNA sequencing, which contains 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and a non-coding control region with the total length of 16,598 bp. Except for eight tRNA and ND6 genes, all other mitochondrial genes are encoded on the H-strand. The codon usage followed the typical vertebrate mitochondrial pattern (ATG or GTG for start codon and TAA or TAG for stop codon). The overall nucleotide composition was 30.0% A, 27.0% T, 25.8% C and 17.2% G, with an A + T bias of 57.0%. The complete mitochondrial genome sequence will be useful for phylogenetic analysis and studies of population genetics of G. imberbis.

Species diversity of drifting fish eggs in the Yangtze River using molecular identification

The dam constructions greatly changed the hydrologic conditions in the Yangtze River, and then significantly affected the spawning activities of indigenous river fish. Monitoring the species composition of drifting eggs during spawning season is important for protection issues. In this study, we have sampled drifting fish eggs in nine locations from 2014 to 2016. Eggs were identified using the mitochondrial cyt b gene sequence. A total of 7,933 fish eggs were sequenced successfully and blasted into the NCBI database. Thirty-nine fish species were identified, and were assigned to four families and two orders. Approximately 64% of the species identified, and 67% of the eggs, were classified in the Family Cyprinidae. Abundance and Shannon–Wiener diversity index of species were higher in the main river than in tributaries of the river. However, tributaries may be important spawning grounds for some fish species. The Jaccard’s similarity index and river-way distances among sampled stations were negatively correlated suggesting the environment shapes species composition in the sampled spawning grounds. These results showed that mitochondrial DNA sequence is a powerful and effective tool for fish egg identification in Yangtze River and these data are useful for conservation efforts.

The complete mitochondrial genome sequence of Glyptothorax laosensis (Siluriformes, Sisoridae).

Abstract The complete mitogenome sequence of Glyptothorax laosensis was determined using long PCR reactions. The genome is 16 539 bp in length, including 13 typical vertebrate protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and a control region. Except for eight tRNA and ND6 genes, all other mitochondrial genes are encoded on the heavy strand. The gene order and composition of G. laosensis was similar to that of most other vertebrates. The descending order of the base composition on heavy strand was 31.3% A, 27.5% C, 25.9% T, 15.3% G, with a relatively lower level of G and a slight AT bias of 57.2%. The results of phylogenetic reconstruction showed G. laosensis is the sister group with G. trilineatus (Figure 1), and the Glyptothorax genus formed a monophyletic group.

The mitochondrial genome of Mystacoleucus marginatus (Cypriniformes, Cyprinidae)

Abstract The mitochondrial genome of Mystacoleucus marginatus (Cypriniformes, Cyprinidae) has been sequenced. The total sequence is 16,611 bp in size with 56.67% AT content. It contains 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs and 1 putative control region. The gene content and organization are similar to that of most other vertebrates. Most genes are encoded on the heavy strand except ND6 and eight tRNA genes on light strand. This molecular information will contribute to better understand its evolution and population genetics.

The mitochondrial genome of Pseudolaubuca sinensis (Cypriniformes, Cyprinidae)

Abstract In the present study, the complete mitogenome sequence of Pseudolaubuca sinensis was determined using PCR amplificationand DNA sequencing, which contains 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a non-coding control region with the total length of 16,617 bp. Except for eight tRNA and ND6 genes, all other mitochondrial genes are encoded on the heavy strand. The codon usage followed the typical vertebrate mitochondrial pattern (ATG or GTG for start codon and TAA or TAG for stop codon). There are 6 regions of gene share totaling 22 bp and 14 intergenic spacer regions totaling 66 bp. The complete mitochondrial genome sequence is useful for phylogenetic analysis and studies of population genetics of Pseudolaubuca sinensis.

Age structure and genetic diversity of Homatula pycnolepis in the Nujiang River basin

This study examined the age structure of the Loach, Homatula pycnolepis through the otolith growth rings in 204 individual specimens collected from the Xiaomengtong River of the Nujiang River (Salween River) basin in April, 2008. There were only two different age classes, 1 and 2 years of age-no 3 year olds were detected. The age structure of H. pycnolepis was simple. The complete mitochondrial DNA cytochrome b gene sequences (1140) of 80 individuals from 4 populations collected in the Nujiang River drainage were sequenced and a total of 44 variable sites were found among 4 different haplotypes. The global haplotype diversity (Hd) and nucleotide diversity (Pi) were calculated at 0.7595, 0.0151 respectively, and 0, 0 in each population, indicating a consistent lack of genetic diversity in each small population. There was obvious geographic structure in both the Nujiang River basin (NJB) group, and the Nanding River (NDR) group. The genetic distance between NJB and NDR was calculated at 0.0356, suggesting that genetic divergence resulted from long-term isolation of individual population. Such a simple age structure and a lack of genetic diversity in H. pycnolepis may potentially be due to small populations and locale fishing pressures. Accordingly, the results of this study prompt us to recommend that the NJB, NDR and Lancang River populations should be protected as three different evolutionary significant units or separated management units.