Yanhe Li

Population Genetic Structure and Post-Establishment Dispersal Patterns of the Red Swamp Crayfish Procambarus Clarkii in China

The red swamp crayfish (Procambarus clarkii) was introduced to China in the early 20th century. It has been spread to almost all forms of fresh water bodies including lakes, rivers and even paddyfields in most provinces of China. To clarify issues such as the initial entry point(s), dispersal pattern, genetic diversity and genetic structure of Procambarus clarkii in China, the genetic structure and diversity of P. clarkii populations at 37 sampling sites (35 from China, one from the USA and one from Japan) were analyzed using both mitochondrial gene sequences (COI and 16S rRNA) and 12 nuclear microsatellites. Multiple tests including phylogenetic analyses, Bayesian assignment and analysis of isolation by distance showed that (i) the population from Japan and those collected from China, particularly from NanJing (BGt and XG) and its some neighboring sites (CJr, NT and NB), have similar genetic composition, (ii) relatively high genetic diversity was detected in Chinese populations, (iii) the P. clarkii populations in China did not experience significant population expansions. Taken together, Nanjing, Jiangsu province is the presumed initial entry point, and human-mediated dispersal and adaptive variation are likely responsible for the observed genetic pattern of P. clarkii in China.

The expression of prophenoloxidase mRNA in red swamp crayfish, Procambarus clarkii, when it was challenged.

The expression of the prophenoloxidase (proPO) gene was investigated in nine tissues of red swamp crayfish Procambarus clarkii, by real-time PCR after challenges by CpG oligodeoxynucleotide (ODN), Aeromonas hydrophila and white spot syndrome virus (WSSV). The results can be summarized as follows: (i) the expression level of the proPO gene in haemocytes was highest among nine studied tissues before the challenge; (ii) the expression of proPO increased in all studied tissues after stimulation by CpG ODN and WSSV, and also increased in all tissues, except the ovary, after the A. hydrophila challenge; (iii) the whole expression profiles were different, suggesting that different immune mechanisms may exist for crayfish that are resistant to WSSV and A. hydrophila, although the expression in haemocytes was similar before and after the WSSV and A. hydrophila challenges.

Comparative analysis of mitochondrial genomes in distinct nuclear ploidy loach Misgurnus anguillicaudatus and its implications for polyploidy evolution.

Misgurnus anguillicaudatus has several natural ploidy types. To investigate whether nuclear polyploidy have an impact on mitochondrial DNA (mtDNA), the complete mitochondrial genomes (mitogenomes) of five distinct ploidy M. anguillicaudatus (natural diploid, triploid, tetraploid, pentaploid and hexaploid), which were collected in central China, were sequenced and analyzed. The five mitogenomes share the same gene arrangement and have similar gene size, base composition and codon usage pattern. The most variable regions of the mitogenome were the protein-coding genes, especially the ND4L (5.39% mutation rate). Most variations occurred in tetraploids. The phylogenetic tree showed that the tetraploid M. anguillicaudatus separated early from other ploidy loaches. Meanwhile, the mitogenomes from pentaploids, and hexaploids have the closest phylogenetic relations, but far from that of tetraploids, implying that pentaploids and hexaploids could not be formed from tetraploids, possibly from the diploids and triploids. The genus Misgurnus species were divided into two divergent inter-genus clades, and the five ploidy M. anguillicaudatus were monophyletic, which support the hypotheses about the mitochondrial introgression in loach species.

Inferring Invasion History of Red Swamp Crayfish (Procambarus clarkii) in China from Mitochondrial Control Region and Nuclear Intron Sequences.

Identifying the dispersal pathways of an invasive species is useful for adopting the appropriate strategies to prevent and control its spread. However, these processes are exceedingly complex. So, it is necessary to apply new technology and collect representative samples for analysis. This study used Approximate Bayesian Computation (ABC) in combination with traditional genetic tools to examine extensive sample data and historical records to infer the invasion history of the red swamp crayfish, Procambarus clarkii, in China. The sequences of the mitochondrial control region and the proPOx intron in the nuclear genome of samples from 37 sites (35 in China and one each in Japan and the USA) were analyzed. The results of combined scenarios testing and historical records revealed a much more complex invasion history in China than previously believed. P. clarkii was most likely originally introduced into China from Japan from an unsampled source, and the species then expanded its range primarily into the middle and lower reaches and, to a lesser extent, into the upper reaches of the Changjiang River in China. No transfer was observed from the upper reaches to the middle and lower reaches of the Changjiang River. Human-mediated jump dispersal was an important dispersal pathway for P. clarkii. The results provide a better understanding of the evolutionary scenarios involved in the rapid invasion of P. clarkii in China.

A simple and affordable method of DNA extraction from fish scales for polymerase chain reaction.

Most fish studies today are performed at the molecular level, which needs reliable, quick, and cost-effective DNA extraction protocols (Liu et al. 2009; Ming et al. 2010; Shen et al. 2010). Generally, the most widely used materials for DNA extraction in fish are fins or red blood cell samples (Yang et al. 2001; Liu et al. 2009; Zhang et al. 2009; Li et al. 2009). As fins are used by fish in locomotion, their removal would adversely impact survival of sampled fish. Similarly, collection of samples of enough red blood for DNA extraction from small fish would require them to be cultured further, and this would also be difficult for the researcher. Thus, simpler methods of sample collection are needed for DNA extraction. Since collection of fish scale samples is easy and noninvasive (Kumar et al. 2007), there is a need for a simple, rapid, and affordable method of DNA extraction from them. Based on a literature search, only five papers have described methods of DNA isolation from fish scales (Estoup et al. 1996; Nelson et al. 1998; Adcock et al. 2000; Yue and Orban 2001; Kumar et al. 2007). The method described by Nelson et al. (1998) is relatively complicated for DNA isolation from a large number of individuals. Adcock et al. (2000) successfully isolated DNA from old dried scales by the traditional phenol–chloroform procedure. Yue and Orban (2001) found that

Selection shapes the patterns of codon usage in three closely related species of genus Misgurnus

Neutrality plots revealed that selection probably dominates codon bias, whereas mutation plays only a minor role, in shaping the codon bias in three loaches, Misgurnus anguillicaudatus, M. mohoity, and M. bipartitus. These three species also clearly showed similar tendencies in the preferential usage of codons. Nineteen, nine, and 14 preferred codon pairs and 179, 182, and 173 avoided codon pairs were also detected in M. anguillicaudatus, M. bipartitus, and M. mohoity, respectively, and the most frequently avoided type of cP3-cA1 dinucleotide in these species was nnUAnn. The expression-linked patterns of codon usage revealed that higher expression was associated with higher GC3, lower ENC, and a smaller proportion of amino acids with high size/complexity (S/C) scores in these three species. These results elucidate selectively driven codon bias in Misgurnus species, and reveal the potential importance of expression-mediated selection in shaping the genome evolution of fish.

The complete mtDNA genome of Triplophysa dorsalis (Cypriniformes, Balitoridae, Cobitoidea): genome characterization and phylogenetic analysis

Abstract Based upon the morphological characters, the genus Triplophysa (plateau Loach) is a highly diverse group in the family Balitoridae (or Cypriniformes, Cobitoidea) with 133 valid species. Therefore, the taxonomic relationship of this species at the genetic level remains ambiguous. In the present study, we sequenced the complete mitochondrial genome of Triplophysa dorsalis. In order to understand its position and genetic background at the gene level, the characteristics of mitochondrial DNA sequences and phylogenetic relationship were examined. The mitochondrial genome of T. dorsalis is similar to those of the typical vertebrates, 16 572 bp in length, including 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and a non-coding control region (D-loop). All genes were encoded on the heavy strand except for ND6 and 8 tRNA genes. The overall base composition of the heavy strand was 28.16%, 28.41%, 25.62% and 17.82% for A, T, C and G, respectively. Phylogenetic analyses showed that the seven Triplophysa species clustered together with T. dorsalis to form a sister group with Triplophysa strauchii, T. bleekeri, T. stoliczkai and T. bombifrons. The two genera Triplophysa and Barbatula formed a sister-group relationship, the species Homatula potanini located in the intermediate position, and the genus Leptobotia elongata was in the basal position in the subfamily Nemacheilidae. Further investigations with more Triplophysa species need to be performed for better understanding of the evolutionary history of this fascinating genus.

Species identification and evolutionary inference of the genera Megalobrama and Parabramis (Cyprinidae: Cultrinae) in China

Abstract The species boundaries and evolutionary relationships of two closely related genera, Megalobrama and Parabramis, were inferred from the partial mitochondrial cytochrome oxidase subunit I (COI) gene, NADH dehydrogenase subunit 2 (ND2) gene and their concatenated segment. Phylogenetic reconstructions showed that among the three breams, Megalobrama amblycephala and Megalobrama skolkovii are more closely related to each other than either is to Megalobrama terminalis. The taxonomy of M. pellegrini should be reconsidered. The divergence time estimation based on the assumption of a global molecular clock indicated that speciation and dispersal of the two genera might have occurred at approximately Pliocene to Late Pleistocene, due to major paleo-environmental events associated with monsoon evolution and the formation of the Three Gorges of the Yangtze River.