Research Article |
Corresponding author: Feng Lan ( fenglanshangyouju@163.com ) Academic editor: Maria Elina Bichuette
© 2021 Dongqi Liu, Feng Lan, Sicai Xie, Yi Diao, Yi Zheng, Junhui Gong.
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation:
Liu D, Lan F, Xie S, Diao Y, Zheng Y, Gong J (2021) Dynamic genetic diversity and population structure of Coreius guichenoti. ZooKeys 1055: 135-148. https://doi.org/10.3897/zookeys.1055.70117
|
To investigate the genetic effects on the population of Coreius guichenoti of dam constructions in the upper reaches of the Yangtze River, we analyzed the genetic diversity and population structure of 12 populations collected in 2009 and 2019 using mitochondrial DNA (mtDNA) control regions. There was no significant difference in genetic diversity between 2009 and 2019 (P > 0.05), but the population structure tended to become stronger. Genetic differentiation (FST) among five populations (LX, BB, YB, SF and JA) collected in 2009 was not significant (P > 0.05). However, some populations collected in 2019 were significantly differentiated (P < 0.05), indicating that the population structure has undergone change. A correlation analysis showed that the genetic diversity of the seven populations collected in 2019 was significantly negatively correlated with geographical height (r = −0.808, P = 0.028), indicating that the populations at high elevations were more vulnerable than those at low elevations. In order to prevent the further decrease of genetic diversity and population resources, some conservation and restoration suggestions, such as fish passage and artificial breeding, are put forward.
Coreius guichenoti, genetic diversity, mtDNA, population structure
Coreius guichenoti (Sauvage & Dabry de Thiersant, 1874) (Cyprinidae, Cypriniformes) is one of the endemic fishes and an important economic fish in the upper reaches of Yangtze River in China (
Coreius guichenoti were often found in fast currents of rivers and streams near gravel and rock crack habitats, and they feed on small fish (
Population geographic location, sample number and time for each site sampled.
Code | Locality | N1 | N2 | Elevation (m) | Sample time |
---|---|---|---|---|---|
LX | Luxian | 24 | 21 | 245 | Jun 2009 |
BB | Beibei | 21 | 19 | 212 | Sep 2009 |
YB | Yanbian | 22 | 20 | 1003 | Aug 2009 |
SF | Shuifu | 35 | 28 | 431 | May 2009 |
JA | Jiangan | 33 | 28 | 293 | Jun 2009 |
XZ | Xuzhou | 45 | 29 | 284 | Jun 2019 |
JY | Jiangyang | 21 | 20 | 247 | Aug 2019 |
LC | Longchi | 36 | 26 | 323 | Sep 2019 |
LM | Liemian | 30 | 30 | 294 | Oct 2019 |
CB | Caiba | 45 | 35 | 285 | May 2019 |
XQ | Xiqu | 26 | 22 | 1115 | Nov 2019 |
HMC | Hongmenchang | 39 | 30 | 902 | May 2019 |
Total | 377 | 308 |
In view of the current and potential anthropogenic negative factors affecting the population of C. guichenoti, it is necessary to carry out long-term monitoring of the genetic status of wild population dynamics. Especially, after the construction of Xiluodu and Xiangjiaba dams, what is the genetic diversity of the wild population of C. guichenoti? Have these dams affected the population structure of C. guichenoti, and to what extent?
Previous studies have tried to evaluate genetic diversity and population structure of C. guichenoti from other sections of the Yangtze River (
During the period of 2009 and 2019, 377 individuals of C. guichenoti were collected from the upper reaches of the Yangtze river basin. Tissue specimens of C. guichenoti were collected in strict accordance with relevant national laws and animal ethics requirements. During the collection process, a small amount of fish fin tissues was cut off and disinfected, and the fish were released into the river. Sampling sites cover most of the distribution range of the species. To ensure comparability, sample collection was considered using the same or similar as possible sampling points in the same water system or section. A total of five populations were collected in the Yanbian section of the Yalong River (YB), the Xufu section of the Jinsha River (SF), the Jiangan section of the Yangtze River (JA), the Luxian section of the Yangtze River (LX) and the Beibei section of the Jialing River (BB) in 2009. A total of seven populations were collected in the Xiqu section of Jinsha River (XQ), Hongmenchang section of Jinsha River (HMC), Longchi section of Minjiang River (LC), Caiba section of Yangtze River (CB), Xuzhou section of Yangtze River (XZ), Jiangyang section of Yangtze River (JY) and Liemian section of Jialing River (LM) in 2019 (Fig.
To reduce the influence of different ages on the experimental error, 308 samples aged around 3 years were selected from 377 individuals, according to the relationship between age and body length (
Primers DL1 (ACCCCTGLCTCCCAAALC, Ta: 62 °C) and DH2 (ATCTTALCATCTTCAGTG, Ta: 62 °C) (
Haplotype number (H), Haplotype diversity (h), and nucleotide diversity (π) were used to estimate genetic diversity in mtDNA control regions (
Population demography history was tested with mtDNA control region. First, Tajima’s D (
Using the isolation with migration (IM) model in IMA2 program (
To test the correlation between genetic differentiation and geographical distance, we performed Mantel test with mtDNA data. The significance of the correlation (r) between log-transformed genetic distance and log-transformed geographic distance was determined by using 2, 000 permutations of Distance Isolation (IBD) Web Service v. 3.1.6 (
Genetic diversity analysis of 12 populations was performed based on mtDNA control region. Sequencing of 899 bp revealed 301 variable loci. The average base composition is A = 28.5%, T = 31.4%, C = 22.4% and G = 17.7%. A total of 65 haplotypes were identified from the control region sequences extracted from 308 individuals. Each population has some private haplotypes. However, with the exception of JY, Hap1 is shared in every population. LC, JA, XZ, HMC, and CB shared Hap3. YB, JA, SF, XZ, CB, and XQ share Hap4. All populations shared Hap5, except LC and YB. Each population shared Hap7, except for LX and JY. BB, JY, YB, JA, LC, and XZ shared Hap8 (Fig.
Phylogenetic trees of the mtDNA control region haplotypes in C. guichenoti reconstructed with Bayesian inference. Numbers at nodes represent Bayesian posterior probabilities and neighbor-joining tree. At the right side of the figure, the numbers represent the total of individuals from different sampling locations in each haplotype.
Population genetic diversity and structure statistics for the mitochondrial control region.
Population | H | h | π | Fis |
---|---|---|---|---|
LX | 9 | 0.897 | 0.0038 | 0.146 |
BB | 11 | 0.894 | 0.0042 | 0.254 |
YB | 16 | 0.901 | 0.0047 | 0.114 |
SF | 27 | 0.899 | 0.0038 | 0.112 |
JA | 23 | 0.884 | 0.0044 | 0.227 |
XZ | 28 | 0.874 | 0.0041 | 0.328 |
JY | 13 | 0.891 | 0.0042 | 0.208 |
LC | 25 | 0.878 | 0.0037 | 0.228 |
LM | 30 | 0.876 | 0.0031 | 0.663* |
CB | 27 | 0.892 | 0.0038 | 0.377 |
XQ | 19 | 0.869 | 0.0045 | 0.317 |
HMC | 23 | 0.873 | 0.0044 | 0.757* |
According to the sampling sites, the 12 populations were divided into three groups: upper group (YB, XQ and HMC), middle group (LX, JA, SF, JY, LC, CB, and XZ), and lower group (BB and LM). AMOVA analysis of five populations (JA, YB, BB, SF, and LX) collected in 2009 showed no significant molecular differences in mtDNA among populations, between populations and within populations (P > 0.05; Suppl. material
The FST values of five populations (LX, BB, YB, SF, and JA) collected in 2009 were not significant (P > 0.05). The genetic differentiation between XQ and JA, HMC, and BB was not significant. Two neighborhood link trees were constructed based on the FST values in five populations (2009) and seven populations (2019). BB and LX populations clustered together, and SF, JA, and YB populations clustered in adjacency trees (Suppl. material
The results of mtDNA haplotype sequence analysis showed that there were four clades in the tree (Fig.
Matrix of pairwise FST values calculated from the mtDNA control region data.
LX | BB | YB | SF | JA | XZ | JY | LC | LM | CB | XQ | |
---|---|---|---|---|---|---|---|---|---|---|---|
LX | |||||||||||
BB | 0.026 | ||||||||||
YB | 0.036 | 0.013 | |||||||||
SF | 0.030 | 0.042 | 0.011 | ||||||||
JA | 0.023 | 0.064 | 0.032 | 0.043 | |||||||
XZ | 0.037 | 0.052 | 0.034 | 0.032 | 0.016 | ||||||
JY | 0.056 | 0.036 | 0.024 | 0.051 | 0.044 | 0.045 | |||||
LC | 0.012 | 0.057 | 0.057 | 0.041 | 0.015 | 0.043 | 0.034 | ||||
LM | 0.015 | 0.047 | 0.042 | 0.053 | 0.064 | 0.028 | 0.068 | 0.022 | |||
CB | 0.032 | 0.045 | 0.038 | 0.064 | 0.052 | 0.053 | 0.028 | 0.063 | 0.032 | ||
XQ | 0.061 | 0.026 | 0.018 | 0.074 | 0.064 | 0.065 | 0.046 | 0.059 | 0.118* | 0.022 | |
HMC | 0.023 | 0.067 | 0.054 | 0.024 | 0.017 | 0.014 | 0.028 | 0.113* | 0.044 | 0.032 | 0.026 |
Probabilities from tests (Wilconxon’s) for mutation drift equilibrium (bottlenecks) under three mutation models (IAM, TPM and SMM).
Population | Probability of Wilcoxon test | ||
---|---|---|---|
I.A.M | S.M.M | T.P.M | |
LX | 0.1253 | 0.5441 | 0.3320 |
BB | 0.0555 | 0.6762 | 0.7860 |
YB | 0.0315* | 0.7348 | 0.7327 |
SF | 0.2237 | 0.2657 | 0.3388 |
JA | 0.1436 | 0.9686 | 0.3026 |
XZ | 0.0538 | 0.3246 | 0.1752 |
JY | 0.1708 | 0.1028 | 0.1929 |
LC | 0.0258* | 0.0413* | 0.0738 |
LM | 0.0257* | 0.0402* | 0.0629 |
CB | 0.1114 | 0.2026 | 0.1088 |
XQ | 0.0452* | 0.2324 | 0.0526 |
HMC | 0.0384* | 0.0438* | 0.0635 |
Mantel test showed that geographical distance was significantly associated with genetic differentiation in five populations (2009; Fig.
The multichannel mismatch distribution, insignificant Tajima’s D and Fu’s FS values, and BSP analysis showed that SF, LX, BB, JA, YB, and XQ populations were relatively stable. However, LC and LM suffer genetic bottlenecks and XZ suffers dilatations. The bottleneck trend in the JY population and a weak population growth trend in the HMC and CB population.
In this study, we assessed genetic variation in twelve populations of C. guichenoti to understand the dynamics of the species’ genetic variability and its population structure and explore whether the rapid reduction of genetic variability will be observed in this species. Adaptive potential is related to genetic diversity, and the loss of genetic diversity can increase the possibility of population extinction. Previous work has highlighted the possible importance of genetic variability in determining the health of both individuals and, perhaps by implication, populations (
The results of AMOVA analysis showed that the genetic differentiation between populations and between populations was limited (P > 0.05), and most of the total genetic variation occurred among individuals within groups, which was insignificant neither (P > 0.05). The FST values showed that the population structure of each sampling site was not significant. Moreover, these five groups do not form independent groups in terms of population structure, and each individual actually has an equal probability of belonging to any of these groups in any analysis. There was no obvious systematic geographic structure among the haplotypes of the samples from different geographical locations. The sequence differences within and between groups were small, indicating high genetic similarity among different groups and relatively shallow population history. The genetic differentiation of the five populations was significantly correlated with geographical distance. After spawning, this species usually flows downstream with floods, and when rivers are in flood, juvenile and adult fish subsequently swim upstream (
However, different population structures were found in seven populations collected from 2019. There were significant differences in FST values between some populations collected from 2019. The seven populations did not form an independent cluster in population structure, but the composition of each population was different. Our AMOVA analysis showed that although the genetic differentiation between populations was very limited, there was significant genetic variation among individuals within populations (P < 0.05). Significant differences among all populations have not yet developed, but differences among individuals within populations are emerging. To explain this, the dam restricted the genetic links between the upstream and downstream populations of C. guichenoti, splitting them into small, isolated populations. A strong, though occasionally permeable, barrier to transmission may exist to limit the flow of genes between sites. In this case, the species’ habitat becomes fragmented, which not only affects the spawning and development environment of C. guichenoti, but also impedes upstream and downstream migration and gene exchange. Thus, weak correlation between the observed genetic differentiations and geographical distances was found in seven populations (2019, P > 0.05) while it is significant negative correlation in five populations (2009, P < 0.05). As the hydrological environment changes, the individuals within the population become different. Then there may be a strong demographic structure in the future. Furthermore, compared with large populations, small populations are more prone to inbreeding and loss of genetic diversity due to genetic drift and bottlenecks (
Though the decrease of genetic diversity was not significant from 2009 to 2019, the population structure of C. guichenoti showed a trend of change. If conservation and restoration measures will be not carried out, a loss of genetic diversity may occur in the future. Loss of genetic diversity will impair the ability of the population to respond to environmental changes, so conservation of genetic variation should be a priority in the recovery efforts of C. guichenoti, especially in light of recent habitat fragmentation due to dams.
Migration (increased gene exchange) can lead to gene rescue or recovery (
Furthermore, in order to maintain heterozygosity and genetic diversity, mature adults should be collected for artificial propagation from different locations across the distribution, especially considering the high genetic diversity among groups (
This work was supported by Upper Changjiang River Burean of Hydrological and Water Resources Survey (no. 035001203), Sichuan Province Key Laboratory of Characteristic Biological Resources of Dry and Hot River Valley (no. GR-2020-C-04), Science & Technology Department of Sichuan Province (no. 2021YFN0101) and Panzhihua University (no. HJK2019, no. SFKC2046, no. 2020cxcy004, and no. 2021cxcy076).
Tables S1, S2, Figures S1, S2
Data type: MS Word file
Explanation note: Table S1. Results of hierarchical AMOVA for five populations sampled in 2009 based on mitochondrial control region. Table S2. Results of hierarchical AMOVA for seven populations sampled in 2019 based on mitochondrial control region. Figure S1. Neighbor-joining tree based on FST. Figure S2. History in IM analyses for C. guichenoti. The boxes represent sampled and ancestral populations, horizontal lines represent splitting times and curved arrows represent migration.