Strong population structure of Schizopygopsis chengi and the origin of S. chengi baoxingensis revealed by mtDNA and microsatellite markers

Evaluation of genetic diversity and population structure in Leptobotiamicrophthalma Fu & Ye, 1983 (Cypriniformes, Cobitidae)

This paper reports the first account about dynamic changes on genetic diversity and population structure of Leptobotiamicrophthalma in the Yangtze River drainage due to dam constructions. The genetic diversity and population structure of twelve populations of L.microphthalma collected in 2010 and 2020 were estimated using 12 nuclear microsatellite markers. Reduction of genetic diversity between 2010 and 2020 was not significant in a paired t-test (p > 0.05), but population structure of L.microphthalma had a tendency to change: the genetic differentiation (Fst) among the five populations collected in 2010 were all insignificant (p > 0.05). However, differentiation (Fst) among some populations collected in 2020 were significant (p < 0.05), which indicated the population structure of L.microphthalma was changing. Correlation analysis indicated that negative correlations between the genetic diversities and geographical elevations among populations were significant for seven populations collected in 2020 (r = -0.819, p = 0.039), which means that populations of L.microphthalma in high elevation regions were more vulnerable than those in low elevation regions. Finally, some suggestions for conservation and restoration are proposed, such as artificial propagation, to prevent the further reduction of genetic diversity and population resources.

Dynamic genetic diversity and population structure of Coreiusguichenoti

To investigate the genetic effects on the population of Coreiusguichenoti 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.

Phylogeography of Schizopygopsis malacanthus Herzenstein (Cypriniformes, Cyprinidae) in relation to the tectonic events and Quaternary climatic oscillations in the Shaluli Mountains Region

The tectonic events and Quaternary climatic oscillations in the Shaluli Mountains (the margin of the southeastern Tibetan Plateau) had an extensive effect on the genetic structure and distribution patterns of this region's terrestrial fauna and flora. It is not yet clear whether similar mechanisms influence this region's fish fauna. Schizopygopsis malacanthus is limited to high-elevation rivers and lakes, and exhibits distinct adaptations to the mountains of, and near to, the Qinghai-Tibet Plateau (QTP). Therefore, this species is a good candidate for investigating patterns of genetic variation resulting from palaeoenvironmental fluctuations in the Shaluli Mountains (China). Here, we used microsatellite and mitochondrial DNA control region sequences to analyze six populations of S. malacanthus collected from the Jinsha and Yalong River drainages. Genealogical analyses identified four maternal lineages and perhaps even four putative species, of which the Ouqu River lineage played a pivotal role during the course of the species' evolution. Two lineages from the Yalong River drainage did not cluster together, whereas those from different drainages grouped together, suggesting tectonic event impacts that possibly altered regional river drainages have been highly influential in population connectivity and gene flow. Population genetic analysis indicated that the geographic barriers and this species preference for higher elevations both played key roles in the divergence of S. malacanthus populations. Demographic tests suggested large-scale spatial synchrony in population fluctuations of S. malacanthus, accompanying dramatic Pleistocene climatic oscillations. It appears that palaeoenvironmental changes in the Shaluli Mountains influenced the distribution and evolution of studied S. malacanthus populations, which provide important information about the factors that influenced the phylogeographic history of this region's fish fauna. Additionally, our study also has implications for ongoing conservation of this vulnerable fish.

Evolutionary History of Rhus chinensis (Anacardiaceae) From the Temperate and Subtropical Zones of China Based on cpDNA and Nuclear DNA Sequences and Ecological Niche Model

To explore the origin and evolution of local flora and vegetation, we examined the evolutionary history of Rhus chinensis, which is widely distributed in China’s temperate and subtropical zones, by sequencing three maternally inherited chloroplast DNAs (cpDNA: trnL-trnF, psbA-trnH, and rbcL) and the biparentally inherited nuclear DNA (nuDNA: LEAFY) from 19 natural populations of R. chinensis as well as the ecological niche modeling. In all, 23 chloroplast haplotypes (M1–M23) and 15 nuclear alleles (N1–N15) were detected. The estimation of divergence time showed that the most recent common ancestor dated at 4.2 ± 2.5 million years ago (Mya) from cpDNA, and the initial divergence of genotypes occurred at 4.8 ± 3.6 Mya for the nuDNA. Meanwhile, the multimodality mismatch distribution curves and positive Tajima’s D values indicated that R. chinensis did not experience population expansion after the last glacial maximum. Besides, our study was also consistent with the hypothesis that most refugia in the temperate and subtropical zones of China were in situ during the glaciation.

Phylogeography of the threatened tetraploid fish, Schizothorax waltoni, in the Yarlung Tsangpo River on the southern Qinghai-Tibet Plateau: implications for conservation

The phylogeography of Schizothorax waltoni, an endemic and endangered tetraploid schizothoracine fish in the Yarlung Tsangpo River (YLTR) on southern margin of Qinghai-Tibet Plateau (QTP), was investigated using two mitochondrial DNA regions and eleven microsatellite loci. Analyses of concatenated sequences of cytochrome b (1141 bp) and the control region (712 bp) revealed high haplotype diversity and moderate nucleotide diversity. High genetic diversity was observed based on microsatellite variation. Both mtDNA and microsatellite analyses revealed significant genetic differentiation between the eastern population (Mainling) and the other four populations to the west, and non-significant genetic differentiation amongst the three central populations in the west. Significant genetic differentiation was observed between the western population (Shigatse) and the three central populations based on microsatellite analyses alone. Bayesian skyline plot analyses showed that S. waltoni experienced a pronounced population expansion 0.05 to 0.10 Ma. Hierarchical structure analyses of microsatellite data indicated that S. waltoni could be split into three groups (western, central and eastern YLTR). The results indicate that three management units should be considered for S. waltoni. Our findings highlight the need for the conservation and effective management of S. waltoni, which is a key member of the endemic and highly threatened fishes of the QTP.

Low genetic diversity in broodstocks of endangered Chinese sucker, Myxocyprinusasiaticus: implications for artificial propagation and conservation

The releasing program of Chinese sucker (Myxocyprinusasiaticus) has been conducted for years in China. To prevent loss of genetic variation in wild populations, it is important to assess and monitor genetic diversity of broodstocks before release of offspring. Three broodstocks (Pixian Base of Sichuan Fisheries Research Institute, China (PBS), Yibin Base of Sichuan Fisheries Research Institute, China (YBS) and Yibin Rare Aquatic Animal Research Institute, China (YRA)) were investigated using mitochondrial control region and 12 microsatellites. The relatively low genetic diversities of these broodstocks were detected (PBS, haplotype diversity (h) = 0.877, observed heterozygosity (Ho) = 0.416; YBS, h = 0.812, Ho = 0.392; YRA, h = 0.818, Ho = 0.365). PBS showed higher Ho than YBS and YRA (P < 0.05). Genetic divergence (F_ST) based on microsatellites between PBS and YRA was significant (F_ST = 0.1270, P < 0.05), the same situation happened between YBS and YRA (F_ST = 0.1319, P < 0.05). However, divergence between PBS and YBS was not significant (F_ST = 0.0029, P > 0.05). Structure analysis revealed that YRA were distinct from PBS and YBS. Based on these results, it is important to propose some suggestions of genetic management for artificial propagation of Chinese sucker, such as broodstock exchange among hatcheries and broodstock supplement from wild.