| 1. |
- Gao, Hongkai, et al.
(author)
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Fish communities and diversity in river ecosystems on the Qinghai-Tibet Plateau revealed by environmental DNA (eDNA) method
- 2023
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In: Ecological Indicators. - 1470-160X. ; 156
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Journal article (peer-reviewed)abstract
- The Qinghai-Tibet Plateau (QTP) serves as the source of many large rivers in Asia, and also serves as a natural habitat for rare wildlife and a genetic reservoir for plateau species. The exceptional ecological environment of the QTP has fostered diverse fish species. However, due to climate change and human activities, fish species in this area are facing serious threats, while large spatial scale investigation is a big challenge. Environmental DNA (eDNA) metabarcoding, as an innovative monitoring technology, offers a simple, fast, and environmentally friendly approach to explore fish communities on the QTP. This study utilized eDNA technology to assess the diversity, composition, and potential environmental influences of riverine fish communities across the QTP. A total of 90 fish species were identified belonging to 79 genera, 34 families, and 18 orders. The dominant species were Schizothorax chongi, Gymnocypris przewalskii, Carassius carassius, and Botia striata. PCoA and ADONIS indicated significant differences among fish community in different river basins of the Qinghai-Tibet Plateau. Canonical correspondence analysis (CCA) revealed that the ratio of SRP to TP, average NDVI, average elevation, and proportion of bare land significantly influenced the distribution of fish community. This study provided a novel monitoring method and insight for fish communities and implied potential species invasion on the QTP.
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| 2. |
- Ni, Jingwen, et al.
(author)
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天山典型流域水文多要素模拟与气候变化影响预估
- 2023
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In: Journal of Glaciology and Geocryology. - 1000-0240. ; 45:6, s. 1875-1886
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Journal article (peer-reviewed)abstract
- Because of varied topography and landscape heterogeneity，Tianshan Mountain has extremely complex hydrological processes. Considering that the climate change poses a great threat to the water security，it’s necessary to simulate the change of water elements quantitatively and systematically along with elevation. In this study，we applied the modified FLEXG-Δh model to four classic river basins in Tianshan Mountain in consideration of glacier area changes. The results suggested that：（1）FLEXG-Δh model has high simulation accuracy for the historical runoff process because the average Kling-Gupta coefficient（IKGE）in calibration is 0. 75 and IKGE in validation is 0. 60. （2）Precipitation increases along with elevation while runoff and evaporation increase first but then decreased，with the maximum values at 4 000 m and 2 000 m respectively. The height zone with the greatest runoff is mainly affected by the glacier cover，while it is the distribution of forest for the greatest evaporation. （3）By 2100，the glaciers at low altitudes will melt significantly，while there will be a little melting above 4 500 m. Under SSP1-RCP2. 6 and SSP5-RCP8. 5 scenarios，145 and 222 glaciers will completely melt and the volume of glaciers will decrease 1. 81×104 km3（54% of the existing glaciers）and 2. 44×104 km3（73% of the existing glaciers），respectively. In the SSP5-RCP8. 5 scenario，the rise of temperature will increase the evap⁃ oration but lead to the fact that the runoff depth will decrease 0. 16~1. 40 mm·a-1 below 4 000 m and increase 0. 20~0. 67 mm·a-1 above 4 000 m ，causing the height of peak value will go up by about 500 m. Under SSP1-RCP2. 6 scenario，there will be few obvious changes. This study presented the vertical zonal law of hydrology and vegetation，and predicted the impact of global changes on the Tianshan Mountains，which provided theoreti⁃ cal support for water utilization and sustainable development.
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| 3. |
- Zhang, Hongkai, et al.
(author)
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Evidence of Site-Specific and Male-Biased Germline Mutation Rate in a Wild Songbird
- 2023
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In: Genome Biology and Evolution. - 1759-6653. ; 15:11
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Journal article (peer-reviewed)abstract
- Germline mutations are the ultimate source of genetic variation and the raw material for organismal evolution. Despite their significance, the frequency and genomic locations of mutations, as well as potential sex bias, are yet to be widely investigated in most species. To address these gaps, we conducted whole-genome sequencing of 12 great reed warblers (Acrocephalus arundinaceus) in a pedigree spanning 3 generations to identify single-nucleotide de novo mutations (DNMs) and estimate the germline mutation rate. We detected 82 DNMs within the pedigree, primarily enriched at CpG sites but otherwise randomly located along the chromosomes. Furthermore, we observed a pronounced sex bias in DNM occurrence, with male warblers exhibiting three times more mutations than females. After correction for false negatives and adjusting for callable sites, we obtained a mutation rate of 7.16 × 10−9 mutations per site per generation (m/s/g) for the autosomes and 5.10 × 10−9 m/s/g for the Z chromosome. To demonstrate the utility of species-specific mutation rates, we applied our autosomal mutation rate in models reconstructing the demographic history of the great reed warbler. We uncovered signs of drastic population size reductions predating the last glacial period (LGP) and reduced gene flow between western and eastern populations during the LGP. In conclusion, our results provide one of the few direct estimates of the mutation rate in wild songbirds and evidence for male-driven mutations in accordance with theoretical expectations.
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| 4. |
- Zhang, Hongkai
(author)
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Genomic studies of sex differences : On mutations, recombination, and sexual antagonism in songbirds
- 2023
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Doctoral thesis (other academic/artistic)abstract
- Many organisms have separate sexes, i.e., males and females. The presence of separate sexes causes sex-specific selection regimes and sexual antagonism, which can lead to sex differences in morphology, physiology, and behaviours. Sex and sex differences can be genetically governed and regulated by a pair of sex chromosomes (e.g., X and Y, or Z and W), on which there often are regions without recombination. In this thesis, I used genomic approaches to study sex differences in a songbird, the great reed warbler (Acrocephalus arundinaceus), in which male and females are monochromatic and genetically determined by a pair of sex chromosomes. The thesis starts with a study presenting and evaluating two alternative phylogenetic approaches (the expected likelihood weight (ELW) and the BEAST approach) to determine when different parts of the sex chromosomes stop recombining. My findings highlight the benefits of using fixed topologies to estimate the timing of recombination cessation as done by these approaches. Thereafter, I focus on molecular sex differences using genomic and bioinformatic methods to specifically investigate sex biases in de novo mutations and in recombination patterns, and search for sexually antagonistic loci in the genome.By using whole genome sequencing data from a three-generation pedigree of the great reed warbler, I found a strong sex bias in the numbers of de novo mutations, with males having three times as many mutations as females. Regarding recombination, I found no statistical support for sex-specific recombination rates, but the recombination landscape differed between sexes, with males having more crossovers towards the chromosome ends compared to females. Besides, I developed an interactive R application, RecView ShinyApp, to implement the methodology of locating recombination for future studies within similar topic.Finally, I used statistical approaches based on allele frequency differences and associations with sex per se to search for sexually antagonistic loci with whole genome sequencing data from 100 old great reed warblers that aged between 3 and 5 years. By comparing the top 100 SNPs with the strongest allelic differentiation between the sexes, and the most significant associations with sex, I discovered 50 overlapping SNPs that constitute candidates for future studies of sexual antagonistic selection. To conclude, this thesis has improved the methodology for studying the timing of recombination cessation on sex chromosomes as well as to study recombination per se, identified sex-specific de novo mutation rates and sexually dimorphic recombination landscapes, and obtained candidate loci for sexual antagonism.
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| 5. |
- Zhang, Hongkai, et al.
(author)
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RecView : an interactive R application for locating recombination positions using pedigree data
- 2023
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In: BMC Genomics. - 1471-2164. ; 24:1
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Journal article (peer-reviewed)abstract
- Background: Recombination reshuffles alleles at linked loci, allowing genes to evolve independently and consequently enhancing the efficiency of selection. This makes quantifying recombination along chromosomes an important goal for understanding how selection and drift are acting on genes and chromosomes. Results: We present RecView, an interactive R application and its homonymous R package, to facilitate locating recombination positions along chromosomes or scaffolds using whole-genome genotype data of a three-generation pedigree. RecView analyses and plots the grandparent-of-origin of all informative alleles along each chromosome of the offspring in the pedigree, and infers recombination positions with either of two built-in algorithms: one based on change in the proportion of the alleles with specific grandparent-of-origin, and one on the degree of continuity of alleles with the same grandparent-of-origin. RecView handles multiple offspring and chromosomes simultaneously, and all putative recombination positions are reported in base pairs together with an estimated precision based on the local density of informative alleles. We demonstrate RecView using genotype data of a passerine bird with an available reference genome, the great reed warbler (Acrocephalus arundinaceus), and show that recombination events can be located to specific positions. Conclusions: RecView is an easy-to-use and highly effective application for locating recombination positions with high precision. RecView is available on GitHub (https://github.com/HKyleZhang/RecView.git).
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