Population structure and genetic differentiation of tea green leafhopper, Empoasca (Matsumurasca) onukii, in China based on microsatellite markers

Zhang, Li; Wang, Fuping; Qiao, Li; Dietrich, Christopher H.; Matsumura, Masaya; Qin, Dao‐Zheng

doi:10.1038/s41598-018-37881-0

Cited by 12 publications

(34 citation statements)

References 43 publications

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“…Our analyses of phylogenetic and genetic structure confirmed the genetic differences between group I (samples from Yunnan) and the other groups, as shown in a previous study based on microsatellites [5]. However, this previous study suggested four main genetic groups (K = 4) [5]. This may be because the present study collected much more samples around China (54 locations in 22 provinces) than the other one (22 19 locations in 13 provinces) and used a greater number of genetic markers (whole-genome SNPs vs. microsatellite markers).…”

Section: Evolutionary History Is Inconsistent Between Tgl and Tea Cultivarssupporting

confidence: 90%

“…This may be because the present study collected much more samples around China (54 locations in 22 provinces) than the other one (22 19 locations in 13 provinces) and used a greater number of genetic markers (whole-genome SNPs vs. microsatellite markers). We observed that individuals from different groups were interspersed (Figures 4B and C), possibly reflecting gene flow across location, as observed in the previous study [5].…”

Section: Evolutionary History Is Inconsistent Between Tgl and Tea Cultivarssupporting

confidence: 80%

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Genomic variation in the tea leafhopper reveals the basis of adaptive evolution

Zhao

Shi

et al. 2021

Preprint

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The tea green leafhopper (TGL), Empoasca onukii, is of biological and economic interest. Despite numerous studies, the mechanisms underlying its adaptation and evolution remain enigmatic. Here, we used previously untapped genome and population genetics approaches to examine how this pest so rapidly has adapted to different environmental variables and thus has expanded geographically. We complete a chromosome-level assembly and annotation of the E. onukii genome, showing notable expansions of gene families associated with adaptation to chemoreception and detoxification. Genomic signals indicating balancing selection highlight metabolic pathways involved in adaptation to a wide range of tea varieties grown across ecologically diverse regions. Patterns of genetic variation among 54 E. onukii samples unveil the population structure and evolutionary history across different tea-growing regions in China. Our results demonstrate that the genomic change in key pathways, including those linked to metabolism, circadian rhythms and immune system function, may underlie the successful spread and adaptation of E. onukii. This work highlights the genetic and molecular bases underlying the evolutionary success of a species with broad economic impact, and provides insight into insect adaptation to host plants, which will ultimately facilitate more sustainable pest management.

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Section: Evolutionary History Is Inconsistent Between Tgl and Tea Cultivarssupporting

confidence: 90%

Section: Evolutionary History Is Inconsistent Between Tgl and Tea Cultivarssupporting

confidence: 80%

Genomic variation in the tea leafhopper reveals the basis of adaptive evolution

Zhao

Shi

et al. 2021

Preprint

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“…The observed level of heterozygosity was compared to the expected HetEQ using the intermediate two-phased model (TPM), due to its suitability for microsatellite data 81 , 82 . The TPM was applied with 95% of the mutations following a two-phase mutation pattern and a variance among multiple steps of 12 83 , with deviations from equilibrium determined using Wilcoxon’s Sign Rank tests, which are most suitable in instances where less than 20 loci are used 81 . Effective population size ( N e ) was estimated assuming a closed population with discrete generations and random variance in reproductive success using the program NeEstimator v2.01 84 .…”

Section: Methodsmentioning

confidence: 99%

Conservation concerns associated with low genetic diversity for K’gari–Fraser Island dingoes

Conroy

Lamont

Bridges

et al. 2021

Sci Rep

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The dingo population on world heritage-listed K’gari-Fraser Island (K’gari) is amongst the most well-known in Australia. However, an absence of population genetic data limits capacity for informed conservation management. We used 9 microsatellite loci to compare the levels of genetic diversity and genetic structure of 175 K’gari dingo tissue samples with 264 samples from adjacent mainland regions. Our results demonstrated that the K'gari population has significantly lower genetic diversity than mainland dingoes (AR, HE, PAR; p < 0.05) with a fourfold reduction in effective population size (Ne = 25.7 vs 103.8). There is also strong evidence of genetic differentiation between the island and mainland populations. These results are in accordance with genetic theory for small, isolated, island populations, and most likely the result of low initial diversity and founder effects such as bottlenecks leading to decreased diversity and drift. As the first study to incorporate a large sample set of K’gari dingoes, this provides invaluable baseline data for future research, which should incorporate genetic and demographic monitoring to ensure long-term persistence. Given that human-associated activities will continue to result in dingo mortality, it is critical that genetic factors are considered in conservation management decisions to avoid deleterious consequences for this iconic dingo population.

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“…Recent studies demonstrate the importance of quantifying phylogenetic relatedness between species to understand how evolutionary history and colonization dynamics influence diversity within communities [9,10]. Phylogenetic diversity (PD) also plays an important role in conservation [11], for better prioritizing phylogenetically diverse areas, as well as for preserving ecosystem function and associated ecosystem services [12].…”

Section: Introductionmentioning

confidence: 99%

Building a Robust, Densely-Sampled Spider Tree of Life for Ecosystem Research

et al. 2020

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Phylogenetic relatedness is a key diversity measure for the analysis and understanding of how species and communities evolve across time and space. Understanding the nonrandom loss of species with respect to phylogeny is also essential for better-informed conservation decisions. However, several factors are known to influence phylogenetic reconstruction and, ultimately, phylogenetic diversity metrics. In this study, we empirically tested how some of these factors (topological constraint, taxon sampling, genetic markers and calibration) affect phylogenetic resolution and uncertainty. We built a densely sampled, species-level phylogenetic tree for spiders, combining Sanger sequencing of species from local communities of two biogeographical regions (Iberian Peninsula and Macaronesia) with a taxon-rich backbone matrix of Genbank sequences and a topological constraint derived from recent phylogenomic studies. The resulting tree constitutes the most complete spider phylogeny to date, both in terms of terminals and background information, and may serve as a standard reference for the analysis of phylogenetic diversity patterns at the community level. We then used this tree to investigate how partial data affect phylogenetic reconstruction, phylogenetic diversity estimates and their rankings, and, ultimately, the ecological processes inferred for each community. We found that the incorporation of a single slowly evolving marker (28S) to the DNA barcode sequences from local communities, had the highest impact on tree topology, closely followed by the use of a backbone matrix. The increase in missing data resulting from combining partial sequences from local communities only had a moderate impact on the resulting trees, similar to the difference observed when using topological constraints. Our study further revealed substantial differences in both the phylogenetic structure and diversity rankings of the analyzed communities estimated from the different phylogenetic treatments, especially when using non-ultrametric trees (phylograms) instead of time-stamped trees (chronograms). Finally, we provide some recommendations on reconstructing phylogenetic trees to infer phylogenetic diversity within ecological studies.

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Population structure and genetic differentiation of tea green leafhopper, Empoasca (Matsumurasca) onukii, in China based on microsatellite markers

Cited by 12 publications

References 43 publications

Genomic variation in the tea leafhopper reveals the basis of adaptive evolution

Genomic variation in the tea leafhopper reveals the basis of adaptive evolution

Conservation concerns associated with low genetic diversity for K’gari–Fraser Island dingoes

Building a Robust, Densely-Sampled Spider Tree of Life for Ecosystem Research

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