Montane cloud forests (MCFs), with their isolated nature, offer excellent opportunities to study ... more Montane cloud forests (MCFs), with their isolated nature, offer excellent opportunities to study the long-term effects of habitat fragmentation and the impacts of climate change. Quercus arbutifolia is a rare oak in MCFs of southern China and Vietnam. Its isolated populations, small population size and unique ecological niche make this species vulnerable to climate change and habitat loss. In this study, we used chloroplast (cpDNA) and nuclear (ITS) DNA sequences to investigate genetic divergence patterns and demographic history of five of the six known populations of Q. arbutifolia. Considering its small population size and fragmentation, Q. arbutifolia has unexpectedly high genetic diversity. The time since the most recent common ancestor of all cpDNA haplotypes was c. 10.25 Ma, and the rapid diversification of haplotypes occurred during the Quaternary. The maximum clade credibility chronogram of cpDNA haplotypes suggests that the DM population (Daming Mountain, Guangxi province) diverged early and rapidly became isolated from other populations. The Pearl River drainage system may have been the main geographic barrier between DM and other populations since the late Miocene. ITS data suggests that population expansion occurred during the last interglacial of the Quaternary. The combined effects of pre-Quaternary and Quaternary climatic and geological changes were the main drivers to the current genetic diversity and distribution pattern of Q. arbutifolia. Because of the high between-population genetic differentiation and high within-population genetic diversity of Q. arbutifolia, conservation efforts should be implemented for all populations, but if conservation resources are limited, populations DM, YZ (Mang Mountain, Hunan province) and ZZ (Daqin Mountain, Fujian province) should have priority.
Yunnan Plateau and its adjacent areas (YPA) with typical subtropical evergreen broad-leaved fores... more Yunnan Plateau and its adjacent areas (YPA) with typical subtropical evergreen broad-leaved forests (SEBF) have a rich number of vascular plants and high endemism. However, how ancient geological and climatic events in YPA have shaped the SEBF remains poorly understood. In this study, we integrated multilocus phylogeography, species distribution models (SDMs), and regression analysis to investigate the effects of paleoenvironmental changes on the contemporary genetic patterns of Quercus schottkyana, an en-demic and dominant evergreen oak in the YPA. A total of 380 samples were taken from 29 populations, covering the natural geographical distribution of Q. schottkyana. Molecular dating indicated that haplotype divergence began at late Miocene; this finding supported the hypothesis that major uplifting of YPA occurred after late Miocene, which led to the speciation and divergence of Q. schottkyana. Unlike previous biome reconstruction studies based on paly-nology data, our SDM analysis indicated that the distribution ranges of Q. schottkyana was comparatively stable after the Last Glacial Maximum (LGM) and experienced only a slight northward expansion afterward. Species genetic diversity showed a significant negative correlation to the habitat stability using regression analysis. These analyses suggested the admixture of individuals from genetically differentiated populations in the unstable habitats, which in turn increased the genetic diversity of Q. schottkyana. We also found that climate gradient along the latitude cline influenced the genetic structure of Q. schottkyana. This study provides new insights into the understanding of the evolutionary history of SEBF in YPA.
Some taxa are good indicators of particular climates because their distribution is determined by ... more Some taxa are good indicators of particular climates because their distribution is determined by specific temperature or precipitation requirements. Ring-cupped oaks (Quercus L. subgenus Cyclobalanopsis (Oersted) Schneider) are mainly distributed in tropical and subtropical climates in southeastern and eastern Asia. Recently, we collected many leaf fossils of ring-cupped oaks from the Upper Miocene Lawula Formation of eastern Tibet at an elevation of 3910 m. No modern species of ring-cupped oaks could survive at such a high elevation under current climate conditions. Based on detailed morphological comparisons with extant and fossil species, we propose a new species, Quercus tibetensis H. Xu, T. Su et Z.K. Zhou sp. nov., representing the first fossil record of ring-cupped oaks in Tibet. We investigated the climate requirements of the nearest living relatives (NLRs) of Q. tibetensis, and the ranges of mean annual temperature (MAT) and mean annual precipitation (MAP) are 7.9 °C to 21.7 °C, and 733.0 mm to 2536.8 mm, respectively, compared with the current climate at the fossil site with MAT of 4.4 °C and MAP of 516.5 mm. The NLRs of Q. tibetensis are distributed at elevations from 70 m to 3000 m, much lower than the fossil locality (3910 m). The altitudinal difference of the fossil site is 161 m to 3091 m between the late Miocene and today, even considering the warmer global climate during the late Mio-cene. Our results indicate that the climate conditions at the fossil site during the late Miocene were warmer and more humid than the current climate. Meanwhile, this new fossil finding corroborates results from previous studies that the southeastern part of the Qinghai–Tibetan Plateau experienced continued uplift since the late Miocene.
The commonly found oak species Quercus kerrii and the rare species Quercus austrocochinchinensis ... more The commonly found oak species Quercus kerrii and the rare species Quercus austrocochinchinensis (subgenus Cyclobalanopsis) are genetically close and found in sympatry in Indo-China with morphological evidences of hybridization. The two species provide an opportunity to investigate the mechanism of speciation and to study how species integrity is maintained in the subgenus Cyclobalanopsis. However, the genomic resources are lacking in Cyclobalanopsis to produce enough molecular markers. We performed RNA-seq on Q. austrocochinchinensis and Q. kerrii by pooling tissues of new and old leaves, roots, and stems. A total of 14,247,444/ 12,900,500 (Q. austrocochinchinensis/Q. kerrii) clean reads were obtained from 2 × 300 bp Illumina MiSeq sequencing platform. De novo assembly produced 79,312/81,921 contigs representing 49,845/50,767 unigenes. The Ka/Ks estimation and following enrichment analysis identified 24 genes. Most of them were related to biosynthesis and growth, which may be involved in the process of speciation. 5196/5021 primer pairs were successfully designated from 13,762/13,430 puta-tive loci with microsatellite repeats. We selectively screened 215 polymorphic simple sequence repeat (SSR) loci according to the list of 29,893 pairwise orthologous genes predicted by a reciprocal best hits algorithm. From the 215 loci, we selected 102 well-amplified SSR primers for poly-morphic SSR locus analysis. We found 18 highly polymor-phic loci and suitable for population genetic analysis, with 10 loci that had a diagnostic power that may be useful in studying hybridization. Finally, in silico PCR was performed using two Fagaceae species Quercus robur and Castanea mollissima. Our study provides a set of useful SSR markers and can enable further functional and comparative genomic research on the Quercus subgenus Cyclobalanopsis.
Montane cloud forests (MCFs), with their isolated nature, offer excellent opportunities to study ... more Montane cloud forests (MCFs), with their isolated nature, offer excellent opportunities to study the long-term effects of habitat fragmentation and the impacts of climate change. Quercus arbutifolia is a rare oak in MCFs of southern China and Vietnam. Its isolated populations, small population size and unique ecological niche make this species vulnerable to climate change and habitat loss. In this study, we used chloroplast (cpDNA) and nuclear (ITS) DNA sequences to investigate genetic divergence patterns and demographic history of five of the six known populations of Q. arbutifolia. Considering its small population size and fragmentation, Q. arbutifolia has unexpectedly high genetic diversity. The time since the most recent common ancestor of all cpDNA haplotypes was c. 10.25 Ma, and the rapid diversification of haplotypes occurred during the Quaternary. The maximum clade credibility chronogram of cpDNA haplotypes suggests that the DM population (Daming Mountain, Guangxi province) diverged early and rapidly became isolated from other populations. The Pearl River drainage system may have been the main geographic barrier between DM and other populations since the late Miocene. ITS data suggests that population expansion occurred during the last interglacial of the Quaternary. The combined effects of pre-Quaternary and Quaternary climatic and geological changes were the main drivers to the current genetic diversity and distribution pattern of Q. arbutifolia. Because of the high between-population genetic differentiation and high within-population genetic diversity of Q. arbutifolia, conservation efforts should be implemented for all populations, but if conservation resources are limited, populations DM, YZ (Mang Mountain, Hunan province) and ZZ (Daqin Mountain, Fujian province) should have priority.
Yunnan Plateau and its adjacent areas (YPA) with typical subtropical evergreen broad-leaved fores... more Yunnan Plateau and its adjacent areas (YPA) with typical subtropical evergreen broad-leaved forests (SEBF) have a rich number of vascular plants and high endemism. However, how ancient geological and climatic events in YPA have shaped the SEBF remains poorly understood. In this study, we integrated multilocus phylogeography, species distribution models (SDMs), and regression analysis to investigate the effects of paleoenvironmental changes on the contemporary genetic patterns of Quercus schottkyana, an en-demic and dominant evergreen oak in the YPA. A total of 380 samples were taken from 29 populations, covering the natural geographical distribution of Q. schottkyana. Molecular dating indicated that haplotype divergence began at late Miocene; this finding supported the hypothesis that major uplifting of YPA occurred after late Miocene, which led to the speciation and divergence of Q. schottkyana. Unlike previous biome reconstruction studies based on paly-nology data, our SDM analysis indicated that the distribution ranges of Q. schottkyana was comparatively stable after the Last Glacial Maximum (LGM) and experienced only a slight northward expansion afterward. Species genetic diversity showed a significant negative correlation to the habitat stability using regression analysis. These analyses suggested the admixture of individuals from genetically differentiated populations in the unstable habitats, which in turn increased the genetic diversity of Q. schottkyana. We also found that climate gradient along the latitude cline influenced the genetic structure of Q. schottkyana. This study provides new insights into the understanding of the evolutionary history of SEBF in YPA.
Some taxa are good indicators of particular climates because their distribution is determined by ... more Some taxa are good indicators of particular climates because their distribution is determined by specific temperature or precipitation requirements. Ring-cupped oaks (Quercus L. subgenus Cyclobalanopsis (Oersted) Schneider) are mainly distributed in tropical and subtropical climates in southeastern and eastern Asia. Recently, we collected many leaf fossils of ring-cupped oaks from the Upper Miocene Lawula Formation of eastern Tibet at an elevation of 3910 m. No modern species of ring-cupped oaks could survive at such a high elevation under current climate conditions. Based on detailed morphological comparisons with extant and fossil species, we propose a new species, Quercus tibetensis H. Xu, T. Su et Z.K. Zhou sp. nov., representing the first fossil record of ring-cupped oaks in Tibet. We investigated the climate requirements of the nearest living relatives (NLRs) of Q. tibetensis, and the ranges of mean annual temperature (MAT) and mean annual precipitation (MAP) are 7.9 °C to 21.7 °C, and 733.0 mm to 2536.8 mm, respectively, compared with the current climate at the fossil site with MAT of 4.4 °C and MAP of 516.5 mm. The NLRs of Q. tibetensis are distributed at elevations from 70 m to 3000 m, much lower than the fossil locality (3910 m). The altitudinal difference of the fossil site is 161 m to 3091 m between the late Miocene and today, even considering the warmer global climate during the late Mio-cene. Our results indicate that the climate conditions at the fossil site during the late Miocene were warmer and more humid than the current climate. Meanwhile, this new fossil finding corroborates results from previous studies that the southeastern part of the Qinghai–Tibetan Plateau experienced continued uplift since the late Miocene.
The commonly found oak species Quercus kerrii and the rare species Quercus austrocochinchinensis ... more The commonly found oak species Quercus kerrii and the rare species Quercus austrocochinchinensis (subgenus Cyclobalanopsis) are genetically close and found in sympatry in Indo-China with morphological evidences of hybridization. The two species provide an opportunity to investigate the mechanism of speciation and to study how species integrity is maintained in the subgenus Cyclobalanopsis. However, the genomic resources are lacking in Cyclobalanopsis to produce enough molecular markers. We performed RNA-seq on Q. austrocochinchinensis and Q. kerrii by pooling tissues of new and old leaves, roots, and stems. A total of 14,247,444/ 12,900,500 (Q. austrocochinchinensis/Q. kerrii) clean reads were obtained from 2 × 300 bp Illumina MiSeq sequencing platform. De novo assembly produced 79,312/81,921 contigs representing 49,845/50,767 unigenes. The Ka/Ks estimation and following enrichment analysis identified 24 genes. Most of them were related to biosynthesis and growth, which may be involved in the process of speciation. 5196/5021 primer pairs were successfully designated from 13,762/13,430 puta-tive loci with microsatellite repeats. We selectively screened 215 polymorphic simple sequence repeat (SSR) loci according to the list of 29,893 pairwise orthologous genes predicted by a reciprocal best hits algorithm. From the 215 loci, we selected 102 well-amplified SSR primers for poly-morphic SSR locus analysis. We found 18 highly polymor-phic loci and suitable for population genetic analysis, with 10 loci that had a diagnostic power that may be useful in studying hybridization. Finally, in silico PCR was performed using two Fagaceae species Quercus robur and Castanea mollissima. Our study provides a set of useful SSR markers and can enable further functional and comparative genomic research on the Quercus subgenus Cyclobalanopsis.
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