Browsing by Author "Liu, Yang"
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- Carbon density in boreal forests responds non-linearly to temperature: an example from the Greater Khingan Mountains, northeast ChinaPublication . Liu, Yang; Trancoso, Ralph; Ma, Qin; Ciais, Philippe; Gouvêa, Lidiane; Yue, Chaofang; Assis, Jorge; Blanco, Juan A.Boreal forests play a crucial role in the global carbon (C) cycle and in climate stabilization. To better predict global C budgets, it is important to accurately estimate the size of forest C pools, and to identify the factors affecting them. We used national forest inventory data for the Greater Khingan Mountains, northeast China from 1999 to 2018 and 149 additional field plots to estimate C storage and its changes in forest vegetation, excluding C stored in soils, and to calculate the total C density in forest ecosystems. From 1999 to 2018, the vegetation C storage and density increased by 92.22 Tg and 4.30 Mg C ha-1, respectively, while the mean C sink was 4.61 Tg C yr-1. Carbon storage and density showed the same pattern, with the largest stocks in trees, followed by herbs, shrubs, and then litter. Mean C density was higher in mature forests than in young forests. The maximum C density was recorded in Populus davidiana forests, and was 2.2-times larger than in Betula davurica forests (the minimum). The mean (& PLUSMN; standard error) total C density of forest ecosystems was 111.3 & PLUSMN; 2.9 Mg C ha-1, including C stored in soils. Mean annual temperature (MAT) controlled total C density, as MAT had positive effects when it was lower than the temperature of the inflection point (-2.1 to -4.6 degrees C) and negative effects when it was above the inflection point. The rate of change in the total C density depended on the quantile points of the conditional distribution of total C density. Natural and anthropogenic disturbances had weaker effects on C density than temperature and precipitation. In conclusion, our results indicate that there might be a temperatureinduced pervasive decrease in C storage and an increase in tree mortality across Eastern Asian boreal forests with future climate warming.
- Mitochondrial genes from 18 angiosperms fill sampling gaps for phylogenomic inferences of the early diversification of flowering plantsPublication . Xue, Jia-Yu; Dong, Shan-Shan; Wang, Ming-Qiang; Song, Tian-Qiang; Zhou, Guang-Can; Li, Zhen; Van de Peer, Yves; Shao, Zhu-Qing; Wang, Wei; Chen, Min; Zhang, Yan-Mei; Sun, Xiao-Qin; Chen, Hong-Feng; Zhang, Yong-Xia; Zhang, Shou-Zhou; Chen, Fei; Zhang, Liang-Sheng; Cox, Cymon; Liu, Yang; Wang, Qiang; Hang, Yue-YuThe early diversification of angiosperms is thought to have been a rapid process, which may complicate phylogenetic analyses of early angiosperm relationships. Plastid and nuclear phylogenomic studies have raised several conflicting hypotheses regarding overall angiosperm phylogeny, but mitochondrial genomes have been largely ignored as a relevant source of information. Here we sequenced mitochondrial genomes from 18 angiosperms to fill taxon-sampling gaps in Austrobaileyales, magnoliids, Chloranthales, Ceratophyllales, and major lineages of eudicots and monocots. We assembled a data matrix of 38 mitochondrial genes from 107 taxa to assess how well mitochondrial genomic data address current uncertainties in angiosperm relationships. Although we recovered conflicting phylogenies based on different data sets and analytical methods, we also observed congruence regarding deep relationships of several major angiosperm lineages: Chloranthales were always inferred to be the sister group of Ceratophyllales, Austrobaileyales to mesangiosperms, and the unplaced Dilleniales was consistently resolved as the sister to superasterids. Substitutional saturation, GC compositional heterogeneity, and codon-usage bias are possible reasons for the noise/conflict that may impact phylogenetic reconstruction; and angiosperm mitochondrial genes may not be substantially affected by these factors. The third codon positions of the mitochondrial genes appear to contain more parsimony-informative sites than the first and second codon positions, and therefore produced better resolved phylogenetic relationships with generally strong support. The relationships among these major lineages remain incompletely resolved, perhaps as a result of the rapidity of early radiations. Nevertheless, data from mitochondrial genomes provide additional evidence and alternative hypotheses for exploring the early evolution and diversification of the angiosperms.
- Organellar phylogenomics of an emerging model system: Sphagnum (peatmoss)Publication . Shaw, A. Jonathan; Devos, Nicolas; Liu, Yang; Cox, C. J.; Goffinet, B.; Flatberg, Kjell Ivar; Shaw, BlankaBackground and Aims Sphagnum-dominated peatlands contain approx. 30 % of the terrestrial carbon pool in the form of partially decomposed plant material (peat), and, as a consequence, Sphagnum is currently a focus of studies on biogeochemistry and control of global climate. Sphagnum species differ in ecologically important traits that scale up to impact ecosystem function, and sequencing of the genome from selected Sphagnum species is currently under-way. As an emerging model system, these resources for Sphagnum will facilitate linking nucleotide variation to plant functional traits, and through those traits to ecosystem processes. A solid phylogenetic framework for Sphagnum is crucial to comparative analyses of species-specific traits, but relationships among major clades within Sphagnum have been recalcitrant to resolution because the genus underwent a rapid radiation. Herein a well-supported hypothesis for phylogenetic relationships among major clades within Sphagnum based on organellar genome sequences (plastid, mitochondrial) is provided.Methods We obtained nucleotide sequences (273 753 nucleotides in total) from the two organellar genomes from 38 species (including three outgroups). Phylogenetic analyses were conducted using a variety of methods applied to nucleotide and amino acid sequences. The Sphagnum phylogeny was rooted with sequences from the related Sphagnopsida genera, Eosphagnum and Flatbergium.Key Results Phylogenetic analyses of the data converge on the following subgeneric relationships: (Rigida (((Subsecunda) (Cuspidata)) ((Sphagnum) (Acutifolia))). All relationships were strongly supported. Species in the two major clades (i.e. Subsecunda + Cuspidata and Sphagnum + Acutifolia), which include > 90 % of all Sphagnum species, differ in ecological niches and these differences correlate with other functional traits that impact biogeochemical cycling. Mitochondrial intron presence/absence are variable among species and genera of the Sphagnopsida. Two new nomenclatural combinations are made, in the genera Eosphagnum and Flatbergium.Conclusions Newly resolved relationships now permit phylogenetic analyses of morphological, biochemical and ecological traits among Sphagnum species. The results clarify long-standing disagreements about subgeneric relationships and intrageneric classification.
- Resolution of the ordinal phylogeny of mosses using targeted exons from organellar and nuclear genomesPublication . Liu, Yang; Johnson, Matthew G.; Cox, Cymon; Medina, Rafael; Devos, Nicolas; Vanderpoorten, Alain; Hedenäs, Lars; Bell, Neil E.; Shevock, James R.; Aguero, Blanka; Quandt, Dietmar; Wickett, Norman J.; Shaw, A. Jonathan; Goffinet, B.Mosses are a highly diverse lineage of land plants, whose diversification, spanning at least 400 million years, remains phylogenetically ambiguous due to the lack of fossils, massive early extinctions, late radiations, limited morphological variation, and conflicting signal among previously used markers. Here, we present phylogenetic reconstructions based on complete organellar exomes and a comparable set of nuclear genes for this major lineage of land plants. Our analysis of 142 species representing 29 of the 30 moss orders reveals that relative average rates of non-synonymous substitutions in nuclear versus plastid genes are much higher in mosses than in seed plants, consistent with the emerging concept of evolutionary dynamism in mosses. Our results highlight the evolutionary significance of taxa with reduced morphologies, shed light on the relative tempo and mechanisms underlying major cladogenic events, and suggest hypotheses for the relationships and delineation of moss orders.