Figures S1 and S2, Table S1 and Methods from Divergence in cryptic leaf colour provides local camouflage in an alpine plant

Natural history of Corydalis and Apollo butterfly, population information and methods in determine pigment distributio

Molecular Phylogeny of <i>Gueldenstaedtia</i> and <i>Tibetia</i> (Fabaceae) and Their Biogeographic Differentiation within Eastern Asia

<div><p><i>Tibetia</i> and <i>Gueldenstaedtia</i> are two morphologically similar and small genera in Fabaceae, with distributions largely corresponding to the Sino-Himalayan and Sino-Japanese subkingdoms in eastern Asia, respectively. These two genera have confusing relationships based on morphology; therefore, we aimed to provide a clear understanding of their phylogenetic and biogeographic evolution within eastern Asia. In our investigations we included 88 samples representing five <i>Gueldenstaedtia</i> species, five <i>Tibetia</i> species, and outgroup species were sequenced using five markers (nuclear: ITS; chloroplast: <i>matK</i>, <i>trnL-F</i>, <i>psbA-trnH</i> and <i>rbcL</i>). Our phylogenetic results support (1) the monophyly of <i>Tibetia</i> and of <i>Gueldenstaedtia</i>, respectively; and (2) that <i>Tibetia</i> and <i>Gueldenstaedtia</i> are sister genera. Additionally, our data identified that <i>Tibetia</i> species had much higher sequence variation than <i>Gueldenstaedtia</i> species. Our results suggest that the two genera were separated from each other about 17.23 million years ago, which is congruent with the Himalayan orogeny and the uplift of the Tibetan Plateau in the mid Miocene. The divergence of <i>Tibetia</i> and <i>Gueldenstaedtia</i> is strongly supported by the separation of the Sino-Himalayan and Sino-Japanese region within eastern Asia. In addition, the habitat heterogeneity may accelerate the molecular divergence of <i>Tibetia</i> in the Sino-Himalayan region.</p></div

Sequence characteristics of <i>Tibetia</i> and <i>Gueldenstaedtia</i>, and sequence divergence values, which were estimated with pairwise distance.

<p>Sequence characteristics of <i>Tibetia</i> and <i>Gueldenstaedtia</i>, and sequence divergence values, which were estimated with pairwise distance.</p

Appendix S1 from Camouflaged plants are shorter than non-camouflaged plants in the alpine zone

Fig. S1. The phylogenetic tree of 621 seed plant of the alpine sub-nival belt from the Hengduan Mountains, with the information of plant colour (cryptic or not), plant height and mean elevation. Table S1 The results of the model selection based on MCMCglmm

Chronogram of <i>Tibetia</i>, <i>Gueldenstaedtia</i> and other related taxa from the Papilionoideae based on <i>matK</i> data.

<p>Divergence times are shown using the computer program BEAST. The calibration nodes 1 (34±0.1 Ma), 2 (56±0.1 Ma), and 3 (40±0.4 Ma) are marked by arrows based on the fossil records. The root of the tree was set to no more than 60 Ma.</p

Morphological, cytological and ecological differences among <i>Tibetia</i> and <i>Gueldenstaedtia</i> s.str. and <i>Chesneya</i> (Fabaceae).

<p>Morphological, cytological and ecological differences among <i>Tibetia</i> and <i>Gueldenstaedtia</i> s.str. and <i>Chesneya</i> (Fabaceae).</p

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A Bayesian consensus tree of <i>Tibetia</i> and <i>Gueldenstaedtia</i> based on combined nuclear and chloroplast sequences (tree length = 1224 steps, CI = 0.81, and RI = 0.97).

<p>The bootstrap values in 1000 replicates are shown under the branches and Bayesian posterior probabilities higher than 95% are indicated above the lines. Maximum likelihood topology is displayed at the bottom left.</p

Data_Sheet_1_Horizontal Gene Transfer From Bacteria and Plants to the Arbuscular Mycorrhizal Fungus Rhizophagus irregularis.PDF

<p>Arbuscular mycorrhizal fungi (AMF) belong to Glomeromycotina, and are mutualistic symbionts of many land plants. Associated bacteria accompany AMF during their lifecycle to establish a robust tripartite association consisting of fungi, plants and bacteria. Physical association among this trinity provides possibilities for the exchange of genetic materials. However, very few horizontal gene transfer (HGT) from bacteria or plants to AMF has been reported yet. In this study, we complement existing algorithms by developing a new pipeline, Blast2hgt, to efficiently screen for putative horizontally derived genes from a whole genome. Genome analyses of the glomeromycete Rhizophagus irregularis identified 19 fungal genes that had been transferred between fungi and bacteria/plants, of which seven were obtained from bacteria. Another 18 R. irregularis genes were found to be recently acquired from either plants or bacteria. In the R. irregularis genome, gene duplication has contributed to the expansion of three foreign genes. Importantly, more than half of the R. irregularis foreign genes were expressed in various transcriptomic experiments, suggesting that these genes are functional in R. irregularis. Functional annotation and available evidence showed that these acquired genes may participate in diverse but fundamental biological processes such as regulation of gene expression, mitosis and signal transduction. Our study suggests that horizontal gene influx through endosymbiosis is a source of new functions for R. irregularis, and HGT might have played a role in the evolution and symbiotic adaptation of this arbuscular mycorrhizal fungus.</p

The distribution area and sample sites of <i>Tibetia</i> and <i>Gueldenstaedtia</i> in eastern Asia.

<p>The map is from the website <a href="http://www.naturalearthdata.com/" target="_blank">http://www.naturalearthdata.com/</a>.</p