Diverse assemblages of seed-dispersing megafauna once existed in Asian rainforests, but are now almost solely represented by elephants. Asia’s rhinos persist in remnant, ecologically-extinct populations and the most threatened of these is the Sumatran rhino, Dicerorhinus sumatrensis. To understand the seed dispersal role of Sumatran rhinos, we consolidated information on fruit consumption, seed dispersal and fruit traits from a two-month field study (Sumatra), local ecological knowledge (Peninsular Malaysia), and published and unpublished accounts. We evaluated...

Understanding the mechanisms that drive community assembly in species-rich tropical forest remains a fundamental challenge in ecology. Here, we integrated multivariate functional trait dimensions, phylogeny, and metabolomics to test fundamental predictions concerning the role of differentiation with respect to abiotic and biotic niche axes in the maintenance of high local diversity of woody plants in the Euphorbiaceae. We measured 40 functional traits related to resource acquisition, photosynthetic capacity, hydraulic efficiency, and secondary-metabolite profiles generated using...

1. Lianas account for a small fraction of forest biomass, but their contribution to leaf or litter biomass and thus to food webs can be substantial. Globally liana exhibit fast life history traits. Thus liana litter may decompose faster than tree litter, and could enhance decomposition of tree litter (complementarity effect). The differences in decomposition may also vary with mesofauna access or across forest communities. The contribution of these factors to nutrient biogeochemical cycling is...

Bats provide an excellent case study for studying evolution due to their remarkable flight and echolocation capabilities. In this study, we sought to understand the phenotypic evolution of key traits in Rhinolophidae (horseshoe bats) using phylogenetic comparative methods. We aim to test the phylogenetic signals of traits and evaluated the best-fit evolutionary models given the data for each trait considering different traits may evolve under different models (i.e., Brownian Motion (BM), Ornstein-Uhlenbeck (OU) and Early...

Additional file 23: Table S1. Clinicopathologic Information and Multi-omics Data in PDAC Cohort. Table S1A Multi-omics information of PDAC cohort. Table S1B Clinicopathologic information of the 229 PDAC.

Genetic variation determines the evolutionary potential of a species and is vital for fully understanding the evolution of a species, as well as for developing optimal conservation strategies. Horsfieldia tetratepala is an economically important rainforest tree which has declined steadily, mainly though habitat destruction, and an endangered, narrow endemic in China where it is also classified as a Plant Species with Extremely Small Populations (PSESP). Effective conservation strategies for H. tetratepala are required urgently, but...

Conspecific negative distance- and density-dependence is believed to be one of the most important mechanisms controlling forest community assembly and species diversity globally. Plant pathogens, and insect and mammalian herbivores, are the most common natural enemy types that have been implicated in this phenomenon, but their general effects at different plant life stages are still unclear. Here, we conduct a meta-analysis of studies that involved robust manipulative experiments, using fungicides, insecticides, or exclosures, to assess...

1. The coexistence of closely related species is key to understanding the nature of biodiversity hotspots where in situ diversification has yielded rich communities of close relatives. Limiting similarity predicts that co-occurring species are differentiated in their niches; identifying the axes of differentiation in sympatric close relatives can thus help reveal the eco-evolutionary dynamics of community assembly. For flowering plants, these axes may be temporal (related to reproductive phenology) or morphological (related to functional traits)....

Additional file 26: Table S4. The Effects of Diabetes on the Proteogenomic Characteristics of PDAC. Table S4A Mutations and arm events information in PDAC patients with or without diabetes history. Table S4B Matrix of differential pathway enrichment in patients with or without diabetes history at mRNA level. Table S4C Matrix of differential pathway enrichment in patients with or without diabetes history at protein level.

Bottom-up effects from host plants and top-down effects from predators on herbivore abundance and distribution vary with physical environment, plant chemistry, predator and herbivore trait and diversity. Tri-trophic interactions in tropical ecosystems may follow different patterns from temperate ecosystems due to differences in above abiotic and biotic conditions. We sampled leaf-chewing larvae of Lepidoptera (caterpillars) from a dominant host tree species in a seasonal rainforest in Southwest China. We reared out parasitoids and grouped herbivores...

Additional file 23: Table S1. Clinicopathologic Information and Multi-omics Data in PDAC Cohort. Table S1A Multi-omics information of PDAC cohort. Table S1B Clinicopathologic information of the 229 PDAC.

Additional file 24: Table S2. The Impacts of Somatic Copy Number Alterations in PDAC Cohort. Table S2A Matrix of amplification peaks, followed by the genes contained in them, 95% confidence level. Table S2B Matrix of deletion peaks, followed by the genes contained in them, 95% confidence level. Table S2C Matrix of the top 10 mutated genes in PDAC of Fudan cohort. Table S2D Matrix of the 10 mutated genes used in Figure 1C of ICGC,...

Additional file 26: Table S4. The Effects of Diabetes on the Proteogenomic Characteristics of PDAC. Table S4A Mutations and arm events information in PDAC patients with or without diabetes history. Table S4B Matrix of differential pathway enrichment in patients with or without diabetes history at mRNA level. Table S4C Matrix of differential pathway enrichment in patients with or without diabetes history at protein level.

Additional file 28: Table S6. Proteomic Subtypes of PDAC Patients. Table S6A Proteomic subtypes, transcriptomic subtypes and phosphoproteomic subtypes of PDAC patients. Table S6B A list of differentially expressed proteins among three subtypes. Table S6C Pathway alterations in the proteomic subtypes of the PDAC cohort. Table S6D Matrix of protein expression and kinase activity of kinase activated in S-III. Table S6E Matrix of differential pathway enrichment between patients located in H-PDAC and BT-PDAC. Table S6F...

Additional file 29: Table S7. Characterization of Immune Infiltration in PDAC. Table S7A Matrix of xCell signatures significantly altered in 5 immune subgroups. Table S7B Matrix describing the expression of proteins in 5 immune subgroups. Table S7C Matrix of GSVA scores of pathways significantly altered in 5 immune subgroups, transcriptome level. Table S7D Matrix of amplification/deletion events of genes in 5 immune subgroups. Table S7E Matrix describing the expression of proteins involved in TCA cycle.

Additional file 30: Table S8. HOGA1 inactivation promotes pancreatic cancer growth through activating LARP7-CDK1 pathway. Table S8A Quantified western blot results of 12 pairs of samples. Table S8B Proliferation of PANC-1 and BxPC-3 cells associated with HOGA1 knocked down. Table S8C Proliferation of PANC-1 and BxPC-3 cells associated with HOGA1 overexpressed. Table S8D Proliferation of PANC-1 and BxPC-3 cells associated with metabolic enzyme treatment. Table S8E A list of 773 different proteins detected in PANC-1...

1. Protected Areas (PAs) are a cornerstone of global conservation strategies. PAs, however, are not equally effective for all threatened taxa, and it is important to understand taxa-specific effectiveness of PAs networks. 2. In this study we evaluate the role of the PAs network on the protection of Asian elephants (Elephas maximus) and their habitats in Southeast Asia’s Sundaic region. Since Asian elephants tend to prefer secondary forests or forest gaps, we predicted that PAs...

Assessing the heat tolerance (CTmax) of organisms is central to understand the impact of climate change on biodiversity. While both environment and evolutionary history affect CTmax, it is unclear how these factors and their interplay influence ecological interactions, communities, and ecosystems under climate change. We collected and reared caterpillars and parasitoids from canopy and ground layers in different seasons in a tropical rainforest. We tested the CTmax and Thermal Safety Margins (TSM) of these food...

Additional file 30: Table S8. HOGA1 inactivation promotes pancreatic cancer growth through activating LARP7-CDK1 pathway. Table S8A Quantified western blot results of 12 pairs of samples. Table S8B Proliferation of PANC-1 and BxPC-3 cells associated with HOGA1 knocked down. Table S8C Proliferation of PANC-1 and BxPC-3 cells associated with HOGA1 overexpressed. Table S8D Proliferation of PANC-1 and BxPC-3 cells associated with metabolic enzyme treatment. Table S8E A list of 773 different proteins detected in PANC-1...

The molecular events underlying the lactation curve of dairy animals have long been a biological conundrum for mammary biologists, and a cause of a considerable loss of income for dairy farmers. To better understand the regulatory mechanisms and developmental processes of the mammary gland during the lactation cycle, whole-genome transcriptome profiles of bovine mammary tissues at five different lactation stages were investigated using the RNA-Seq technique. The differentially expressed genes were identified by comparing different...

Additional file 25: Table S3. Integrated Multi-omics Features in Tumor Tissues Compared with NATs of the PDAC. Table S3A Matrix of 7,055 protein groups and their relative intensities in at least 1/6 of the samples (226 tumors and 220 NATs). Table S3B 19,992 mRNA and their ratio of tumors/NATs (54 tumors and 51 NATs). Table S3C A list of protein identified both in protein and mRNA level. Table S3D A list of phosphosites used for...

Additional file 25: Table S3. Integrated Multi-omics Features in Tumor Tissues Compared with NATs of the PDAC. Table S3A Matrix of 7,055 protein groups and their relative intensities in at least 1/6 of the samples (226 tumors and 220 NATs). Table S3B 19,992 mRNA and their ratio of tumors/NATs (54 tumors and 51 NATs). Table S3C A list of protein identified both in protein and mRNA level. Table S3D A list of phosphosites used for...

Additional file 28: Table S6. Proteomic Subtypes of PDAC Patients. Table S6A Proteomic subtypes, transcriptomic subtypes and phosphoproteomic subtypes of PDAC patients. Table S6B A list of differentially expressed proteins among three subtypes. Table S6C Pathway alterations in the proteomic subtypes of the PDAC cohort. Table S6D Matrix of protein expression and kinase activity of kinase activated in S-III. Table S6E Matrix of differential pathway enrichment between patients located in H-PDAC and BT-PDAC. Table S6F...

The molecular events underlying the lactation curve of dairy animals have long been a biological conundrum for mammary biologists, and a cause of a considerable loss of income for dairy farmers. To better understand the regulatory mechanisms and developmental processes of the mammary gland during the lactation cycle, whole-genome transcriptome profiles of bovine mammary tissues at five different lactation stages were investigated using the RNA-Seq technique. The differentially expressed genes were identified by comparing different...

Additional file 24: Table S2. The Impacts of Somatic Copy Number Alterations in PDAC Cohort. Table S2A Matrix of amplification peaks, followed by the genes contained in them, 95% confidence level. Table S2B Matrix of deletion peaks, followed by the genes contained in them, 95% confidence level. Table S2C Matrix of the top 10 mutated genes in PDAC of Fudan cohort. Table S2D Matrix of the 10 mutated genes used in Figure 1C of ICGC,...