Effects of lianas on forest biogeochemistry during their lives and afterlives.

Climate change and other anthropogenic disturbances are increasing liana abundance and biomass in many tropical and subtropical forests. While the effects of living lianas on species diversity, ecosystem carbon, and nutrient dynamics are receiving increasing attention, the role of dead lianas in forest ecosystems has been little studied and is poorly understood. Trees and lianas coexist as the major woody components of forests worldwide, but they have very different ecological strategies, with lianas relying on trees for mechanical support. Consequently, trees and lianas have evolved highly divergent stem, leaf, and root traits. Here we show that this trait divergence is likely to persist after death, into the afterlives of these organs, leading to divergent effects on forest biogeochemistry. We introduce a conceptual framework combining horizontal, vertical, and time dimensions for the effects of liana proliferation and liana tissue decomposition on ecosystem carbon and nutrient cycling. We propose a series of empirical studies comparing traits between lianas and trees to answer questions concerning the influence of trait afterlives on the decomposability of liana and tree organs. Such studies will increase our understanding of the contribution of lianas to terrestrial biogeochemical cycling, and help predict the effects of their increasing abundance.

Hemiepiphytic figs kill their host trees: acquiring phosphorus is a driving factor.

Hemiepiphytic figs killing their host trees is an ecological process unique to the tropics. Yet the benefits and adaptive strategies of their special life history remain poorly understood. We compared leaf phosphorus (P) content data of figs and palms worldwide, and functional traits and substrate P content of hemiepiphytic figs (Ficus tinctoria), their host palm and nonhemiepiphytic conspecifics at different growth stages in a common garden. We found that leaf P content of hemiepiphytic figs and their host palms significantly decreased when they were competing for soil resources, but that of hemiepiphytic figs recovered after host death. P availability in the canopy humus and soil decreased significantly with the growth of hemiepiphytic figs. Functional trait trade-offs of hemiepiphytic figs enabled them to adapt to the P shortage while competing with their hosts. From the common garden to a global scale, the P competition caused by high P demand of figs may be a general phenomenon. Our results suggest that P competition is an important factor causing host death, except for mechanically damaging and shading hosts. Killing hosts benefits hemiepiphytic figs by reducing interspecific P competition and better acquiring P resources in the P-deficient tropics, thereby linking the life history strategy of hemiepiphytic figs to the widespread P shortage in tropical soils.

Plastid NDH Pseudogenization and Gene Loss in a Recently Derived Lineage from the Largest Hemiparasitic Plant Genus Pedicularis (Orobanchaceae).

The plastid genome (plastome) is highly conserved in both gene order and content and has a lower mutation rate than the nuclear genome. However, the plastome is more variable in heterotrophic plants. To date, most such studies have investigated just a few species or only holoheterotrophic groups, and few have examined plastome evolution in recently derived lineages at an early stage of transition from autotrophy to heterotrophy. In this study, we investigated the evolutionary dynamics of plastomes in the monophyletic and recently derived Pedicularis sect. Cyathophora (Orobanchaceae). We obtained 22 new plastomes, 13 from the six recognized species of section Cyathophora, six from hemiparasitic relatives and three from autotrophic relatives. Comparative analyses of gene content, plastome structure and selection pressure showed dramatic differences among species in section Cyathophora and in Pedicularis as a whole. In comparison with autotrophic relatives and other Pedicularis spp., we found that the inverted repeat (IR) region in section Cyathophora had expansions to the small single-copy region, with a large expansion event and two independent contraction events. Moreover, NA(D)H dehydrogenase, accD and ccsA have lost function multiple times, with the function of accD being replaced by nuclear copies of an accD-like gene in Pedicularis spp. The ccsA and ndhG genes may have evolved under selection in association with IR expansion/contraction events. This study is the first to report high plastome variation in a recently derived lineage of hemiparasitic plants and therefore provides evidence for plastome evolution in the transition from autotrophy to heterotrophy.

Enemies mediate distance- and density-dependent mortality of tree seeds and seedlings: a meta-analysis of fungicide, insecticide and exclosure studies.

Conspecific negative distance- and density-dependence is often assumed 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 and exclosures, to assess the contributions of different natural enemy types to distance- and density-dependent effects at seed and seedling stages. We found that distance- and density-dependent mortality caused by natural enemies was most likely at the seedling stage and was greater at higher mean annual temperatures. Conspecific negative distance- and density-dependence at the seedling stage is significantly weakened when fungicides were applied. By contrast, negative conspecific distance- and density-dependence is not a general pattern at the seed stage. High seed mass reduced distance- and density-dependent mortality at the seed stage. Seed studies excluding only large mammals found significant negative conspecific distance-dependent mortality, but exclusion of all mammals resulted in a non-significant effect of conspecifics. Our study suggests that plant pathogens are a major cause of distance- and density-dependent mortality at the seedling stage, while the impacts of herbivores on seedlings have been understudied. At the seed stage, large and small mammals, respectively, weaken and enhance negative conspecific distance-dependent mortality. Future research should identify specific agents of mortality, investigate the interactions among different enemy types and assess how global change may affect natural enemies and thus influence the strength of conspecific distance- and density-dependence.

Conservation planning on China's borders with Myanmar, Laos, and Vietnam.

Transboundary conservation is playing an increasingly important role in maintaining ecosystem integrity and halting biodiversity loss caused by anthropogenic activities. However, lack of information on species distributions in transboundary regions and understanding of the threats in these areas impairs conservation. We developed a spatial conservation plan for the transboundary areas between Yunnan province, southwestern China, and neighboring Myanmar, Laos, and Vietnam in the Indo-Burma biodiversity hotspot. To identify priority areas for conservation and restoration, we determined species distribution patterns and recent land-use changes and examined the spatiotemporal dynamics of the connected natural forest, which supports most species. We assessed connectivity with equivalent connected area (ECA), which is the amount of reachable habitat for a species. An ECA incorporates the presence of habitat in a patch and the amount of habitat in other patches within dispersal distance. We analyzed 197,845 locality records from specimen collections and monographs for 21,004 plant and vertebrate species. The region of Yunnan immediately adjacent to the international borders had the highest species richness, with 61% of recorded species and 56% of threatened vertebrates, which suggests high conservation value. Satellite imagery showed the area of natural forest in the border zone declined by 5.2% (13,255 km2 ) from 1995 to 2018 and monoculture plantations increased 92.4%, shrubland 10.1%, and other cropland 6.2%. The resulting decline in connected natural forest reduced the amount of habitat, especially for forest specialists with limited dispersal abilities. The most severe decline in connectivity was along the Sino-Vietnamese border. Many priority areas straddle international boundaries, indicating demand and potential for establishing transboundary protected areas. Our results illustrate the importance of bi- and multilateral cooperation to protect biodiversity in this region and provide guidance for future conservation planning and practice.

Planeación de la Conservación en las Fronteras de China con Myanmar, Laos y Vietnam Resumen La conservación transfronteriza cada vez juega un papel más importante en la preservación de la integridad del ecosistema y en el freno a la pérdida local de la biodiversidad causada por las actividades antropogénicas. Sin embargo, la falta de información sobre la distribución de las especies en las regiones transfronterizas y de la comprensión de las amenazas en estas áreas obstaculiza la conservación. Desarrollamos un plan de conservación espacial para las áreas transfronterizas entre la provincia de Yunnan, al suroeste de China, y los países vecinos Myanmar, Laos y Vietnam localizadas en el punto caliente de biodiversidad Indo-Burma. Para identificar las áreas prioritarias para la conservación y la restauración, determinamos los patrones de distribución de las especies y los recientes cambios en el uso de suelo y examinamos las dinámicas espaciotemporales del bosque natural conectado, el cual mantiene a la mayoría de las especies. Evaluamos la conectividad con el área equivalente conectada (AEC), que es la cantidad de hábitat accesible para una especie. Un AEC incorpora la presencia del hábitat en un fragmento y la cantidad de hábitat en otros fragmentos dentro de la distancia de dispersión. Analizamos 197,845 registros de localidades desde colecciones de especímenes y monografías para 21,004 especies de plantas y de vertebrados. La región de Yunnan inmediatamente adyacente a las fronteras internacionales tuvo la riqueza de especies más alta con el 61% de las especies registradas y el 56% de los vertebrados amenazados, lo que sugiere un elevado valor de conservación. Las imágenes satelitales mostraron que el área del bosque natural en la zona fronteriza declinó en un 5.2% (13,255 km2 ) entre 1995 y 2018 y que los sembradíos de monocultivos incrementaron en un 92.4%, los matorrales en un 10.1% y otras tierras de cultivo en un 6.2%. La declinación resultante en el bosque natural conectado redujo la cantidad del hábitat, especialmente para los especialistas del bosque con habilidades limitadas de dispersión. La declinación más grave en la conectividad ocurrió a lo largo de la frontera entre China y Vietnam. Muchas áreas prioritarias atraviesan las fronteras internacionales, lo que indica una demanda y un potencial para el establecimiento de áreas protegidas transfronterizas. Nuestros resultados ejemplifican la importancia de la cooperación bi- y multilateral para proteger la biodiversidad en esta región y proporciona información para la planeación y práctica de la conservación en el futuro.

Climate change promotes transitions to tall evergreen vegetation in tropical Asia.

Vegetation in tropical Asia is highly diverse due to large environmental gradients and heterogeneity of landscapes. This biodiversity is threatened by intense land use and climate change. However, despite the rich biodiversity and the dense human population, tropical Asia is often underrepresented in global biodiversity assessments. Understanding how climate change influences the remaining areas of natural vegetation is therefore highly important for conservation planning. Here, we used the adaptive Dynamic Global Vegetation Model version 2 (aDGVM2) to simulate impacts of climate change and elevated CO2 on vegetation formations in tropical Asia for an ensemble of climate change scenarios. We used climate forcing from five different climate models for representative concentration pathways RCP4.5 and RCP8.5. We found that vegetation in tropical Asia will remain a carbon sink until 2099, and that vegetation biomass increases of up to 28% by 2099 are associated with transitions from small to tall woody vegetation and from deciduous to evergreen vegetation. Patterns of phenology were less responsive to climate change and elevated CO2 than biomes and biomass, indicating that the selection of variables and methods used to detect vegetation changes is crucial. Model simulations revealed substantial variation within the ensemble, both in biomass increases and in distributions of different biome types. Our results have important implications for management policy, because they suggest that large ensembles of climate models and scenarios are required to assess a wide range of potential future trajectories of vegetation change and to develop robust management plans. Furthermore, our results highlight open ecosystems with low tree cover as most threatened by climate change, indicating potential conflicts of interest between biodiversity conservation in open ecosystems and active afforestation to enhance carbon sequestration.

Drivers of bird beta diversity in the Western Ghats-Sri Lanka biodiversity hotspot are scale dependent: roles of land use, climate, and distance.

In the last 50 years, intensive agriculture has replaced large tracts of rainforests. Such changes in land use are driving niche-based ecological processes that determine local community assembly. However, little is known about the relative importance of these anthropogenic niche-based processes, in comparison to climatic niche-based processes and spatial processes such as dispersal limitation. In this study, we use a variation partitioning approach to determine the relative importance of land-use change (ranked value of forest loss), climatic variation (temperature and precipitation), and distance between transects, on bird beta diversity at two different spatial scales within the Western Ghats-Sri Lanka biodiversity hotspot. Our results show that the drivers of local community assembly are scale dependent. At the larger spatial scale, distance was more important than climate and land use for bird species composition, suggesting that dispersal limitation over the Palk Strait, which separates the Western Ghats and Sri Lanka, is the main driver of local community assembly. At the smaller scale, climate was more important than land use, suggesting the importance of climatic niches. Therefore, to conserve all species in a biodiversity hotspot, it is important to consider geographic barriers and climatic variation along with land-use change.

Chemical Composition and the Cytotoxic, Antimicrobial, and Anti-Inflammatory Activities of the Fruit Peel Essential Oil from Spondias pinnata (Anacardiaceae) in Xishuangbanna, Southwest China.

Spondias pinnata (Linn. f.) Kurz (Anacardiaceae) is widely distributed in tropical Asia, where it is commonly used as a vegetable and fruit, and is attracting increasing research attention. In this study, we investigated the chemical composition and the cytotoxic, antimicrobial, and anti-inflammatory activities of the fruit peel essential oil of S. pinnata (EOSP), which has been consumed as a medicine and condiment in Xishuangbanna, southwest China. A total of 40 components were identified by Gas Chromatography/Mass spectrometry (GC-MS), representing 95.19% of the EOSP, with furfural (17.14%), α-terpineol (13.09%), and ethyl benzoate (9.05%) as the main constituents. EOSP has moderate cytotoxic activity against five cancer cells and obvious antimicrobial activity against five pathogenic strains. In particular, EOSP (Minimal Inhibitory and Fungicidal Concentration, MIC and MFC, 16‒32 µg/mL) showed a 32-times higher inhibition effect against Aspergillus fumigatus than the positive control Tigecycline (MIC and MBC 512‒1024 µg/mL). EOSP also showed strong anti-inflammatory activity by significantly inhibiting nitric oxide (NO) production induced by lipopolysaccharide (LPS) in RAW 264.7 cell lines at 0.08‱, with no effect on cell viability. These bioactivities of S. pinnata fruit peel validate its traditional uses and suggest that it could be a new source of natural antimicrobial and anti-inflammatory agents for food or medical industries.

Exceptionally high rates of positive selection on the rbcL gene in the genus Ilex (Aquifoliaceae).

BACKGROUND: The genus Ilex (Aquifoliaceae) has a near-cosmopolitan distribution in mesic habitats from tropical to temperate lowlands and in alpine forests. It has a high rate of hybridization and plastid capture, and comprises four geographically structured plastid groups. A previous study showed that the plastid rbcL gene, coding for the large subunit of Rubisco, has a particularly high rate of non-synonymous substitutions in Ilex, when compared with other plant lineages. This suggests a strong positive selection on rbcL, involved in yet unknown adaptations. We therefore investigated positive selection on rbcL in 240 Ilex sequences from across the global range. RESULTS: The rbcL gene shows a much higher rate of positive selection in Ilex than in any other plant lineage studied so far (> 3000 species) by tests in both PAML and SLR. Most positively selected residues are on the surface of the folded large subunit, suggesting interaction with other subunits and associated chaperones, and coevolution between positively selected residues is prevalent, indicating compensatory mutations to recover molecular stability. Coevolution between positively selected sites to restore global stability is common. CONCLUSIONS: This study has confirmed the predicted high incidence of positively selected residues in rbcL in Ilex, and shown that this is higher than in any other plant lineage studied so far. The causes and consequences of this high incidence are unclear, but it is probably associated with the similarly high incidence of hybridization and introgression in Ilex, even between distantly related lineages, resulting in large cytonuclear discordance in the phylogenies.

Horizontal and vertical species turnover in tropical birds in habitats with differing land use.

Large tracts of tropical rainforests are being converted into intensive agricultural lands. Such anthropogenic disturbances are known to reduce species turnover across horizontal distances. But it is not known if they can also reduce species turnover across vertical distances (elevation), which have steeper climatic differences. We measured turnover in birds across horizontal and vertical sampling transects in three land-use types of Sri Lanka: protected forest, reserve buffer and intensive-agriculture, from 90 to 2100 m a.s.l. Bird turnover rates across horizontal distances were similar across all habitats, and much less than vertical turnover rates. Vertical turnover rates were not similar across habitats. Forest had higher turnover rates than the other two habitats for all bird species. Buffer and intensive-agriculture had similar turnover rates, even though buffer habitats were situated at the forest edge. Therefore, our results demonstrate the crucial importance of conserving primary forest across the full elevational range available.

Orchid conservation in the biodiversity hotspot of southwestern China.

Xishuangbanna is on the northern margins of tropical Asia in southwestern China and has the largest area of tropical forest remaining in the country. It is in the Indo-Burma hotspot and contains 16% of China's vascular flora in <0.2% of the country's total area (19,690 km(2) ). Rapid expansion of monoculture crops in the last 20 years, particularly rubber, threatens this region's exceptional biodiversity. To understand the effects of land-use change and collection on orchid species diversity and determine protection priorities, we conducted systematic field surveys, observed markets, interviewed orchid collectors, and then determined the conservation status of all orchids. We identified 426 orchid species in 115 genera in Xishuangbanna: 31% of all orchid species that occur in China. Species richness was highest at 1000-1200 m elevation. Three orchid species were assessed as possibly extinct in the wild, 15 as critically endangered, 82 as endangered, 124 as vulnerable, 186 as least concern, and 16 as data deficient. Declines over 20 years in harvested species suggested over-collection was the major threat, and utility value (i.e., medicinal or ornamental value) was significantly related to endangerment. Expansion of rubber tree plantations was less of a threat to orchids than to other taxa because only 75 orchid species (17.6%) occurred below the 1000-m-elevation ceiling for rubber cultivation, and most of these (46) occurred in nature reserves. However, climate change is projected to lift this ceiling to around 1300 m by 2050, and the limited area at higher elevations reduces the potential for upslope range expansion. The Xishuangbanna Tropical Botanical Garden is committed to achieving zero plant extinctions in Xishuangbanna, and orchids are a high priority. Appropriate in and ex situ conservation strategies, including new protected areas and seed banking, have been developed for every threatened orchid species and are being implemented.

Plant species with extremely small populations conservation program: achieving Kunming-Montreal global biodiversity targets.

Conservation programs for plant species with extremely small populations (PSESP) have been successfully implemented for several decades in China. Here we highlight how their inclusion in several national conservation policies helps meet targets of the Kunming-Montreal Global Biodiversity Framework (KMGBF) and show how lessons from these programs can be applied more widely.

Comparative analyses of mitogenomes in the social bees with insights into evolution of long inverted repeats in the Meliponini.

The insect mitogenome is typically a compact circular molecule with highly conserved gene contents. Nonetheless, mitogenome structural variations have been reported in specific taxa, and gene rearrangements, usually the tRNAs, occur in different lineages. Because synapomorphies of mitogenome organizations can provide information for phylogenetic inferences, comparative analyses of mitogenomes have been given increasing attention. However, most studies use a very few species to represent the whole genus, tribe, family, or even order, overlooking potential variations at lower taxonomic levels, which might lead to some incorrect inferences. To provide new insights into mitogenome organizations and their implications for phylogenetic inference, this study conducted comparative analyses for mitogenomes of three social bee tribes (Meliponini, Bombini, and Apini) based on the phylogenetic framework with denser taxonomic sampling at the species and population levels. Comparative analyses revealed that mitogenomes of Apini and Bombini are the typical type, while those of Meliponini show diverse variations in mitogenome sizes and organizations. Large inverted repeats (IRs) cause significant gene rearrangements of protein coding genes (PCGs) and rRNAs in Indo-Malay/Australian stingless bee species. Molecular evolution analyses showed that the lineage with IRs have lower d N/ d S ratios for PCGs than lineages without IRs, indicating potential effects of IRs on the evolution of mitochondrial genes. The finding of IRs and different patterns of gene rearrangements suggested that Meliponini is a hotspot in mitogenome evolution. Unlike conserved PCGs and rRNAs whose rearrangements were found only in the mentioned lineages within Meliponini, tRNA rearrangements are common across all three tribes of social bees, and are significant even at the species level, indicating that comprehensive sampling is needed to fully understand the patterns of tRNA rearrangements, and their implications for phylogenetic inference.

Genomic variation, environmental adaptation, and feralization in ramie, an ancient fiber crop.

Feralization is an important evolutionary process, but the mechanisms behind it remain poorly understood. Here, we use the ancient fiber crop ramie (Boehmeria nivea (L.) Gaudich.) as a model to investigate genomic changes associated with both domestication and feralization. We first produced a chromosome-scale de novo genome assembly of feral ramie and investigated structural variations between feral and domesticated ramie genomes. Next, we gathered 915 accessions from 23 countries, comprising cultivars, major landraces, feral populations, and the wild progenitor. Based on whole-genome resequencing of these accessions, we constructed the most comprehensive ramie genomic variation map to date. Phylogenetic, demographic, and admixture signal detection analyses indicated that feral ramie is of exoferal or exo-endo origin, i.e., descended from hybridization between domesticated ramie and the wild progenitor or ancient landraces. Feral ramie has higher genetic diversity than wild or domesticated ramie, and genomic regions affected by natural selection during feralization differ from those under selection during domestication. Ecological analyses showed that feral and domesticated ramie have similar ecological niches that differ substantially from the niche of the wild progenitor, and three environmental variables are associated with habitat-specific adaptation in feral ramie. These findings advance our understanding of feralization, providing a scientific basis for the excavation of new crop germplasm resources and offering novel insights into the evolution of feralization in nature.