Phylogenomic Analyses Reveal an Allopolyploid Origin of Core Didymocarpinae (Gesneriaceae) Followed by Rapid Radiation

Allopolyploid plants have long been regarded as possessing genetic advantages under certain circumstances due to the combined effects of their hybrid origins and duplicated genomes. However, the evolutionary consequences of allopolyploidy in lineage diversification remain to be fully understood. Here, we investigate the evolutionary consequences of allopolyploidy using 138 transcriptomic sequences of Gesneriaceae, including 124 newly sequenced, focusing particularly on the largest subtribe Didymocarpinae. We estimated the phylogeny of Gesneriaceae using concatenated and coalescent-based methods based on five different nuclear matrices and 27 plastid genes, focusing on relationships among major clades. To better understand the evolutionary affinities in this family, we applied a range of approaches to characterize the extent and cause of phylogenetic incongruence. We found that extensive conflicts between nuclear and chloroplast genomes and among nuclear genes were caused by both incomplete lineage sorting (ILS) and reticulation, and we found evidence of widespread ancient hybridization and introgression. Using the most highly supported phylogenomic framework, we revealed multiple bursts of gene duplication throughout the evolutionary history of Gesneriaceae. By incorporating molecular dating and analyses of diversification dynamics, our study shows that an ancient allopolyploidization event occurred around the Oligocene-Miocene boundary, which may have driven the rapid radiation of core Didymocarpinae.

Damage by typhoon Hato compared among three different plant communities in Macau, China

Tropical cyclones are among the major climatic disasters threatening human survival and development. They are also responsible in part for forest taxonomic composition and dynamics and may lead to catastrophic succession between ecosystems. In this study, we aimed to investigate the extensiveness and severity of the effect caused by Typhoon Hato among the three primary plant communities in Macau, China, including Guia Hill, Taipa Grande, and Ka Ho. The plants' damage was classified into seven categories, ranging from Degree 6, which represents the most severe damage, to Degree 0, which represents almost no damage. The impact of Typhoon Hato was evaluated at different levels, including sample plots, species, DBH, and community structure. Our results show that the sub-climax community of Guia Hill was most disturbed, with the highest damage index (DI) of 55.28%. Similarly, the Ka Ho shoreline shrub community was also considerably influenced, with a DI of 48.14%. By contrast, the managed secondary forest around Taipa Grande was the least affected, with a DI of 32.66%. Additionally, from the tree layer perspective, the tall trees at Guia Hill canopy layer were directly affected by wind, while the dense understory layer suffered from severe secondary damage due to the fallen trees and branches. For Taipa Grande, the dominant species in the canopy layer were shorter and had less direct damage; the secondary damage was also small as a consequence. Ka Ho had more dwarfed and multibranched species surviving from the sea breeze since Ka Ho was close to the sea. The dense plant structure in Ka Ho protected plants from being easily broken by typhoons, but some twigs and leaves were lost. Some less damaged local species and easily recovered species found in this study could inform the selection of wind-resistant species for the typhoon-affected communities.

Cheilolejeunea zhui (Lejeuneaceae, Marchantiophyta), a new species with moniliate ocelli from Guangxi, China

A new ocellate liverwort species, Cheilolejeunea zhui (Lejeuneaceae), is described from Guangxi, China. The new species is similar to the neotropical C. urubuensis in having moniliate ocelli in the leaf lobes and in general appearances but differs in having obliquely spreading leaves, obtuse to subacute leaf apex, thin-walled leaf cells with distinct trigones, shallowly bifid female bracteole apex, and numerous ocelli in its perianths. Molecular phylogeny of data from three regions (nrITS, trnL-F, and trnG) confirmed the systematic position of this new species to be sister to C. urubuensis, well apart from the remaining members of the genus. Based on morphological and molecular evidence, Cheilolejeunea sect. Moniliocella sect. nov. is proposed to accommodate C. urubuensis and C. zhui. The discovery of C. zhui represents the fourth known species in Cheilolejeunea with linearly arranged ocelli.

How does spatial extent and environmental limits affect the accuracy of species richness estimates from ecological niche models? A case study with North American Pinaceae and Cactaceae

Measuring species richness at varying spatial extents can be challenging, especially at large extents where exhaustive species surveys are difficult or impossible. Our work aimed at determining the reliability of species richness estimates from stacked ecological niche models at different spatial extents for taxonomic groups with vastly different environmental dependencies and interactions. To accomplish this, we generated ecological niche models for the species of Cactaceae and Pinaceae that occur within 180 published floras from North America north of Mexico. We overlaid or stacked the resulting species' potential distribution estimates over the bounding boxes representing each of the 180 floras to generate predictions of species richness. In general, our stacked models of Cactaceae and Pinaceae were poor predictors of species richness. The relationships between observed and predicted values improved noticeably with the size of spatial extents. However, the stacked models tended to overpredict the richness of Cactaceae and over- and underpredict the richness of Pinaceae. Cactaceae stacked models showed higher sensitivity and lower specificity than those for Pinaceae. We conclude that stacked ecological niche models may be somewhat poor predictors of species richness at smaller spatial extents and should be used with caution for this purpose. Perhaps more importantly, abilities to compensate for their limitations or apply corrections to their reliability may vary with taxonomic groups.

Adaptive radiation in Orinus, an endemic alpine grass of the Qinghai-Tibet Plateau, based on comparative transcriptomic analysis

The species of Orinus (Poaceae) are important alpine plants with a variety of phenotypic traits and potential usages in molecular breeding toward drought-tolerant forage crops. However, the genetic basis of evolutionary adaption and diversification in the genus is still unclear. In the present study, we obtained transcriptomes for the two most divergent species, O. thoroldii and O. kokonoricus, using the Illumina platform and de novo assembly. In total, we generated 23,029 and 24,086 unigenes with N50 values of 1188 and 1203 for O. thoroldii and O. kokonoricus respectively, and identified 19,005 pairs of putative orthologs between the two species of Orinus. For these orthologs, estimations of non-synonymous/synonymous substitution rate ratios indicated that 568 pairs may be under strongly positive selection (Ka/Ks > 1), and Gene Ontogeny (GO) enrichment analysis revealed that significantly enriched pathways were in DNA repair and resistance to abiotic stress. Meanwhile, the divergence times of species between O. thoroldii and O. kokonoricus occurred 3.2 million years ago (Mya), and the recent evolutionary branch is an allotetraploid species, Cleistogenes songorica. We also detected a Ks peak of ∼0.60 for Orinus. Additionally, we identified 188 pairs of differentially expressed genes (DEGs) between the two species of Orinus, which were significantly enrich in stress resistance and lateral root development. Thus, we considered that the species diversification and evolutionary adaption of this genus was initiated by environmental selection, followed by phenotypic differentiation, finally leading to niche separation in the Qinghai-Tibet Plateau.

Jackfruit genome and population genomics provide insights into fruit evolution and domestication history in China

As the largest known tree-borne fruit in the world, jackfruit (Artocarpus heterophyllus) is an important cultivated crop in tropical regions of South and Southeast Asia. The species has been cultivated in China for more than 1000 years, but the history of its introduction to the country remains unclear. We assembled a high-quality chromosome-level genome of jackfruit into 985.63 Mb with scaffold N50 of 32.81 Mb. We analyzed whole-genome resequencing data of 295 landraces to investigate the domestication history in China and agronomic trait evolution of jackfruit. Population structure analysis revealed that jackfruits of China could be traced back to originate from Southeast Asia and South Asia independently. Selection signals between jackfruit and its edible congener, cempedak (Artocarpus integer), revealed several important candidate genes associated with fruit development and ripening. Moreover, analyses of selective sweeps and gene expression revealed that the AhePG1 gene may be the major factor in determining fruit texture. This study not only resolves the origins of jackfruit of China, but also provides valuable genomic resources for jackfruit breeding improvement and offers insights into fruit size evolution and fruit texture changes.

A consensus view of the proteome of the last universal common ancestor

The availability of genomic and proteomic data from across the tree of life has made it possible to infer features of the genome and proteome of the last universal common ancestor (LUCA). A number of studies have done so, all using a unique set of methods and bioinformatics databases. Here, we compare predictions across eight such studies and measure both their agreement with one another and with the consensus predictions among them. We find that some LUCA genome studies show a strong agreement with the consensus predictions of the others, but that no individual study shares a high or even moderate degree of similarity with any other individual study. From these observations, we conclude that the consensus among studies provides a more accurate depiction of the core proteome of the LUCA and its functional repertoire. The set of consensus LUCA protein family predictions between all of these studies portrays a LUCA genome that, at minimum, encoded functions related to protein synthesis, amino acid metabolism, nucleotide metabolism, and the use of common, nucleotide‐derived organic cofactors.

Comparative transcriptomic analysis of genes in the triterpene saponin biosynthesis pathway in leaves and roots of Ardisia kteniophylla A. DC., a plant used in traditional Chinese medicine

Ardisia kteniophylla (Primulaceae) is highly valued in traditional medicine due to its production of the pharmacologically active secondary metabolites, especially triterpenoid saponins in its roots. Although A. kteniophylla is very important in traditional medicine, the genetic basis for its production of triterpenoid saponins remains largely unknown. Therefore, we sequenced transcriptomes of A. kteniophylla to identify putative genes involved in production of triterpenoid saponins in both leaves and roots, and we used the transcriptomes to compare expression levels of these genes between the two organ systems. The production of triterpenoid saponins in plants is usually induced through hormonal signaling on account of the presence of pests. Thus, we treated plants with the hormones salicylic acid (SA) and methyl jasmonate (MeJA) and used quantitative real‐time PCR (qRT‐PCR) to investigate expression levels of genes involved in triterpenoid saponin biosynthesis. In total, we obtained transcriptomes for leaf and root tissues representing 52,454 unigenes. Compared with the leaf transcriptome, we found that 6092 unigenes were upregulated in the root, especially enzymes involved in the direct synthesis of triterpenoid saponins, while 6001 genes appeared downregulated, including those involved in precursory steps in the triterpenoid saponin biosynthesis pathway. Our results from qRT‐PCR indicate that genes within the upstream parts of the triterpenoid saponin biosynthesis pathway may be upregulated under exposure to the applied hormones, but downstream genes are downregulated. This suggests possible conflicting effects of SA and MeJA in promoting the production of secondary metabolites on the one hand, and, on the other, limiting plant growth processes to devote energy to combating pests. We also performed an analysis of transcription factors (TFs) and found 997 unique transcripts belonging to 16 TF families. Our data may help to facilitate future work on triterpene saponins biosynthesis in A. kteniophylla with potential pharmacological and molecular breeding applications.

Closing the Gap: Horizontal Transfer of Mariner Transposons between Rhus Gall Aphids and Other Insects

Horizontal transfer of transposons (HTT) is an essential source of genomic evolution in eukaryotes. The HTT dynamics are well characterized in eukaryotes, including insects; however, there is a considerable gap in knowledge about HTT regarding many eukaryotes' species. In this study, we analyzed the events of the HTT between Rhus gall aphids (Hemiptera) and other insects. We analyzed the Mariner-like transposable elements (MLEs) belonging to Rhus gall aphids for the possible HT events. The MLEs have a patchy distribution and high similarity over the entire element length with insect MLEs from different orders. We selected representative sequences from the Rhus gall MLEs and identified five events of HT between MLEs of Rhus gall aphids and other insects from five different orders. We also found multiple HTT events among the MLEs of insects from the five orders, demonstrating that these Mariner elements have been involved in recurrent HT between Rhus gall aphids and other insects. Our current study closed the knowledge gap surrounding HTT and reported the events between Rhus gall aphids and other insects for the first time. We believe that this study about HTT events will help us understand the evolution and spread of transposable elements in the genomes of Rhus gall aphids.

Identification of genes involved in drought tolerance in seedlings of the desert grass, Psammochloa villosa (Poaceae), based on full-length isoform sequencing and de novo assembly from short reads

Psammochloa villosa is a perennial herbaceous plant that is dominant within arid regions of the Inner Mongolian Plateau and the Qinghai-Tibet Plateau in China, where it is an endemic species and exhibits strong drought tolerance and wind resistance. To study drought tolerance in P. villosa and determine its molecular basis, we simulated high and moderate drought stress in a controlled environment and then analyzed transcriptome sequences by combining long-read sequences from a representative, wild-grown individual with short reads from the treatment groups. We obtained 184,076 high-quality isoforms as a reference and 168,650 genes (91.6%), which we were able to annotate according to public databases. Ultimately, we obtained 119,005 unigenes representing the transcriptome of P. villosa under drought stress and, among these, we identified 3089 differentially expressed genes and 1484 transcription factors. Physiologically, P. villosa that was exposed to high and moderate drought stress had reduced germination rates and shorter buds but generated more chlorophyll, which is atypical under drought stress and possibly reflects an adaptation of these plants to their arid environment. We inferred that significantly upregulated genes were annotated as 'Chlorophyll a-b binding protein' and 'Light-harvesting chlorophyll-protein' among drought and control groups. Broadly, our analyses revealed that drought stress triggered many genome-level responses, especially related to mitigation of radical oxygen species (ROS), which increase in concentration under drought stress. In particular, in the high drought stress group compared with the control, GO enrichment analysis revealed a significant enrichment of upregulated genes (n = 10) involved in mitigation of oxidative stress. Similarly, using KEGG we found significant enrichment of genes in the phenylpropanoid biosynthesis pathway (11 genes), which yields phenols that scavenge ROS. We also inferred that many genes involved in metabolism of arginine and proline, which may serve as both scavengers of ROS and osmoprotectants that interact with stress response genes based on our protein-protein interaction network analysis. We verified the relative expression levels of eight genes associated with mitigation of ROS, DNA repair, and transmembrane transporter activity using qRT-PCR, and the results were consistent with our inferences from transcriptomes. This study provides insights into the genomic and physiological basis of drought tolerance in P. villosa and represents a resource for development of the species as a forage crop via molecular breeding within arid lands.

Socio-Ecological Effects on the Patterns of Non-native Plant Distributions on Hainan Island

Non-native plants spread to recipient areas via natural or human-mediated modes of dispersal, and, if the non-native species are invasive, introduction potentially causes impacts on native plants and local ecosystems as well as economic losses. Therefore, we studied the diversity and distributional patterns of non-native plant species diversity in the tropical island province of Hainan, China and its relationships with environmental and socioeconomic factors by generating a checklist of species and subsequently performing an analysis of phylogenetic diversity. To generate the checklist, we began with the available, relevant literature representing 19 administrative units of Hainan and determined the casual, naturalized, or invasive status of each species by conducting field surveys within 14 administrative units. We found that non-native plants of Hainan comprise 77 casual species, 42 naturalized species, and 63 invasive species. Moreover, we found that non-native plant species had diverse origins from North and South America, Africa, and Asia and that the most common species across administrative areas belong to the plant families Asteraceae and Fabaceae. Moreover, the numbers of non-native species distributed in the areas of Hainan bording the coast arer greater than those within interior areas of the province. Among the coastal areas, Haikou has the highest species richness and, simultaneously, the highest values for significantly, positively correlated predictor variables, population and GDP (R2 = 0.60, P < 0.01; R2 = 0.64, P < 0.01, respectively). In contrast, the landlocked administrative units of Tunchang and Ding’an have the smallest number of non-native species, while their populations are less than a quarter of that of Haikou and their GDP less than one tenth. Among natural environmental variables, we determined that the number of non-native species had the strongest correlation with the minimum temperature in the coldest month, which predicts a smaller number of non-native species. Additionally, non-native species are primarily distributed in urban and rural built-up areas and agricultural areas; areas that are dominated by human activities. Overall, our study provides a working checklist of the non-native plants of Hainan as well as a theoretical framework and reference for the control of invasive plants of the province.

Genome size evolution of the extant lycophytes and ferns

Ferns and lycophytes have remarkably large genomes. However, little is known about how their genome size evolved in fern lineages. To explore the origins and evolution of chromosome numbers and genome size in ferns, we used flow cytometry to measure the genomes of 240 species (255 samples) of extant ferns and lycophytes comprising 27 families and 72 genera, of which 228 species (242 samples) represent new reports. We analyzed correlations among genome size, spore size, chromosomal features, phylogeny, and habitat type preference within a phylogenetic framework. We also applied ANOVA and multinomial logistic regression analysis to preference of habitat type and genome size. Using the phylogeny, we conducted ancestral character reconstruction for habitat types and tested whether genome size changes simultaneously with shifts in habitat preference. We found that 2C values had weak phylogenetic signal, whereas the base number of chromosomes (x) had a strong phylogenetic signal. Furthermore, our analyses revealed a positive correlation between genome size and chromosome traits, indicating that the base number of chromosomes (x), chromosome size, and polyploidization may be primary contributors to genome expansion in ferns and lycophytes. Genome sizes in different habitat types varied significantly and were significantly correlated with habitat types; specifically, multinomial logistic regression indicated that species with larger 2C values were more likely to be epiphytes. Terrestrial habitat is inferred to be ancestral for both extant ferns and lycophytes, whereas transitions to other habitat types occurred as the major clades emerged. Shifts in habitat types appear be followed by periods of genomic stability. Based on these results, we inferred that habitat type changes and multiple whole-genome duplications have contributed to the formation of large genomes of ferns and their allies during their evolutionary history.

The genome of the Paleogene relic tree Bretschneidera sinensis: insights into trade-offs in gene family evolution, demographic history, and adaptive SNPs

Among relic species, genomic information may provide the key to inferring their long-term survival. Therefore, in this study, we investigated the genome of the Paleogene relic tree species, Bretschneidera sinensis, which is a rare endemic species within southeastern Asia. Specifically, we assembled a high-quality genome for B. sinensis using PacBio high-fidelity and high-throughput chromosome conformation capture reads and annotated it with long and short RNA sequencing reads. Using the genome, we then detected a trade-off between active and passive disease defences among the gene families. Gene families involved in salicylic acid and MAPK signalling pathways expanded as active defence mechanisms against disease, but families involved in terpene synthase activity as passive defences contracted. When inferring the long evolutionary history of B. sinensis, we detected population declines corresponding to historical climate change around the Eocene–Oligocene transition and to climatic fluctuations in the Quaternary. Additionally, based on this genome, we identified 388 single nucleotide polymorphisms (SNPs) that were likely under selection, and showed diverse functions in growth and stress responses. Among them, we further found 41 climate-associated SNPs. The genome of B. sinensis and the SNP dataset will be important resources for understanding extinction/diversification processes using comparative genomics in different lineages.

Anthropogenic factors are stronger drivers of patterns of endemic plant diversity on Hainan Island of China than natural environmental factors

The roles of natural and anthropogenic factors in contributing to the organization of biodiversity at large and small scales have long been challenging to disentangle, and doing so has never been attempted for the island province of Hainan in China based on patterns of taxonomic and phylogenetic diversity. Therefore, in this study, we evaluated the taxonomic and phylogenetic diversity of endemic plants on the island as a function of anthropogenic and natural variables based on non-metric multi-dimensional scaling (NMDS) ordination and generated generalized linear models (GLMs). We found that the highest phylogenetic diversity (1006) and the lowest mean phylogenetic distance (515.5) was in the provincial capital, Haikou. The NMDS analyses indicated that taxonomic diversity was significantly correlated with industrial revenue (p = 0.006) and population (p = 0.004). Furthermore, most phylogenetic diversity indices were strongly correlated with population and agricultural revenue, while the sampled natural environmental variables were not significantly correlated with plant diversity indices. These findings indicate that anthropogenic factors are the main present-day driving forces of plant diversity in Hainan, though we did detect a significant latitudinal diversity gradient of richness that likely reflects the historical roles of natural environmental factors in the organization of biodiversity on the island. Overall, our results are alarming for biodiversity of the island and indicate that conservation and sustainable use of endemic plant species must be made a critical priority.

Comparative Chloroplast Genomics and Phylogenetic Analysis of Zygophyllum (Zygophyllaceae) of China

The genus Zygophyllum comprises over 150 species within the plant family Zygophyllaceae. These species predominantly grow in arid and semiarid areas, and about 20 occur in northwestern China. In this study, we sampled 24 individuals of Zygophyllum representing 15 species and sequenced their complete chloroplast (cp) genomes. For comparison, we also sequenced cp genomes of two species of Peganum from China representing the closely allied family, Nitrariaceae. The 24 cp genomes of Zygophyllum were smaller and ranged in size from 104,221 to 106,286 bp, each containing a large single-copy (LSC) region (79,245-80,439 bp), a small single-copy (SSC) region (16,285-17,146 bp), and a pair of inverted repeat (IR) regions (3,792-4,466 bp). These cp genomes contained 111-112 genes each, including 74-75 protein-coding genes (PCGs), four ribosomal RNA genes, and 33 transfer RNA genes, and all cp genomes showed similar gene order, content, and structure. The cp genomes of Zygophyllum appeared to lose some genes such as ndh genes and rRNA genes, of which four rRNA genes were in the SSC region, not in the IR regions. However, the SC and IR regions had greater similarity within Zygophyllum than between the genus and Peganum. We detected nine highly variable intergenic spacers: matK-trnQ, psaC-rps15, psbZ-trnG, rps7-trnL, rps15-trnN, trnE-trnT, trnL-rpl32, trnQ-psbK, and trnS-trnG. Additionally, we identified 156 simple sequence repeat (cpSSR) markers shared among the genomes of the 24 Zygophyllum samples and seven cpSSRs that were unique to the species of Zygophyllum. These markers may be useful in future studies on genetic diversity and relationships of Zygophyllum and closely related taxa. Using the sequenced cp genomes, we reconstructed a phylogeny that strongly supported the division of Chinese Zygophyllum into herbaceous and shrubby clades. We utilized our phylogenetic results along with prior morphological studies to address several remaining taxonomic questions within Zygophyllum. Specifically, we found that Zygophyllum kaschgaricum is included within Zygophyllum xanthoxylon supporting the present treatment of the former genus Sarcozygium as a subgenus within Zygophyllum. Our results provide a foundation for future research on the genetic resources of Zygophyllum.

Positive relationships among aboveground biomass, tree species diversity, and urban greening management in tropical coastal city of Haikou

Within urban green spaces, tree species diversity is believed to correlate with aboveground biomass, though there is some disagreement within the literature on the strength and directionality of the relationship. Therefore, we assessed the relationship between the biodiversity of woody species and the aboveground biomass of woody plant species in the tropical, coastal city of Haikou in southern China. To accomplish this, we obtained comprehensive tree and site data through field sampling of 190 urban functional units (UFUs, or work units) corresponding to six types of land uses governmental-institutional, industrial-commercial, park-recreational, residential, transport infrastructure, and undeveloped area. Based on our field data, we investigated the relationship between tree species diversity and aboveground biomass using multiple regression, which revealed significant relationships across all five types of land uses. Aboveground biomass in green spaces was also correlated with anthropogenic factors, especially time since urban development, or site age, annual maintenance frequency by human caretakers, and human population density. Among these factors, maintenance is the strongest predictor of aboveground biomass in urban green space. Therefore, this study highlights the critical role of maintenance of urban green space in promoting both aboveground biomass and woody biodiversity in urban ecosystems and, consequently, on urban ecosystem services. Our findings contribute to a deeper understanding of the ecosystem services provided by communities of woody plant species in urban areas.

Phylogenomic and Macroevolutionary Evidence for an Explosive Radiation of a Plant Genus in the Miocene

Mountain systems harbor a substantial fraction of global biodiversity and, thus, provide excellent opportunities to study rapid diversification and to understand the historical processes underlying the assembly of biodiversity hotspots. The rich biodiversity in mountains is widely regarded as having arisen under the influence of geological and climatic processes as well as the complex interactions among them. However, the relative contribution of geology and climate in driving species radiation is seldom explored. Here, we studied the evolutionary radiation of Oreocharis (Gesneriaceae), which has diversified extensively throughout East Asia, especially within the Hengduan Mountains (HDM), using transcriptomic data and a time calibrated phylogeny for 88% (111/126) of all species of the genus. In particular, we applied phylogenetic reconstructions to evaluate the extent of incomplete lineage sorting accompanying the early and rapid radiation in the genus. We then fit macroevolutionary models to explore its spatial and diversification dynamics in Oreocharis and applied explicit birth–death models to investigate the effects of past environmental changes on its diversification. Evidence from 574 orthologous loci suggest that Oreocharis underwent an impressive early burst of speciation starting ca. 12 Ma in the Miocene, followed by a drastic decline in speciation toward the present. Although we found no evidence for a shift in diversification rate across the phylogeny of Oreocharis, we showed a difference in diversification dynamics between the HDM and non-HDM lineages, with higher diversification rates in the HDM. The diversification dynamic of Oreocharis is most likely positively associated with temperature-dependent speciation and dependency on the Asian monsoons. We suggest that the warm and humid climate of the mid-Miocene was probably the primary driver of the rapid diversification in Oreocharis, while mountain building of the HDM might have indirectly affected species diversification of the HDM lineage. This study highlights the importance of past climatic changes, combined with mountain building, in creating strong environmental heterogeneity and driving diversification of mountain plants, and suggests that the biodiversity in the HDM cannot directly be attributed to mountain uplift, contrary to many recent speculations.[East Asian monsoons; environmental heterogeneity; Hengduan Mountains; incomplete lineage sorting; Oreocharis; past climate change; rapid diversification; transcriptome.]

Population genetic structure and evolutionary history of Psammochloa villosa (Trin.) Bor (Poaceae) revealed by AFLP marker

Psammochloa villosa is an ecologically important desert grass that occurs in the Inner Mongolian Plateau where it is frequently the dominant species and is involved in sand stabilization and wind breaking. We sought to generate a preliminary demographic framework for P. villosa to support the future studies of this species, its conservation, and sustainable utilization. To accomplish this, we characterized the genetic diversity and structure of 210 individuals from 43 natural populations of P. villosa using amplified fragment length polymorphism (AFLP) markers. We obtained 1,728 well-defined amplified bands from eight pairs of primers, of which 1,654 bands (95.7%) were polymorphic. Results obtained from the AFLPs suggested effective alleles among populations of 1.32, a Nei's standard genetic distance value of 0.206, a Shannon index of 0.332, a coefficient of gene differentiation (G ST) of 0.469, and a gene flow parameter (Nm) of 0.576. All these values indicate that there is abundant genetic diversity in P. villosa, but limited gene flow. An analysis of molecular variance (AMOVA) showed that genetic variation mainly exists within populations (64.2%), and we found that the most genetically similar populations were often not geographically adjacent. Thus, this suggests that the mechanisms of gene flow are surprisingly complex in this species and may occur over long distances. In addition, we predicted the distribution dynamics of P. villosa based on the spatial distribution modeling and found that its range has contracted continuously since the last interglacial period. We speculate that dry, cold climates have been critical in determining the geographic distribution of P. villosa during the Quaternary period. Our study provides new insights into the population genetics and evolutionary history of P. villosa in the Inner Mongolian Plateau and provides a resource that can be used to design in situ conservation actions and prioritize sustainable utilization.

Tracing the Diploid Ancestry of the Cultivated Octoploid Strawberry

The commercial strawberry, Fragaria × ananassa, is a recent allo-octoploid that is cultivated worldwide. However, other than Fragaria vesca, which is universally accepted one of its diploid ancestors, its other early diploid progenitors remain unclear. Here, we performed comparative analyses of the genomes of five diploid strawberries, F. iinumae, F. vesca, F. nilgerrensis, F. nubicola, and F. viridis, of which the latter three are newly sequenced. We found that the genomes of these species share highly conserved gene content and gene order. Using an alignment-based approach, we show that F. iinumae and F. vesca are the diploid progenitors to the octoploid F. × ananassa, whereas the other three diploids that we analyzed in this study are not parental species. We generated a fully resolved, dated phylogeny of Fragaria, and determined that the genus arose ∼6.37 Ma. Our results effectively resolve conflicting hypotheses regarding the putative diploid progenitors of the cultivated strawberry, establish a reliable backbone phylogeny for the genus, and provide genetic resources for molecular breeding.

Spatial phylogenetics of the native woody plant species in Hainan, China

To better identify biodiversity hotspots for conservation on Hainan Island, a tropical island in southern China, we assessed spatial variation in phylogenetic diversity and species richness using 18,976 georeferenced specimen records and a newly reconstructed molecular phylogeny of 957 native woody plants. Within this framework, we delineated bioregions based on vegetation composition and mapped areas of neoendemism and paleoendemism to identify areas of priority for conservation. Our results reveal that the southwest of Hainan is the most important hot spot for endemism and plant diversity followed by the southeast area. The distribution of endemic species showed a scattered, rather than clustered, pattern on the island. Based on phylogenetic range-weighted turnover metrics, we delineated three major vegetational zones in Hainan. These largely correspond to natural secondary growth and managed forests (e.g., rubber and timber forests) in central Hainan, old-growth forests and natural secondary growth forest at the margins of Hainan, and nature reserves on the island (e.g., Jianfeng and Diaoluo National Nature Reserves). Our study helps to elucidate potential botanical conservation priorities for Hainan within an evolutionary, phylogenetic framework.

The very early evolution of protein translocation across membranes

In this study, we used a computational approach to investigate the early evolutionary history of a system of proteins that, together, embed and translocate other proteins across cell membranes. Cell membranes comprise the basis for cellularity, which is an ancient, fundamental organizing principle shared by all organisms and a key innovation in the evolution of life on Earth. Two related requirements for cellularity are that organisms are able to both embed proteins into membranes and translocate proteins across membranes. One system that accomplishes these tasks is the signal recognition particle (SRP) system, in which the core protein components are the paralogs, FtsY and Ffh. Complementary to the SRP system is the Sec translocation channel, in which the primary channel-forming protein is SecY. We performed phylogenetic analyses that strongly supported prior inferences that FtsY, Ffh, and SecY were all present by the time of the last universal common ancestor of life, the LUCA, and that the ancestor of FtsY and Ffh existed before the LUCA. Further, we combined ancestral sequence reconstruction and protein structure and function prediction to show that the LUCA had an SRP system and Sec translocation channel that were similar to those of extant organisms. We also show that the ancestor of Ffh and FtsY that predated the LUCA was more similar to FtsY than Ffh but could still have comprised a rudimentary protein translocation system on its own. Duplication of the ancestor of FtsY and Ffh facilitated the specialization of FtsY as a membrane bound receptor and Ffh as a cytoplasmic protein that could bind nascent proteins with specific membrane-targeting signal sequences. Finally, we analyzed amino acid frequencies in our ancestral sequence reconstructions to infer that the ancestral Ffh/FtsY protein likely arose prior to or just after the completion of the canonical genetic code. Taken together, our results offer a window into the very early evolutionary history of cellularity.

Hybrid Speciation and Introgression Both Underlie the Genetic Structures and Evolutionary Relationships of Three Morphologically Distinct Species of Lilium (Liliaceae) Forming a Hybrid Zone Along an Elevational Gradient

We studied hybrid interactions of Lilium meleagrinum, Lilium gongshanense, and Lilium saluenense using an integrative approach combining population genetics, fieldwork, and phenological research. These three species occur along an elevational gradient, with L. meleagrinum occurring at lower elevations, L. saluenense at higher elevations, and L. gongshanense between them. The species show strong morphological differentiation despite there being no clear environmental barriers to gene flow among them. Lilium gongshanense is likely to have a hybrid origin based on our prior work, but its progenitors remain uncertain. We sought to determine whether gene flow occurs among these three parapatric species, and, if so, whether L. gongshanense is a hybrid of L. meleagrinum and/or L. saluenense. We analyzed data from multiple chloroplast genes and spacers, nuclear internal transcribed spacer (ITS), and 18 nuclear Expressed Sequence Tag-Simple Sequence Repeat (EST-SSR) microsatellites for accessions of the three species representing dense population-level sampling. We also inferred phenology by examining species in the field and using herbarium specimens. We found that there are only two types of chloroplast genomes shared among the three species and that L. gongshanense forms two distinct groups with closest links to other species of Lilium based on ITS. Taken together, L. gongshanense is unlikely to be a hybrid species resulting from a cross between L. meleagrinum and L. saluenense, but gene flow is occurring among the three species. The gene flow is likely to be rare according to evidence from all molecular datasets, and this is corroborated by detection of only one putative hybrid individual in the field and asynchronous phenology. We suspect that the rarity of hybridization events among the species facilitates their continued genetic separation.

Nuclear and Chloroplast Sequences Resolve the Enigmatic Origin of the Concord Grape

Despite the commercial importance of the Concord grape, its origin has remained unresolved for over 150 years without a comprehensive phylogenetic analysis. In this study we aimed to reconstruct the evolutionary history of the Concord grape using sequence data from four nuclear markers (AT103, GAI1, PHYA, and SQD1), six plastid markers (matK, psbA-trnH, petN-trnC, ycf1, trnL-F, and trnS-G), and the plastid genome. We sampled extensively the Vitis species native to northeastern North America as well as representative species from Europe and Asia, including the commercially important Vitis vinifera (wine grape), a native European species with hermaphroditic flowers, and its wild progenitor, V. vinifera subsp. sylvestris. We also sequenced the plastid genome of one accession of the Concord grape and compared the plastid genome data to the recently published data set of Vitis plastomes. Phylogenetic analyses of the plastid and nuclear data using maximum likelihood and Bayesian inference support the hybrid origin of the Concord grape. The results clearly pinpoint the wine grape, V. vinifera, as the maternal donor and the fox grape, Vitis labrusca, which is common in northeastern North America, as the paternal donor. Moreover, we infer that the breeding history of the Concord grape must have involved the backcrossing of the F1 hybrid with the paternal parent V. labrusca. This backcrossing also explains the higher morphological similarity of the Concord grape to V. labrusca than to V. vinifera. This study provides concrete genetic evidence for the hybrid origin of a widespread Vitis cultivar and is, therefore, promising for similar future studies focused on resolving ambiguous origins of major crops or to create successful hybrid fruit crops.

A population genetics perspective on the evolutionary histories of three clonal, endemic, and dominant grass species of the Qinghai-Tibet Plateau: Orinus (Poaceae)

We performed analyses of amplified fragment length polymorphism (AFLP) in order to characterize the evolutionary history of Orinus according to its population genetic structure, as well as to investigate putative hybrid origins of O. intermedius and to provide additional insights into relationships among species. The genus Orinus comprises three clonal grasses that are dominant species within xeric alpine grasslands of the Qinghai-Tibet Plateau (QTP). Here, we used eight selectively obtained primer pairs of EcoRI/MseI to perform amplifications in 231 individuals of Orinus representing 48 populations and all three species. We compared our resulting data to genetic models of hybridization using a Bayesian algorithm within NewHybrids software. We determined that genetic variation in Orinus was 56.65% within populations while the among-species component was 30.04% using standard population genetics statistics. Nevertheless, we detected that species of Orinus were clustered into three highly distinct genetic groups corresponding to classic species identities. Our results suggest that there is some introgression among species. Thus, we tested explicit models of hybridization using a Bayesian approach within NewHybrids software. However, O. intermedius likely derives from a common ancestor with O. kokonoricus and is probably not the result of hybrid speciation between O. kokonoricus and O. thoroldii. We suspect that recent isolation of species of Orinus in allopatry via vicariance may explain the patterns in diversity that we observed, and this is corroborated by a Mantel test that showed significant positive correlation between geographic and genetic distance (r = 0.05, p < 0.05). Recent isolation may explain why Orinus differs from many other clonal species by exhibiting the highest diversity within populations rather than among them.

Congruent phylogenetic relationships of Melaphidina aphids (Aphididae: Eriosomatinae: Fordini) according to nuclear and mitochondrial DNA data with taxonomic implications on generic limits

Melaphidina aphids (Rhus-gall aphids; Eriosomatinae: Fordini) comprise five genera from eastern Asia and one monotypic genus from eastern North America. Melaphidina are unique in feeding on plant species of Rhus subgenus Rhus (Anacardiaceae), on which they form galls during the summer. The phylogenetic relationships among some species of Melaphidina aphids remain controversial. In this study, we sought to resolve the backbone phylogeny of Melaphidina aphids by sampling 15 accessions representing all six genera, all species, and all subspecies except Meitanaphis microgallis using 20 gene regions: five nuclear genes as well as 13 protein-coding genes and two rRNA genes of the mitochondrial genome. Phylogenetic analyses included Bayesian and maximum likelihood methods. Independent analyses of nuclear and mitochondrial genes returned congruent topologies, and analyses of all gene regions combined showed well-supported relationships among Melaphidina species. In particular, these were: (1) Nurudea (excluding N. ibofushi) is sister to a clade composed of the five remaining genera; (2) the monotypic North American genus Melaphis is sister to a clade comprising the four remaining genera; and (3) (Schlechtendalia + N. ibofushi) is sister to the clade (Floraphis (Meitanaphis + Kaburagia). Our results support the transfer of Meitanaphis flavogallis to Kaburagia as an additional subspecies or species, and the recognition of Floraphis as a distinct genus. This study provides important molecular resources for subsequent evolutionary studies using more nuclear genes on the Melaphidina aphids and their close allies.

Plastid Phylogenomics Resolve Deep Relationships among Eupolypod II Ferns with Rapid Radiation and Rate Heterogeneity

The eupolypods II ferns represent a classic case of evolutionary radiation and, simultaneously, exhibit high substitution rate heterogeneity. These factors have been proposed to contribute to the contentious resolutions among clades within this fern group in multilocus phylogenetic studies. We investigated the deep phylogenetic relationships of eupolypod II ferns by sampling all major families and using 40 plastid genomes, or plastomes, of which 33 were newly sequenced with next-generation sequencing technology. We performed model-based analyses to evaluate the diversity of molecular evolutionary rates for these ferns. Our plastome data, with more than 26,000 informative characters, yielded good resolution for deep relationships within eupolypods II and unambiguously clarified the position of Rhachidosoraceae and the monophyly of Athyriaceae. Results of rate heterogeneity analysis revealed approximately 33 significant rate shifts in eupolypod II ferns, with the most heterogeneous rates (both accelerations and decelerations) occurring in two phylogenetically difficult lineages, that is, the Rhachidosoraceae–Aspleniaceae and Athyriaceae clades. These observations support the hypothesis that rate heterogeneity has previously constrained the deep phylogenetic resolution in eupolypods II. According to the plastome data, we propose that 14 chloroplast markers are particularly phylogenetically informative for eupolypods II both at the familial and generic levels. Our study demonstrates the power of a character-rich plastome data set and high-throughput sequencing for resolving the recalcitrant lineages, which have undergone rapid evolutionary radiation and dramatic changes in substitution rates.

Genetic Structure of the Bacterial Endosymbiont Buchnera aphidicola from Its Host Aphid Schlechtendalia chinensis and Evolutionary Implications

Buchnera aphidicola is a primary symbiotic bacterium which provides essential amino acids to aphids. In this study, we sequenced nuclear 16s rDNA and atpAGD genes for 156 individuals of B. aphidicola from eight geographically distant populations to investigate the genetic diversity and structure of B. aphidicola associated to the sumac gall aphid Schlechtendalia chinensis in central and southern China. Our analyses of the combined sequences showed that B. aphidicola from S. chinensis had high haplotype and nucleotide diversity (h = 0.893; π = 0.00164). One of the 16 haplotypes detected had a wide geographic distribution across the central and southern China and was probably the ancestral haplotype of B. aphidicola from S. chinensis. A network and phylogenetic analysis revealed a geographic structure in which the 16 haplotypes of B. aphidicola were divided into the northern and southern clades separated by the Yangtze River. The two clades diverged from each other at 22.1 ± 3.7 Mya according to our divergence time estimations. Therefore, the modern genetic structure in B. aphidicola from S. chinensis has been probably impacted by historical geological events. Combined with the data from GenBank, we also reconstructed the phylogenetic relationships of three aphid subfamilies and their symbiont bacteria. The results indicated significant topological correlations between the aphid and bacterial phylogenies at interspecific levels.

Both temperature fluctuations and East Asian monsoons have driven plant diversification in the karst ecosystems from southern China

Karst ecosystems in southern China are species-rich and have high levels of endemism, yet little is known regarding the evolutionary processes responsible for the origin and diversification of karst biodiversity. The genus Primulina (Gesneriaceae) comprises ca. 170 species endemic to southern China with high levels of ecological (edaphic) specialization, providing an exceptional model to study the plant diversification in karsts. We used molecular data from nine chloroplast and 11 nuclear regions and macroevolutionary analyses to assess the origin and cause of species diversification due to palaeoenvironmental changes and edaphic specialization in Primulina. We found that speciation was positively associated with changes in past temperatures and East Asian monsoons through the evolutionary history of Primulina. Climatic change around the mid-Miocene triggered an early burst followed by a slowdown of diversification rate towards the present with the climate cooling. We detected different speciation rates among edaphic types, and transitions among soil types were infrequently and did not impact the overall speciation rate. Our findings suggest that both global temperature changes and East Asian monsoons have played crucial roles in floristic diversification within the karst ecosystems in southern China, such that speciation was higher when climate was warmer and wetter. This is the first study to directly demonstrate that past monsoon activity is positively correlated with speciation rate in East Asia. This case study could motivate further investigations to assess the impacts of past environmental changes on the origin and diversification of biodiversity in global karst ecosystems, most of which are under threat.

On merging Acer sections Rubra and Hyptiocarpa: Molecular and morphological evidence

In this study, we expanded Acer sect. Rubra Pax to include A. sect. Hyptiocarpa Fang. Traditionally, section Rubra comprises two iconic species, Acer rubrum Linnaeus (red maple) and A. saccharinum Linnaeus (silver maple), of eastern North American forests as well as the rare Japanese montane species, A. pycnanthum K. Koch. Section Hyptiocarpa consists of A. laurinum Hasskarl and A. pinnatinervium Merrill, which occur in subtropical and tropical regions of southwestern China to southeast Asia. Here, we confirm prior phylogenetic results showing the close relationship between sects. Rubra and Hyptiocarpa, and we use scanning electron microscopy to demonstrate that leaves of species within these sections have similar arrangements of cuticular waxes, which account for the silvery color of their abaxial surfaces. We describe that the sections also share labile sex expression; inflorescences that range from compound racemose thyrses, to racemes or umbels and that may have undergone evolutionary reduction; and several features of their fruits, such as seed locules without keels, basal portion of wings straight, acute attachment angle between mericarps, and production of some mericarps that are seedless and partially developed at maturity. Our expansion of sect. Rubra to include sect. Hyptiocarpa better elucidates the biogeographic and evolutionary history of these species. Additionally, we show that A. laurinum and A. pinnatinervium have intergrading morphology and are probably synonymous, but we note that further studies are required to conclude their taxonomic status.

Development of SSR markers from transcriptomes for Orinus (Poaceae), an endemic of the Qinghai-Tibetan Plateau

PREMISE OF THE STUDY

Transcriptomes were used to develop microsatellite markers for the plant genus Orinus (Poaceae), which comprises three species of grasses (O. thoroldii, O. kokonoricus, and O. intermedius) that are widely distributed in the Qinghai-Tibetan Plateau.

METHODS AND RESULTS

Primer pairs were developed for 16 high-quality simple sequence repeats (SSRs) using transcriptomes. SSRs were amplified in 248 individuals representing the three species of Orinus; the number of alleles per locus ranged from one to seven, with an average of 2.6. The expected and observed heterozygosity per locus varied from 0.00 to 0.83 and from 0.00 to 1.00, respectively, with respective mean values of 0.32 and 0.34.

CONCLUSIONS

These newly developed SSR markers will be valuable for evaluating the population genetic structure of Orinus throughout its range.

Plastid Phylogenomics Resolve Deep Relationships among Eupolypod II Ferns with Rapid Radiation and Rate Heterogeneity

The eupolypods II ferns represent a classic case of evolutionary radiation and, simultaneously, exhibit high substitution rate heterogeneity. These factors have been proposed to contribute to the contentious resolutions among clades within this fern group in multilocus phylogenetic studies. We investigated the deep phylogenetic relationships of eupolypod II ferns by sampling all major families and using 40 plastid genomes, or plastomes, of which 33 were newly sequenced with next-generation sequencing technology. We performed model-based analyses to evaluate the diversity of molecular evolutionary rates for these ferns. Our plastome data, with more than 26,000 informative characters, yielded good resolution for deep relationships within eupolypods II and unambiguously clarified the position of Rhachidosoraceae and the monophyly of Athyriaceae. Results of rate heterogeneity analysis revealed approximately 33 significant rate shifts in eupolypod II ferns, with the most heterogeneous rates (both accelerations and decelerations) occurring in two phylogenetically difficult lineages, that is, the Rhachidosoraceae-Aspleniaceae and Athyriaceae clades. These observations support the hypothesis that rate heterogeneity has previously constrained the deep phylogenetic resolution in eupolypods II. According to the plastome data, we propose that 14 chloroplast markers are particularly phylogenetically informative for eupolypods II both at the familial and generic levels. Our study demonstrates the power of a character-rich plastome data set and high-throughput sequencing for resolving the recalcitrant lineages, which have undergone rapid evolutionary radiation and dramatic changes in substitution rates.

Another look at the phylogenetic relationships and intercontinental biogeography of eastern Asian - North American Rhus gall aphids (Hemiptera: Aphididae: Eriosomatinae): Evidence from mitogenome sequences via genome skimming

The Rhus gall aphids are sometimes referred to as subtribe Melaphidina (Aphididae: Eriosomatinae: Fordini) and comprise a unique group that forms galls on the primary host plants, Rhus. We examined the evolutionary relationships within the Melaphidina aphids using sequences of the complete mitochondrial genome and with samples of 11 of the 12 recognized species representing all six genera. Bayesian, maximum likelihood and parsimony analyses of the mitochondrial genome data support five well-supported clades within Melaphidina: (1) Nurudea (except N. ibofushi), (2) Schlechtendalia-Nurudea ibofushi, (3) Meitanaphis-Kaburagia, (4) Floraphis, and (5) Melaphis. Nurudea shiraii and N. yanoniella are sister to each other, but N. ibofushi is nested within Schlechtendalia. The Nurudea shiraii-N. yanoniella clade is sister to the large clade of the remaining taxa of Melaphidina aphids. The Bayesian and maximum likelihood analyses support the North American Melaphis rhois as sister to the clade of Floraphis-Kaburagia-Meitanaphis-Schlechtendalia from eastern Asia, whereas the parsimony analysis suggests Melaphis sister to Floraphis with low support (bootstrap support 38%), and the amino acid data weakly place it sister to Schlechtendalia-Nurudea ibofushi. The Melaphis position needs to be further tested with nuclear data. Meitanaphis flavogallis is sister to Kaburagia species instead of grouping with Meitanaphis elongallis. Using the Bayesian method, the North American Melaphis was estimated to have diverged from its closest Asian relatives around 64.6 (95% HPD 59.4-69.8) Ma, which is in the early Paleocene near the Cretaceous and Paleogene boundary (K/Pg boundary). At the K/Pg boundary, mass extinctions caused many types of insect-plant associations to disappear, and these extinctions may explain some of the difficulties in the phylogenetic placement of Melaphis within the analyses.

Complete mitochondrial genome of the Rhus gall aphid Schlechtendalia chinensis (Hemiptera: Aphididae: Eriosomatinae)

We sequenced the first complete mitochondrial genome for the aphid subfamily, Eriosomatinae, from a Rhus gall aphid, Schlechtendalia chinensis. The mitogenome of S. chinensis is 16,047  bp in length with a high A + T content of 84.2% and consists of 13 protein-coding genes, 24 tRNA genes including two extra tRNA^Phe, two rRNA genes, a repeat region, and a control region. All protein-coding genes have a typical ATN initiation codon and TAA termination codon except COI and ND4, which terminate with a single T. All 24 tRNAs have the expected clover-leaf secondary structure and range in size from 62 to 73  bp. The lengths of rrnL and rrnS genes are 1274 and 772  bp, respectively. The repeat region is 335 bp and is uncommon among known aphid sequences for starting with a tRNA^Phe. The control region is 705 bp in length and is located between rrnS and tRNA^Ile. We present a phylogeny of mitogenomes showing that S. chinensis is sister to Aphidinae.

Morphological and ecological divergence of Lilium and Nomocharis within the Hengduan Mountains and Qinghai-Tibetan Plateau may result from habitat specialization and hybridization

BACKGROUND

Several previous studies have shown that some morphologically distinctive, small genera of vascular plants that are endemic to the Qinghai-Tibetan Plateau and adjacent Hengduan Mountains appear to have unexpected and complex phylogenetic relationships with their putative sisters, which are typically more widespread and more species rich. In particular, the endemic genera may form one or more poorly resolved paraphyletic clades within the sister group despite distinctive morphology. Plausible explanations for this evolutionary and biogeographic pattern include extreme habitat specialization and hybridization. One genus consistent with this pattern is Nomocharis Franchet. Nomocharis comprises 7-15 species bearing showy-flowers that are endemic to the H-D Mountains. Nomocharis has long been treated as sister to Lilium L., which is comprised of more than 120 species distributed throughout the temperate Northern Hemisphere. Although Nomocharis appears morphologically distinctive, recent molecular studies have shown that it is nested within Lilium, from which is exhibits very little sequence divergence. In this study, we have used a dated molecular phylogenetic framework to gain insight into the timing of morphological and ecological divergence in Lilium-Nomocharis and to preliminarily explore possible hybridization events. We accomplished our objectives using dated phylogenies reconstructed from nuclear internal transcribed spacers (ITS) and six chloroplast markers.

RESULTS

Our phylogenetic reconstruction revealed several Lilium species nested within a clade of Nomocharis, which evolved ca. 12 million years ago and is itself nested within the rest of Lilium. Flat/open and horizon oriented flowers are ancestral in Nomocharis. Species of Lilium nested within Nomocharis diverged from Nomocharis ca. 6.5 million years ago. These Lilium evolved recurved and campanifolium flowers as well as the nodding habit by at least 3.5 million years ago. Nomocharis and the nested Lilium species had relatively low elevation ancestors (<1000 m) and underwent diversification into new, higher elevational habitats 3.5 and 5.5 million years ago, respectively. Our phylogeny reveals signatures of hybridization including incongruence between the plastid and nuclear gene trees, geographic clustering of the maternal (i.e., plastid) lineages, and divergence ages of the nuclear gene trees consistent with speciation and secondary contact, respectively.

CONCLUSIONS

The timing of speciation and ecological and morphological evolutionary events in Nomocharis are temporally consistent with uplift in the Qinghai-Tibetan Plateau and of the Hengduan Mountains 7 and 3-4 million years ago, respectively. Thus, we speculate that the mountain building may have provided new habitats that led to specialization of morphological and ecological features in Nomocharis and the nested Lilium along ecological gradients. Additionally, we suspect that the mountain building may have led to secondary contact events that enabled hybridization in Lilium-Nomocharis. Both the habitat specialization and hybridization have probably played a role in generating the striking morphological differences between Lilium and Nomocharis.

Evidence of decreased muscle protein turnover in gilts selected for low residual feed intake

The objective of this study was to evaluate the contribution of muscle protein turnover (synthesis and degradation) to the biological basis for genetic differences in finisher pigs selected for residual feed intake (RFI). Residual feed intake is defined as the difference between expected feed intake (based on the achieved rate of BW gain and backfat depth of individual pigs) and the observed feed intake of the individual pig. We hypothesized that protein turnover would be reduced in pigs selected for low RFI. Twelve gilts from a line selected for 7 generations for low RFI and 12 from a contemporary line selected for 2 generations for high RFI were paired by age and BW and fed a standard corn-soybean diet for 6 wk. Pigs were euthanized, muscle and liver samples were collected, and insulin signaling, protein synthesis, and protein degradation proteins were analyzed for expression and activities. Muscle from low RFI pigs tended to have less μ- and m-calpain activities (P = 0.10 and 0.09, respectively) and had significantly greater calpastatin activity and a decreased μ-calpain:calpastatin activity ratio (P < 0.05). Muscle from low RFI pigs had less 20S proteasome activity compared with their high RFI counterparts (P < 0.05). No differences in insulin signaling intermediates and translation initiation signaling proteins [mammalian target of rapamycin (mTOR) pathway] were observed (P > 0.05). Postmortem proteolysis was determined in the LM from the eighth generation of the low RFI pigs versus their high RFI counterparts (n = 9 per line). Autolysis of μ-calpain was decreased in the low RFI pigs and less troponin-T degradation product was observed at 3 d postmortem (P < 0.05), indicating slowed postmortem proteolysis during aging in the low RFI pigs. These data provide significant evidence that less protein degradation occurs in pigs selected for reduced RFI, and this may account for a significant portion of the increased efficiency observed in these animals.

Intestinal integrity, endotoxin transport and detoxification in pigs divergently selected for residual feed intake

Microbes and microbial components potentially impact the performance of pigs through immune stimulation and altered metabolism. These immune modulating factors can include endotoxin from gram negative bacterial outer membrane component, commonly referred to as lipopolysaccharide (LPS). In this study, our objective was to examine the relationship between intestinal barrier integrity, endotoxin and inflammation with feed efficiency (FE), using pig lines divergently selected for residual feed intake (RFI) as a model. Twelve gilts (62 ± 3 kg BW) from the low RFI (LRFI, more efficient) and 12 from the high RFI (HRFI, less efficient) were used. Individual performance data was recorded for 5 wk. At the end of the experimental period, ADFI of LRFI pigs was less (P < 0.001), ADG not different between the 2 lines (P = 0.72) but the G:F of LRFI pigs was greater than for HRFI pigs (P = 0.019). Serum endotoxin concentration (P < 0.01) and the acute phase protein haptoglobin (P < 0.05) were greater in HRFI pigs. Transepithelial resistance of the ileum, transport of fluorescein isothiocyanate labeled-Dextran and-LPS in ileum and colon, as well as tight junction protein mRNA expression in ileum, did not differ between the lines, indicating the 2 lines did not differ in transport characteristics at the intestinal level. Ileum inflammatory markers, myeloperoxidase (P < 0.05) and IL-8 (P < 0.10), were found to be greater in HRFI pigs. Alkaline phosphatase (ALP) activity was significantly increased in the LRFI pigs in ileum and liver tissues and negatively correlated with blood endotoxin (P < 0.05). Lysozyme activity in the liver was not different between the lines; however, the LRFI pigs had a twofold greater lysozyme activity in ileum (P < 0.05). Despite the difference in their activity, ALP or lysozyme mRNA expression was not different between the lines in either tissue. Decreased endotoxin and inflammatory markers and the enhanced activities of antimicrobial enzymes in the LRFI line may not fully explain the difference in the FE between the lines, but they have the potential to prevent the growth potential in HRFI pigs. Further studies are needed to identify the other mechanisms that may contribute to the greater endotoxin and acute phase proteins in the HRFI pigs and the greater FE in the LRFI pigs.

The metabolism of the 5HT3antagonists ondansetron, alosetron and GR87442 I: A comparison ofin vitroandin vivometabolism andin vitroenzyme kinetics in rat, dog and human hepatocytes, microsomes and recombinant human enzymes

The metabolism of the structurally related 5HT3 antagonists ondansetron, alosetron and GR87442 in the rat, dog and human was determined in hepatocytes, liver microsomes and human recombinant microsomes. The profiles of phase I metabolites were similar in human hepatocytes and microsomes. The metabolites of all three compounds produced in rat, dog and human microsomes and hepatocytes were similar to those seen in vivo, with the major routes of metabolism being N-dealkylation and/or hydroxylation. There was more extensive metabolic processing in hepatocytes than in microsomes; however, sequential metabolism was less extensive in vitro compared with in vivo. The pharmacokinetics of the three 5HT3 antagonists investigated were dominated by CYP3A4 (and/or 2C9) compared with CYP1A2 in man, possibly determined by enzyme capacity rather than relative enzyme affinity. These data support the use of rat, dog and human hepatocytes for the prediction of in vivo metabolites of ondansetron, alosetron and GR87442.

West African refugee health in rural Australia: complex cultural factors that influence mental health

Health and mental health practitioners in rural and regional Australia are increasingly being presented with the challenge of working cross-culturally. Due to a diversity of cultures, generic approaches are needed that take account of culture without requiring the practitioner to have detailed knowledge of each person's background. However, there are many practitioners from diverse backgrounds now working in Australia at various stages of enculturation into Western practice. The cultural grounding of one practitioner from West Africa is used to highlight potential areas of misunderstanding, and to offer an accessible point of departure for culturally sensitive practice and formal research opportunities.

Tissue interactions and antlerogenesis: new findings revealed by a xenograft approach

Tissue interactions play a pivotal role in organogenesis. Here we describe a xenograft approach to investigate how heterotypic tissue interactions control antler formation in deer. Deciduous antlers grow from the apices of permanent protuberances, called pedicles. Histogenesis of pedicles depends on the antlerogenic periosteum (AP). Pedicles and growing antlers are made up of interior osseocartilage (a mixture of bone and cartilaginous tissue) and exterior skin. In a previous study we hypothesised that pedicle growth may result from mechanical interactions between the interior and exterior components whereas antler generation from a pedicle would involve molecules communicating between the interior and exterior components. To test this hypothesis, we subcutaneously transplanted AP of red deer (Cervus elaphus), either alone or with future pedicle skin, onto nude mice. The results showed that under the nude mouse skin, subcutaneously xenografted AP alone not only could form pedicle-shaped protuberances but also could differentiate into well-organised pedicle-like structures. The overlying mouse skin accommodated the expansion of the grafted AP by initial mechanical stretching and subsequent formation of new skin. Nude mouse skin was not capable of participating in antler tissue formation. However, grafted deer skin together with AP may have successfully rescued this failure after wounding, which highlights the necessity of the specificity of the overlying skin for antler tissue generation. Therefore, we conclude that it is the interaction between the antlerogenic tissue and the overlying skin that results in antlerogenesis: reciprocal mechanical interactions cause pedicle formation, whereas reciprocal instructive interactions induce first antler generation.