Genome assemblies of 11 bamboo species highlight diversification induced by dynamic subgenome dominance.

Polyploidy (genome duplication) is a pivotal force in evolution. However, the interactions between parental genomes in a polyploid nucleus, frequently involving subgenome dominance, are poorly understood. Here we showcase analyses of a bamboo system (Poaceae: Bambusoideae) comprising a series of lineages from diploid (herbaceous) to tetraploid and hexaploid (woody), with 11 chromosome-level de novo genome assemblies and 476 transcriptome samples. We find that woody bamboo subgenomes exhibit stunning karyotype stability, with parallel subgenome dominance in the two tetraploid clades and a gradual shift of dominance in the hexaploid clade. Allopolyploidization and subgenome dominance have shaped the evolution of tree-like lignified culms, rapid growth and synchronous flowering characteristic of woody bamboos as large grasses. Our work provides insights into genome dominance in a remarkable polyploid system, including its dependence on genomic context and its ability to switch which subgenomes are dominant over evolutionary time.

A maceration technique for soft plant tissue without hazardous chemicals.

Premise: Current methods for maceration of plant tissue use hazardous chemicals. The new method described here improves the safety of dissection and maceration of soft plant tissues for microscopic imaging by using the harmless enzyme pectinase. Methods and Results: Leaf material from a variety of land plants was obtained from living plants and dried herbarium specimens. Concentrations of aqueous pectinase and soaking schedules were optimized, and tissues were manually dissected while submerged in fresh solution following a soaking period. Most leaves required 2-4 h of soaking; however, delicate leaves could be macerated after 30 min while tougher leaves required 12 h to 3 days of soaking. Staining techniques can also be used with this method, and permanent or semi-permanent slides can be prepared. The epidermis, vascular tissue, and individual cells were imaged at magnifications of 10× to 400×. Only basic safety precautions were needed. Conclusions: This pectinase method is a cost-effective and safe way to obtain images of epidermal peels, separated tissues, or isolated cells from a wide range of plant taxa.

Intraspeaker Priming across the New Zealand English Short Front Vowel Shift.

A growing body of research in psycholinguistics, corpus linguistics, and sociolinguistics shows that we have a strong tendency to repeat linguistic material that we have recently produced, seen, or heard. The present paper investigates whether priming effects manifest in continuous phonetic variation the way it has been reported in phonological, morphological, and syntactic variation. We analyzed nearly 60,000 tokens of vowels involved in the New Zealand English short front vowel shift (SFVS), a change in progress in which trap/dress move in the opposite direction to kit, from a topic-controlled corpus of monologues (166 speakers), to test for effects that are characteristic of priming phenomena: repetition, decay, and lexical boost. Our analysis found evidence for all three effects. Tokens that were relatively high and front tended to be followed by tokens that were also high and front; the repetition effect weakened with greater time between the prime and target; and the repetition effect was stronger if the prime and target belonged to (different tokens of) the same word. Contrary to our expectations, however, the cross-vowel effects suggest that the repetition effect responded not to the direction of vowel changes within the SFVS, but rather the peripherality of the tokens. We also found an interaction between priming behavior and gender, with stronger repetition effects among men than women. While these findings both indicate that priming manifests in continuous phonetic variation and provide further evidence that priming is among the factors providing structure to intraspeaker variation, they also challenge unitary accounts of priming phenomena.

The Streptochaeta Genome and the Evolution of the Grasses.

In this work, we sequenced and annotated the genome of Streptochaeta angustifolia, one of two genera in the grass subfamily Anomochlooideae, a lineage sister to all other grasses. The final assembly size is over 99% of the estimated genome size. We find good collinearity with the rice genome and have captured most of the gene space. Streptochaeta is similar to other grasses in the structure of its fruit (a caryopsis or grain) but has peculiar flowers and inflorescences that are distinct from those in the outgroups and in other grasses. To provide tools for investigations of floral structure, we analyzed two large families of transcription factors, AP2-like and R2R3 MYBs, that are known to control floral and spikelet development in rice and maize among other grasses. Many of these are also regulated by small RNAs. Structure of the gene trees showed that the well documented whole genome duplication at the origin of the grasses (ρ) occurred before the divergence of the Anomochlooideae lineage from the lineage leading to the rest of the grasses (the spikelet clade) and thus that the common ancestor of all grasses probably had two copies of the developmental genes. However, Streptochaeta (and by inference other members of Anomochlooideae) has lost one copy of many genes. The peculiar floral morphology of Streptochaeta may thus have derived from an ancestral plant that was morphologically similar to the spikelet-bearing grasses. We further identify 114 loci producing microRNAs and 89 loci generating phased, secondary siRNAs, classes of small RNAs known to be influential in transcriptional and post-transcriptional regulation of several plant functions.

Integrated Genomic Analyses From Low-Depth Sequencing Help Resolve Phylogenetic Incongruence in the Bamboos (Poaceae: Bambusoideae).

The bamboos (Bambusoideae, Poaceae) comprise a major grass lineage with a complex evolutionary history involving ancient hybridization and allopolyploidy. About 1700 described species are classified into three tribes, Olyreae (herbaceous bamboos), Bambuseae (tropical woody bamboos), and Arundinarieae (temperate woody bamboos). Nuclear analyses strongly support monophyly of the woody tribes, whereas plastome analyses strongly support paraphyly, with Bambuseae sister to Olyreae. Our objectives were to clarify the origin(s) of the woody bamboo tribes and resolve the nuclear vs. plastid conflict using genomic tools. For the first time, plastid and nuclear genomic information from the same bamboo species were combined in a single study. We sampled 51 species of bamboos representing the three tribes, estimated their genome sizes and generated low-depth sample sequence data, from which plastomes were assembled and nuclear repeats were analyzed. The distribution of repeat families was found to agree with nuclear gene phylogenies, but also provides novel insights into nuclear evolutionary history. We infer two early, independent hybridization events, one between an Olyreae ancestor and a woody ancestor giving rise to the two Bambuseae lineages, and another between two woody ancestors giving rise to the Arundinarieae. Retention of the Olyreae plastome associated with differential dominance of nuclear genomes and subsequent diploidization in some lineages explains the paraphyly observed in plastome phylogenetic estimations. We confirm ancient hybridization and allopolyploidy in the origins of the extant woody bamboo lineages and propose biased fractionation and diploidization as important factors in their evolution.

Notes on leaf micromorphology of the rare herbaceous bamboo Buergersiochloa bambusoides Pilg. (Olyreae, Poaceae) from New Guinea and its taxonomic implications.

We present notes on the leaf micromorphology of Buergersiochloa bambusoides, a rare species from New Guinea and included in Buergersiochloinae, one of three subtribes of the herbaceous bamboos (tribe Olyreae). We used scanning electron microscopy and light microscopy to analyze the microcharacters of both adaxial and abaxial leaf surfaces. Within the Olyreae, saddle-shaped silica bodies in both the costal and intercostal zones are considered unique to Buergersiochloinae. Simple, circular and very small papillae are observed on the adaxial surface, and for the first time, branched papillae on the abaxial surface are observed in B. bambusoides. On the abaxial surface, there are papillae on long cells associated with the stomatal complexes. Bicellular microhairs are the only trichomes present and they are found almost exclusively on the abaxial surface. The saddle-shaped silica bodies are the most taxonomically important among the microcharacters observed on the leaf surface of B. bambusoides.

Draft genome of the herbaceous bamboo Raddia distichophylla.

Bamboos are important nontimber forest plants widely distributed in the tropical and subtropical regions of Asia, Africa, America, and Pacific islands. They comprise the Bambusoideae in the grass family (Poaceae), including approximately 1700 described species in 127 genera. In spite of the widespread uses of bamboo for food, construction, and bioenergy, the gene repertoire of bamboo still remains largely unexplored. Raddia distichophylla (Schrad. ex Nees) Chase, belonging to the tribe Olyreae (Bambusoideae, Poaceae), is a diploid herbaceous bamboo with only slightly lignified stems. In this study, we report a draft genome assembly of the ∼589 Mb whole-genome sequence of R. distichophylla with a contig N50 length of 86.36 Kb. Repeat sequences account for ∼49.08% of the genome assembly, of which LTR retrotransposons occupy ∼35.99% of the whole genome. A total of 30,763 protein-coding genes were annotated in the R. distichophylla genome with an average transcript size of 2887 bp. Access to this herbaceous bamboo genome sequence will provide novel insights into biochemistry, molecular marker-assisted breeding programs, and germplasm conservation for bamboo species worldwide.

3D shape analysis of grass silica short cell phytoliths: a new method for fossil classification and analysis of shape evolution.

Fossil grass silica short cell phytoliths (GSSCP) have been used to reconstruct the biogeography of Poaceae, untangle crop domestication history and detect past vegetation shifts. These inferences depend on accurately identifying the clade to which the fossils belong. Patterns of GSSCP shape and size variation across the family have not been established and current classification methods are subjective or based on a 2D view that ignores important 3D shape variation. Focusing on Poaceae subfamilies Anomochlooideae, Pharoideae, Pueliodieae, Bambusoideae and Oryzoideae, we observed in situ GSSCP to establish their orientation and imaged isolated GSSCP using confocal microscopy to produce 3D models. 3D geometric morphometrics was used to analyze GSSCP shape and size. Classification models were applied to GSSCP from Eocene sediments from Nebraska, USA, and Anatolia, Turkey. There were significant shape differences between nearly all recognized GSSCP morphotypes and between clades with shared morphotypes. Most of the Eocene GSSCP were classified as woody bamboos with some distinctive Nebraska GSSCP classified as herbaceous bamboos. 3D morphometrics hold great promise for GSSCP classification. It accounts for the complete GSSCP shape, automates size measurements and accommodates the complete range of morphotypes within a single analytical framework.

Phylogenetic relationships within Parianinae (Poaceae: Bambusoideae: Olyreae) with emphasis on Eremitis: Evidence from nuclear and plastid DNA sequences, macromorphology, and pollen ectexine patterns.

Eremitis, Pariana, and Parianella are herbaceous bamboos (tribe Olyreae) included in the subtribe Parianinae, which is characterized by the presence of fimbriae at the apex of the leaf sheaths and exclusively spiciform synflorescences. We analyzed 43 samples of herbaceous and woody bamboos in order to infer relationships within the Parianinae, based on combined data from the nuclear ribosomal internal transcribed spacer (ITS) and plastid DNA (rpl32-trnL and trnD-trnT spacers). Bayesian inference, maximum likelihood, and maximum parsimony methods were applied, and macro- and micromorphological aspects were also analyzed, including the ectexine patterns of pollen grains. Parianinae is represented by three well-supported lineages in our analyses: (1) Parianella, endemic to southern Bahia, Brazil; (2) Pariana sensu stricto with a broad distribution in southern Central America and northern South America, especially in the Amazon region; and (3) Eremitis, endemic to the Brazilian Atlantic Forest, from the states of Pernambuco to Rio de Janeiro, including one species previously described as a member of Pariana. Our molecular phylogeny showed that Pariana, as historically circumscribed, is not monophyletic, by recovering Pariana sensu stricto as strongly supported and sister to Eremitis + Pariana multiflora, with Parianella sister to the Pariana-Eremitis clade. Morphological features of their synflorescences and differences in ectexine patterns characterize each lineage. Based on all these characters and the phylogenetic results, Pariana multiflora, endemic to the state of Espírito Santo, Brazil, is transferred to Eremitis.

Leaf shape and size track habitat transitions across forest-grassland boundaries in the grass family (Poaceae).

Grass leaf shape is a strong indicator of their habitat with linear leaves predominating in open areas and ovate leaves distinguishing forest-associated grasses. This pattern among extant species suggests that ancestral shifts between forest and open habitats may have coincided with changes in leaf shape or size. We tested relationships between habitat, climate, photosynthetic pathway, and leaf shape and size in a phylogenetic framework to evaluate drivers of leaf shape and size variation over the evolutionary history of the family. We also estimated the ancestral habitat of Poaceae and tested whether forest margins served as transitional zones for shifts between forests and grasslands. We found that grass leaf shape is converging toward different shape optima in the forest understory, forest margins, and open habitats. Leaf size also varies with habitat. Grasses have smaller leaves in open and drier areas, and in areas with high solar irradiance. Direct transitions between linear and ovate leaves are rare as are direct shifts between forest and open habitats. The most likely ancestral habitat of the family was the forest understory and forest margins along with an intermediate leaf shape served as important transitional habitat and morphology, respectively, for subsequent shifts across forest-grassland biome boundaries.

Fusoid cells in the grass family Poaceae (Poales): a developmental study reveals homologies and suggests new insights into their functional role in young leaves.

Background and Aims: In mature grass leaf blades as seen in cross-section, oblong cell-like structures have been interpreted most recently as intercellular gas spaces delimited by successive collapsed fusoid cells. These cells have been reported in at least seven of 12 subfamilies of Poaceae and are considered a synapomorphy for the family; however, no developmental work has been performed to verify their meristematic origin or to assess possible homologies within the graminid clade (= Flagellariaceae + [(Joinvilleaceae + Ecdeiocoleaceae) + Poaceae]) or among subfamilies of Poaceae. A developmental study was therefore carried out, including 20 species in three families (Flagellariaceae, Joinvilleaceae and Poaceae), representing the earlier-diverging and derived branches within the graminid clade and Poaceae. Methods: Light microscopy was combined with scanning electron microscopy, cryoscanning electron microscopy and transmission electron microscopy to study the development of leaves taken from the shoot apex of young plants. Mature leaf blades also were taken from living or dried plants and the mid-portion was studied. Key Results: Developmental results show that, in mature leaf blades as seen in cross-section, one apparent fusoid cell is typically a cavity resulting from the collapse of the initial fusoid cell and its internal divisions, which are herein interpreted as derivative cells with formation of cell plates only. Each cavity is delimited by successive collapsed fusoid cells arranged perpendicularly to the veins. Fusoid cells in all studied Poaceae members originate from the ground meristem, as do the colourless cells in Joinvillea ascendens (Joinvilleaceae). These two types of mesophyll cell have a strongly similar ontogeny, distinguished mainly by the collapse of the fusoid cells in Poaceae, which is not observed in the colourless cells in J. ascendens. Conclusions: Within the Poaceae, the meristematic origin of fusoid cells is the same in the early-diverging lineages, BOP clade and Panicoideae, and thus they are homologous within the family. The same topography and meristematic origin suggest that fusoid cells in Poaceae and colourless cells in Joinvilleaceae are homologous. The results also suggest that the role played by the fusoid cells in young grass leaves is related to synthesis and storage of starch granules at early stages of development.

A refined method for digitally modeling small and complex plant structures in 3D: An example from the grasses (Poaceae).

PREMISE OF THE STUDY: A refined procedure is described for modeling small, intricate plant structures using computer-aided design software. The procedure facilitates the study of wind pollination in the family Poaceae and provides virtual biological illustrations for public outreach. METHODS AND RESULTS: Spikelets were fixed in gFAA, dehydrated using ethanol and xylene, embedded in paraffin wax, and then sectioned with a rotary microtome. Images of serial sections were used as a reference for modeling the shape of bracts with splines in a computer-aided design program. Virtual models produced by this method have many potential uses; examples include geometric morphometric analyses and simulations of computational fluid dynamics. CONCLUSIONS: This protocol is a synthesis of modern biological illustration and engineering technology. Virtual models facilitate quantitative experiments that may address questions about reproductive biology, conditions shaping the form of anatomical support, or the morphological evolution of structures of biomechanical interest.

Topological Data Analysis as a Morphometric Method: Using Persistent Homology to Demarcate a Leaf Morphospace.

Current morphometric methods that comprehensively measure shape cannot compare the disparate leaf shapes found in seed plants and are sensitive to processing artifacts. We explore the use of persistent homology, a topological method applied as a filtration across simplicial complexes (or more simply, a method to measure topological features of spaces across different spatial resolutions), to overcome these limitations. The described method isolates subsets of shape features and measures the spatial relationship of neighboring pixel densities in a shape. We apply the method to the analysis of 182,707 leaves, both published and unpublished, representing 141 plant families collected from 75 sites throughout the world. By measuring leaves from throughout the seed plants using persistent homology, a defined morphospace comparing all leaves is demarcated. Clear differences in shape between major phylogenetic groups are detected and estimates of leaf shape diversity within plant families are made. The approach predicts plant family above chance. The application of a persistent homology method, using topological features, to measure leaf shape allows for a unified morphometric framework to measure plant form, including shapes, textures, patterns, and branching architectures.

Priming as a Motivating Factor in Sociophonetic Variation and Change.

Understanding how and why pronunciations vary and change has been a dominant theme in variationist sociolinguistics (Labov, , ). Linguistic variability has also been an area of focus in psychology and cognitive science. Work from these two fields has shown that where variation exists in language, an alternative form, once used, persists in working memory and has a greater chance of reuse (Bock, ; Bock & Loebell, ; Branigan, Pickering, & Cleland, ). While there have been efforts to connect priming research with sociolinguistics at the level of grammar (Poplack, ; Travis, ), there has been less work which explicitly considers the potential role of priming as a motivating factor in accent variation and change. This paper explores the role of priming in a socially conditioned sound change. There are two main findings: (a) phonetic variants with the same voicing tend to cluster together in naturally occurring speech and (b) repetition of phonetic form interacts with widely attested sociolinguistic predictors of variation. I argue that there are benefits to both cognitive science and sociolinguistics from this synergy: Incorporating research from cognitive science into sociolinguistics provides us with a better understanding of the factors underpinning a sound change in progress; incorporating insights from sociolinguistics into cognitive science shows that priming does not always operate in the same way for all speakers.

A 250 plastome phylogeny of the grass family (Poaceae): topological support under different data partitions.

The systematics of grasses has advanced through applications of plastome phylogenomics, although studies have been largely limited to subfamilies or other subgroups of Poaceae. Here we present a plastome phylogenomic analysis of 250 complete plastomes (179 genera) sampled from 44 of the 52 tribes of Poaceae. Plastome sequences were determined from high throughput sequencing libraries and the assemblies represent over 28.7 Mbases of sequence data. Phylogenetic signal was characterized in 14 partitions, including (1) complete plastomes; (2) protein coding regions; (3) noncoding regions; and (4) three loci commonly used in single and multi-gene studies of grasses. Each of the four main partitions was further refined, alternatively including or excluding positively selected codons and also the gaps introduced by the alignment. All 76 protein coding plastome loci were found to be predominantly under purifying selection, but specific codons were found to be under positive selection in 65 loci. The loci that have been widely used in multi-gene phylogenetic studies had among the highest proportions of positively selected codons, suggesting caution in the interpretation of these earlier results. Plastome phylogenomic analyses confirmed the backbone topology for Poaceae with maximum bootstrap support (BP). Among the 14 analyses, 82 clades out of 309 resolved were maximally supported in all trees. Analyses of newly sequenced plastomes were in agreement with current classifications. Five of seven partitions in which alignment gaps were removed retrieved Panicoideae as sister to the remaining PACMAD subfamilies. Alternative topologies were recovered in trees from partitions that included alignment gaps. This suggests that ambiguities in aligning these uncertain regions might introduce a false signal. Resolution of these and other critical branch points in the phylogeny of Poaceae will help to better understand the selective forces that drove the radiation of the BOP and PACMAD clades comprising more than 99.9% of grass diversity.

Digital Media, Participatory Politics, and Positive Youth Development.

Research on the social implications of adolescent technology use often focuses on identifying and preventing risk. However, adolescence is also a time of rapidly expanding capacities, expectations of autonomy, and identity exploration. In this article, we highlight findings from research in the field of youth civic development, which point to the importance of youth civic engagement during adolescence for later adult civic engagement as well as for promoting positive developmental outcomes. Researchers suggest that certain forms of Internet use (such as information seeking, social network site use, media production, and participation in online communities) promote civic engagement and that digital tools play an important role in youth empowerment efforts. In this article, we suggest a need for greater attention to efforts to promote digital media competencies among adolescents and for greater coordination of research on adolescent risk and adolescent autonomy and empowerment related to Internet use.

Evolutionary relationships in Panicoid grasses based on plastome phylogenomics (Panicoideae; Poaceae).

BACKGROUND: Panicoideae are the second largest subfamily in Poaceae (grass family), with 212 genera and approximately 3316 species. Previous studies have begun to reveal relationships within the subfamily, but largely lack resolution and/or robust support for certain tribal and subtribal groups. This study aims to resolve these relationships, as well as characterize a putative mitochondrial insert in one linage. RESULTS: 35 newly sequenced Panicoideae plastomes were combined in a phylogenomic study with 37 other species: 15 Panicoideae and 22 from outgroups. A robust Panicoideae topology largely congruent with previous studies was obtained, but with some incongruences with previously reported subtribal relationships. A mitochondrial DNA (mtDNA) to plastid DNA (ptDNA) transfer was discovered in the Paspalum lineage. CONCLUSIONS: The phylogenomic analysis returned a topology that largely supports previous studies. Five previously recognized subtribes appear on the topology to be non-monophyletic. Additionally, evidence for mtDNA to ptDNA transfer was identified in both Paspalum fimbriatum and P. dilatatum, and suggests a single rare event that took place in a common progenitor. Finally, the framework from this study can guide larger whole plastome sampling to discern the relationships in Cyperochloeae, Steyermarkochloeae, Gynerieae, and other incertae sedis taxa that are weakly supported or unresolved.

Simple Web-based interactive key development software (WEBiKEY) and an example key for Kuruna (Poaceae: Bambusoideae).

PREMISE OF THE STUDY: Programs that are user-friendly and freely available for developing Web-based interactive keys are scarce and most of the well-structured applications are relatively expensive. WEBiKEY was developed to enable researchers to easily develop their own Web-based interactive keys with fewer resources. METHODS AND RESULTS: A Web-based multiaccess identification tool (WEBiKEY) was developed that uses freely available Microsoft ASP.NET technologies and an SQL Server database for Windows-based hosting environments. WEBiKEY was tested for its usability with a sample data set, the temperate woody bamboo genus Kuruna (Poaceae). CONCLUSIONS: WEBiKEY is freely available to the public and can be used to develop Web-based interactive keys for any group of species. The interactive key we developed for Kuruna using WEBiKEY enables users to visually inspect characteristics of Kuruna and identify an unknown specimen as one of seven possible species in the genus.

Phylogenetic estimation and morphological evolution of Arundinarieae (Bambusoideae: Poaceae) based on plastome phylogenomic analysis.

We explored phylogenetic relationships among the twelve lineages of the temperate woody bamboo clade (tribe Arundinarieae) based on plastid genome (plastome) sequence data. A representative sample of 28 taxa was used and maximum parsimony, maximum likelihood and Bayesian inference analyses were conducted to estimate the Arundinarieae phylogeny. All the previously recognized clades of Arundinarieae were supported, with Ampelocalamus calcareus (Clade XI) as sister to the rest of the temperate woody bamboos. Well supported sister relationships between Bergbambos tessellata (Clade I) and Thamnocalamus spathiflorus (Clade VII) and between Kuruna (Clade XII) and Chimonocalmus (Clade III) were revealed by the current study. The plastome topology was tested by taxon removal experiments and alternative hypothesis testing and the results supported the current plastome phylogeny as robust. Neighbor-net analyses showed few phylogenetic signal conflicts, but suggested some potentially complex relationships among these taxa. Analyses of morphological character evolution of rhizomes and reproductive structures revealed that pachymorph rhizomes were most likely the ancestral state in Arundinarieae. In contrast leptomorph rhizomes either evolved once with reversions to the pachymorph condition or multiple times in Arundinarieae. Further, pseudospikelets evolved independently at least twice in the Arundinarieae, but the ancestral state is ambiguous.