Phylogenomic resolution of order- and family-level monocot relationships using 602 single-copy nuclear genes and 1375 BUSCO genes.

We assess relationships among 192 species in all 12 monocot orders and 72 of 77 families, using 602 conserved single-copy (CSC) genes and 1375 benchmarking single-copy ortholog (BUSCO) genes extracted from genomic and transcriptomic datasets. Phylogenomic inferences based on these data, using both coalescent-based and supermatrix analyses, are largely congruent with the most comprehensive plastome-based analysis, and nuclear-gene phylogenomic analyses with less comprehensive taxon sampling. The strongest discordance between the plastome and nuclear gene analyses is the monophyly of a clade comprising Asparagales and Liliales in our nuclear gene analyses, versus the placement of Asparagales and Liliales as successive sister clades to the commelinids in the plastome tree.

Riparian areas as a conservation priority under climate change.

Identifying climatic refugia is important for long-term conservation planning under climate change. Riparian areas have the potential to provide climatic refugia for wildlife, but literature remains limited, especially for plants. This study was conducted with the purpose of identifying climatic refugia of plant biodiversity in the portion of the Mekong River Basin located in Xishuangbanna, China.

Down, then up: non-parallel genome size changes and a descending chromosome series in a recent radiation of the Australian allotetraploid plant species, Nicotiana section Suaveolentes (Solanaceae).

Background And Aims: The extent to which genome size and chromosome numbers evolve in concert is little understood, particularly after polyploidy (whole-genome duplication), when a genome returns to a diploid-like condition (diploidization). We study this phenomenon in 46 species of allotetraploid Nicotiana section Suaveolentes (Solanaceae), which formed <6 million years ago and radiated in the arid centre of Australia.

Methods: We analysed newly assessed genome sizes and chromosome numbers within the context of a restriction site-associated nuclear DNA (RADseq) phylogenetic framework.

Assessing candidate DNA barcodes for Chinese and internationally traded timber species.

Accurate identification of species from timber is an essential step to help control illegal logging and forest loss. However, current approaches to timber identification based on morphological and anatomical characteristics have limited species resolution. DNA barcoding is a proven tool for plant species identification, but there is a need to build reliable reference data across broad taxonomic and spatial scales.

Evolution of Lomandroideae: Multiple origins of polyploidy and biome occupancy in Australia.

Asparagaceae: Lomandroideae are a species-rich and economically important subfamily in the monocot order Asparagales, with a center of diversity in Australia. Lomandroideae are ecologically diverse, occupying mesic and arid biomes in Australia and possessing an array of key traits, including sexual dimorphism, storage organs and polyploidy that are potentially adaptive for survival in seasonally arid and fire-dependent habitats. The Lomandroideae phylogeny was reconstructed using maximum likelihood and Bayesian inference criteria, based on plastome data from genome-skimming to infer relationships.

An Akania (Akaniaceae) inflorescence with associated pollen from the early Miocene of New Zealand.

Premise Of The Study: An Akania-like inflorescence, including flowers with in situ pollen was recovered from the remarkable Konservat-Lagerstätte lacustrine diatomite deposit at Foulden Maar, Otago indicating the presence of Akaniaceae in southern New Zealand during the early Miocene. The flowers, although slightly smaller than the sole modern Australian species, A. bidwillii, contain pollen grains that are very like that taxon.

DNA barcoding evaluation and implications for phylogenetic relationships in Lauraceae from China.

Lauraceae are an important component of tropical and subtropical forests and have major ecological and economic significance. Owing to lack of clear-cut morphological differences between genera and species, this family is an ideal case for testing the efficacy of DNA barcoding in the identification and discrimination of species and genera. In this study, we evaluated five widely recommended plant DNA barcode loci matK, rbcL, trnH-psbA, ITS2 and the entire ITS region for 409 individuals representing 133 species, 12 genera from China.

Hedycarya macrofossils and associated Planarpollenites pollen from the early Miocene of New Zealand.

Premise Of The Study: The history of the basal angiosperm family Monimiaceae is based largely on fossil wood and leaf and floral fossils of uncertain affinity. Fossilized leaves with a well-preserved cuticle and Hedycarya-like flowers, including one with in situ pollen tetrads and fruits from an early Miocene lacustrine diatomite deposit in southern New Zealand implies a long record for Hedycarya in New Zealand. The flowers contain pollen grains that are very similar to those of the modern New Zealand species Hedycarya arborea and the Australian H.

Origins and evolution of cinnamon and camphor: A phylogenetic and historical biogeographical analysis of the Cinnamomum group (Lauraceae).

Tropical and subtropical amphi-Pacific disjunction is among the most fascinating distribution patterns, but received little attention. Here we use the fossil-rich Cinnamomum group, a primarily tropical and subtropical Asian lineage with some species distributed in Neotropics, Australasia and Africa to shed light upon this disjunction pattern. Phylogenetic and biogeographic analyses were carried out using sequences of three nuclear loci from 94 Cinnamomum group and 13 outgroup samples.

Transcriptome-derived evidence supports recent polyploidization and a major phylogeographic division in Trithuria submersa (Hydatellaceae, Nymphaeales).

Relatively little is known about species-level genetic diversity in flowering plants outside the eudicots and monocots, and it is often unclear how to interpret genetic patterns in lineages with whole-genome duplications. We addressed these issues in a polyploid representative of Hydatellaceae, part of the water-lily order Nymphaeales. We examined a transcriptome of Trithuria submersa for evidence of recent whole-genome duplication, and applied transcriptome-derived microsatellite (expressed-sequence tag simple-sequence repeat (EST-SSR)) primers to survey genetic variation in populations across its range in mainland Australia.

Plastid genomes reveal support for deep phylogenetic relationships and extensive rate variation among palms and other commelinid monocots.

Despite progress based on multilocus, phylogenetic studies of the palms (order Arecales, family Arecaceae), uncertainty remains in resolution/support among major clades and for the placement of the palms among the commelinid monocots. Palms and related commelinids represent a classic case of substitution rate heterogeneity that has not been investigated in the genomic era. To address questions of relationships, support and rate variation among palms and commelinid relatives, 39 plastomes representing the palms and related family Dasypogonaceae were generated via genome skimming and integrated within a monocot-wide matrix for phylogenetic and molecular evolutionary analyses.

Morphological diversity and evolution of Centrolepidaceae (Poales), a species-poor clade with diverse body plans and developmental patterns.

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Premise Of The Study: The small primarily Australian commelinid monocot family Centrolepidaceae displays remarkably high structural diversity that has been hitherto relatively poorly explored. Data on Centrolepidaceae are important for comparison with other Poales, including grasses and sedges.•

Methods: We examined vegetative and reproductive morphology in a global survey of Centrolepidaceae based on light and scanning electron microscopy of 18 species, representing all three genera.

Application of DNA Barcodes in Asian Tropical Trees--A Case Study from Xishuangbanna Nature Reserve, Southwest China.

Background: Within a regional floristic context, DNA barcoding is more useful to manage plant diversity inventories on a large scale and develop valuable conservation strategies. However, there are no DNA barcode studies from tropical areas of China, which represents one of the biodiversity hotspots around the world.

Methodology And Principal Findings: A DNA barcoding database of an Asian tropical trees with high diversity was established at Xishuangbanna Nature Reserve, Yunnan, southwest China using rbcL and matK as standard barcodes, as well as trnH-psbA and ITS as supplementary barcodes.

Reproductive niche conservatism in the isolated New Zealand flora over 23 million years.

The temporal stability of plant reproductive features on islands has rarely been tested. Using flowers, fruits/cones and seeds from a well-dated (23 Ma) Miocene Lagerstätte in New Zealand, we show that across 23 families and 30 genera of forest angiosperms and conifers, reproductive features have remained constant for more than 20 Myr. Insect-, wind- and bird-pollinated flowers and wind- and bird-dispersed diaspores all indicate remarkable reproductive niche conservatism, despite widespread environmental and biotic change.

Leaf fossils of Luzuriaga and a monocot flower with in situ pollen of Liliacidites contortus Mildenh. & Bannister sp. nov. (Alstroemeriaceae) from the Early Miocene.

Premise Of The Study: The Foulden Maar lake sediments in Otago, South Island, New Zealand, date to the earliest Miocene and provide an important picture of the diversity of the Australasian biota, paleoecology, and climate at a time when New Zealand had a smaller land area than today. The diverse rainforest contains many taxa now restricted to Australia, New Caledonia, or South America. The presence of Luzuriaga-like fossils in these deposits is important for understanding Alstroemeriaceae evolution and the biogeography of genera shared between New Zealand and South America.

A fossil Fuchsia (Onagraceae) flower and an anther mass with in situ pollen from the early Miocene of New Zealand.

Premise Of The Study: Fuchsia (Onagraceae) anthers, pollen, and an ornithophilous Fuchsia-like flower from an earliest Miocene lacustrine diatomite deposit at Foulden Maar, southern New Zealand confirm a long record for Fuchsia in New Zealand and probably an equally long history for its distinctive honeyeater pollination syndrome. The anthers contain in situ pollen of the fossil palynomorph previously assigned to Diporites aspis Pocknall et Mildenh. (Onagraceae: Fuchsia L.

Plastid genomes and deep relationships among the commelinid monocot angiosperms.

The commelinid monocots comprise the orders Arecales (A), Commelinales (C), Poales sensu Angiosperm Phylogeny Group III (APGIII) (P), Zingiberales (Z), plus the unplaced family Dasypogonaceae (D), collectively containing numerous economically and ecologically important species and encompassing enormous morphological diversity. Commelinids are supported as monophyletic based on anatomy and molecular data; however, relationships among major commelinid groupings conflict among previous studies, representing a long-standing problem in monocot systematics, with major implications for interpretations of character evolution. In more recent analyses, with whole-plastome sampling largely focused on Poales, areas of conflict remain, suggesting the need for closer investigation of relationships and support.

Cryptic organisation within an apparently irregular rostrocaudal distribution of interneurons in the embryonic zebrafish spinal cord.

The molecules and mechanisms involved in patterning the dorsoventral axis of the developing vertebrate spinal cord have been investigated extensively and many are well known. Conversely, knowledge of mechanisms patterning cellular distributions along the rostrocaudal axis is relatively more restricted. Much is known about the rostrocaudal distribution of motoneurons and spinal cord cells derived from neural crest but there is little known about the rostrocaudal patterning of most of the other spinal cord neurons.

Earliest orchid macrofossils: Early Miocene Dendrobium and Earina (Orchidaceae: Epidendroideae) from New Zealand.

Fossil leaves of two Early Miocene orchids (Dendrobium and Earina) are reported from New Zealand. The distinctive, raised tetra- to cyclocytic stomatal subsidiary cells of Earina and characteristic papilla-like absorbing glands and "ringed" guard cells of Dendrobium support the placement of the fossils into these genera. These therefore represent the first Orchidaceae macrofossils with cuticular preservation, the oldest records for subfamily Epidendroideae, as well as the first New Zealand and southern hemisphere fossil records for Orchidaceae.

Morphology of Hydatellaceae, an anomalous aquatic family recently recognized as an early-divergent angiosperm lineage.

The family Hydatellaceae was recently reassigned to the early-divergent angiosperm order Nymphaeales rather than the monocot order Poales. This dramatic taxonomic adjustment allows comparison with other early-divergent angiosperms, both extant and extinct. Hydatellaceae possess some monocot-like features that could represent adaptations to an aquatic habit.