Chloroplast variation is incongruent with classification of the Australian bloodwood eucalypts (genus Corymbia, family Myrtaceae)

Towards a species-level phylogeny for Neotropical Myrtaceae: Notes on topology and resources for future studies

PREMISE

Increasingly complete phylogenies underpin studies in systematics, ecology, and evolution. Myrteae (Myrtaceae), with ~2700 species, is a key component of the exceptionally diverse Neotropical flora, but given its complicated taxonomy, automated assembling of molecular supermatrices from public databases often lead to unreliable topologies due to poor species identification.

METHODS

Here, we build a taxonomically verified molecular supermatrix of Neotropical Myrteae by assembling 3909 published and 1004 unpublished sequences from two nuclear and seven plastid molecular markers. We infer a time-calibrated phylogenetic tree that covers 712 species of Myrteae (~28% of the total diversity in the clade) and evaluate geographic and taxonomic gaps in sampling.

RESULTS

The tree inferred from the fully concatenated matrix mostly reflects the topology of the plastid data set and there is a moderate to strong incongruence between trees inferred from nuclear and plastid partitions. Large, species-rich genera are still the poorest sampled within the group. Eastern South America is the best-represented area in proportion to its species diversity, while Western Amazon, Mesoamerica, and the Caribbean are the least represented.

CONCLUSIONS

We provide a time-calibrated tree that can be more reliably used to address finer-scale eco-evolutionary questions that involve this group in the Neotropics. Gaps to be filled by future studies include improving representation of taxa and areas that remain poorly sampled, investigating causes of conflict between nuclear and plastid partitions, and the role of hybridization and incomplete lineage sorting in relationships that are poorly supported.

Phylogenomics reveals extreme gene tree discordance in a lineage of dominant trees: hybridization, introgression, and incomplete lineage sorting blur deep evolutionary relationships despite clear species groupings in Eucalyptus subgenus Eudesmia

Eucalypts are a large and ecologically important group of plants on the Australian continent, and understanding their evolution is important in understanding evolution of the unique Australian flora. Previous phylogenies using plastome DNA, nuclear-ribosomal DNA, or random genome-wide SNPs, have been confounded by limited genetic sampling or by idiosyncratic biological features of the eucalypts, including widespread plastome introgression. Here we present phylogenetic analyses of Eucalyptus subgenus Eudesmia (22 species from western, northern, central and eastern Australia), in the first study to apply a target-capture sequencing approach using custom, eucalypt-specific baits (of 568 genes) to a lineage of Eucalyptus. Multiple accessions of all species were included, and target-capture data were supplemented by separate analyses of plastome genes (average of 63 genes per sample). Analyses revealed a complex evolutionary history likely shaped by incomplete lineage sorting and hybridization. Gene tree discordance generally increased with phylogenetic depth. Species, or groups of species, toward the tips of the tree are mostly supported, and three major clades are identified, but the branching order of these clades cannot be confirmed with confidence. Multiple approaches to filtering the nuclear dataset, by removing genes or samples, could not reduce gene tree conflict or resolve these relationships. Despite inherent complexities in eucalypt evolution, the custom bait kit devised for this research will be a powerful tool for investigating the evolutionary history of eucalypts more broadly.

Plastome sequences fail to resolve shallow level relationships within the rapidly radiated genus Isodon (Lamiaceae)

As one of the largest genera of Lamiaceae and of great medicinal importance, Isodon is also phylogenetically and taxonomically recalcitrant largely ascribed to its recent rapid radiation in the Hengduan Mountains. Previous molecular phylogenetic studies using limited loci have only successfully resolved the backbone topology of the genus, but the interspecific relationships suffered from low resolution, especially within the largest clade (Clade IV) which comprises over 80% species. In this study, we attempted to further elucidate the phylogenetic relationships within Isodon especially Clade IV using plastome sequences with a broad taxon sampling of ca. 80% species of the genus. To reduce systematic errors, twelve different plastome data sets (coding and non-coding regions with ambiguously aligned regions and saturated loci removed or not) were employed to reconstruct phylogeny using maximum likelihood and Bayesian inference. Our results revealed largely congruent topologies of the 12 data sets and recovered major lineages of Isodon consistent with previous studies, but several incongruences are also found among these data sets and among single plastid loci. Most of the shallow nodes within Clade IV were resolved with high support but extremely short branch lengths in plastid trees, and showed tremendous conflicts with the nrDNA tree, morphology and geographic distribution. These incongruences may largely result from stochasticity (due to insufficient phylogenetic signal) and hybridization and plastid capture. Therefore, the uniparental-inherited plastome sequences are insufficient to disentangle relationships within a genus which has undergone recent rapid diversification. Our findings highlight a need for additional data from nuclear genome to resolve the relationships within Clade IV and more focused studies to assess the influences of multiple processes in the evolutionary history of Isodon. Nevertheless, the morphology of the shape and surface sculpture/indumentum of nutlets is of systematic importance that they can distinguish the four major clades of Isodon.

Biodiscoveries within the Australian plant genus Eremophila based on international and interdisciplinary collaboration: results and perspectives on outstanding ethical dilemmas

In a cross-continental research initiative, including researchers working in Australia and Denmark, and based on joint external funding by a 3-year grant from the Novo Nordisk Foundation, we have used DNA sequencing, extensive chemical profiling and molecular networking analyses across the entire Eremophila genus to provide new knowledge on the presence of natural products and their bioactivities using polypharmocological screens. Sesquiterpenoids, diterpenoids and dimers of branched-chain fatty acids with previously unknown chemical structures were identified. The collection of plant material from the Eremophila genus was carried out according to a 'bioprospecting agreement' with the Government of Western Australia. We recognize that several Eremophila species hold immense cultural significance to Australia's First Peoples. In spite of our best intentions to ensure that new knowledge gained about the genus Eremophila and any potential future benefits are shared in an equitable manner, in accordance with the Nagoya Protocol, we encounter serious dilemmas and potential conflicts in making benefit sharing with Australia's First Peoples a reality.

Blumea chishangensis sp. nov. (Asteraceae: Inuleae) from Taiwan and new insights into the phylogeny of Blumea

BACKGROUND

Blumea plants are widely distributed in the tropical areas of Asia, Africa, and Australia, especially tropical Asia. Limited studies left the taxonomy and infrageneric phylogeny of Blumea insubstantial. Here, a new species, Blumea chishangensis S. W. Chung, Z. H. Chen, S. H. Liu & W. J. Huang, from Taiwan is described, and an extended phylogeny is reconstructed to provide new perceptions of Blumea evolution.

RESULTS

The new species is distinguished from B. hieraciifolia by the following features: leaf blade sparsely pilose or glabrescent (vs. silky villous), the leaves margins regularly remote mucronulate (vs. double serrate or dentate), capitula pedicelled (vs. capitula sessile or subsessile), and leaves basal rosette or sub-basal rosette and a few cauline (vs. mostly cauline). Phylogenetic analysis based on the ITS, trnL-trnF, and trnH-psbA regions places the new species in the subclade II in B. lacera clade and shows a close relationship with B. axillaris and B. oxyodonta. A key to Blumea species in Taiwan and the studied species in the subclade II is provided. Moreover, the evolutionary inferences of B. conspicua, B. linearis, and B. sinuata are first reported here. The paraphyly of B. formosana and B. sinuata are also revealed for the first time.

CONCLUSIONS

Both morphological and molecular data support that B. chishangensis is a new species. Our phylogeny highlights the need for further taxonomic and evolutionary studies on Blumea.

Perspectives in Myrtaceae evolution from plastomes and nuclear phylogenies

Myrtaceae is a large and species-rich family of woody eudicots, with prevalent distribution in the Southern Hemisphere. Classification and taxonomy of species belonging to this family is quite challenging, sometimes with difficulty in species identification and producing phylogenies with low support for species relationships. Most of the current knowledge comes from few molecular markers, such as plastid genes and intergenic regions, which can be difficult to handle and produce conflicting results. Based on plastid protein-coding sequences and nuclear markers, we present a topology for the phylogenetic relationships among Myrtaceae tribes. Our phylogenetic estimate offers a contrasting topology over previous analysis with fewer markers. Plastome phylogeny groups the tribes Syzygieae and Eucalypteae and individual chloroplast genes produce divergent topologies, especially among species within Myrteae tribe, but also in regard to the grouping of Syzygieae and Eucalypteae. Results are consistent and reproducible with both nuclear and organellar datasets. It confronts previous data about the deep nodes of Myrtaceae phylogeny.

Navigating through chemical space and evolutionary time across the Australian continent in plant genus Eremophila

Eremophila is the largest genus in the plant tribe Myoporeae (Scrophulariaceae) and exhibits incredible morphological diversity across the Australian continent. The Australian Aboriginal Peoples recognize many Eremophila species as important sources of traditional medicine, the most frequently used plant parts being the leaves. Recent phylogenetic studies have revealed complex evolutionary relationships between Eremophila and related genera in the tribe. Unique and structurally diverse metabolites, particularly diterpenoids, are also a feature of plants in this group. To assess the full dimension of the chemical space of the tribe Myoporeae, we investigated the metabolite diversity in a chemo-evolutionary framework applying a combination of molecular phylogenetic and state-of-the-art computational metabolomics tools to build a dataset involving leaf samples from a total of 291 specimens of Eremophila and allied genera. The chemo-evolutionary relationships are expounded into a systematic context by integration of information about leaf morphology (resin and hairiness), environmental factors (pollination and geographical distribution), and medicinal properties (traditional medicinal uses and antibacterial studies), augmenting our understanding of complex interactions in biological systems.

Resolving species boundaries in a recent radiation with the Angiosperms353 probe set: the Lomatium packardiae/L. anomalum clade of the L. triternatum (Apiaceae) complex

PREMISE

Speciation not associated with morphological shifts is challenging to detect unless molecular data are employed. Using Sanger-sequencing approaches, the Lomatium packardiae/L. anomalum subcomplex within the larger Lomatium triternatum complex could not be resolved. Therefore, we attempt to resolve these boundaries here.

METHODS

The Angiosperms353 probe set was employed to resolve the ambiguity within Lomatium triternatum species complex using 48 accessions assigned to L. packardiae, L. anomalum, or L. triternatum. In addition to exon data, 54 nuclear introns were extracted and were complete for all samples. Three approaches were used to estimate evolutionary relationships and define species boundaries: STACEY, a Bayesian coalescent-based species tree analysis that takes incomplete lineage sorting into account; ASTRAL-III, another coalescent-based species tree analysis; and a concatenated approach using MrBayes. Climatic factors, morphological characters, and soil variables were measured and analyzed to provide additional support for recovered groups.

RESULTS

The STACEY analysis recovered three major clades and seven subclades, all of which are geographically structured, and some correspond to previously named taxa. No other analysis had full agreement between recovered clades and other parameters. Climatic niche and leaflet width and length provide some predictive ability for the major clades.

CONCLUSIONS

The results suggest that these groups are in the process of incipient speciation and incomplete lineage sorting has been a major barrier to resolving boundaries within this lineage previously. These results are hypothesized through sequencing of multiple loci and analyzing data using coalescent-based processes.

A nuclear phylogenomic study of the angiosperm order Myrtales, exploring the potential and limitations of the universal Angiosperms353 probe set

PREMISE

To further advance the understanding of the species-rich, economically and ecologically important angiosperm order Myrtales in the rosid clade, comprising nine families, approximately 400 genera and almost 14,000 species occurring on all continents (except Antarctica), we tested the Angiosperms353 probe kit.

METHODS

We combined high-throughput sequencing and target enrichment with the Angiosperms353 probe kit to evaluate a sample of 485 species across 305 genera (76% of all genera in the order).

RESULTS

Results provide the most comprehensive phylogenetic hypothesis for the order to date. Relationships at all ranks, such as the relationship of the early-diverging families, often reflect previous studies, but gene conflict is evident, and relationships previously found to be uncertain often remain so. Technical considerations for processing HTS data are also discussed.

CONCLUSIONS

High-throughput sequencing and the Angiosperms353 probe kit are powerful tools for phylogenomic analysis, but better understanding of the genetic data available is required to identify genes and gene trees that account for likely incomplete lineage sorting and/or hybridization events.

Pests, diseases, and aridity have shaped the genome of Corymbia citriodora

Corymbia citriodora is a member of the predominantly Southern Hemisphere Myrtaceae family, which includes the eucalypts (Eucalyptus, Corymbia and Angophora; ~800 species). Corymbia is grown for timber, pulp and paper, and essential oils in Australia, South Africa, Asia, and Brazil, maintaining a high-growth rate under marginal conditions due to drought, poor-quality soil, and biotic stresses. To dissect the genetic basis of these desirable traits, we sequenced and assembled the 408 Mb genome of Corymbia citriodora, anchored into eleven chromosomes. Comparative analysis with Eucalyptus grandis reveals high synteny, although the two diverged approximately 60 million years ago and have different genome sizes (408 vs 641 Mb), with few large intra-chromosomal rearrangements. C. citriodora shares an ancient whole-genome duplication event with E. grandis but has undergone tandem gene family expansions related to terpene biosynthesis, innate pathogen resistance, and leaf wax formation, enabling their successful adaptation to biotic/abiotic stresses and arid conditions of the Australian continent.

Genomic divergence in sympatry indicates strong reproductive barriers and cryptic species within Eucalyptus salubris

Genetic studies are increasingly detecting cryptic taxa that likely represent a significant component of global biodiversity. However, cryptic taxa are often criticized because they are typically detected serendipitously and may not receive the follow-up study required to verify their geographic or evolutionary limits. Here, we follow-up a study of Eucalyptus salubris that unexpectedly detected two divergent lineages but was not sampled sufficiently to make clear interpretations. We undertook comprehensive sampling for an independent genomic analysis (3,605 SNPs) to investigate whether the two purported lineages remain discrete genetic entities or if they intergrade throughout the species' range. We also assessed morphological and ecological traits, and sequenced chloroplast DNA. SNP results showed strong genome-wide divergence (F ST = 0.252) between two discrete lineages: one dominated the north and one the southern regions of the species' range. Within lineages, gene flow was high, with low differentiation (mean F ST = 0.056) spanning hundreds of kilometers. In the central region, the lineages were interspersed but maintained their genomic distinctiveness: an indirect demonstration of reproductive isolation. Populations of the southern lineage exhibited significantly lower specific leaf area and occurred on soils with lower phosphorus relative to the northern lineage. Finally, two major chloroplast haplotypes were associated with each lineage but were shared between lineages in the central distribution. Together, these results suggest that these lineages have non-contemporary origins and that ecotypic adaptive processes strengthened their divergence more recently. We conclude that these lineages warrant taxonomic recognition as separate species and provide fascinating insight into eucalypt speciation.

Out of the OCBILs: new hypotheses for the evolution, ecology and conservation of the eucalypts

OCBIL theory is a multi-hypothesis formulation aimed towards an understanding of the evolution, ecology and conservation of biological and cultural diversity on old, climatically buffered, infertile landscapes (OCBILs). OCBILs have been in existence contemporaneously with rainforest since Gondwanan times. Such landscapes are common in areas of eucalypt species richness embraced by Australia’s two Global Biodiversity Hotspots, the Southwest Australian Floristic Region and the Forests of East Australia. Here, I summarize evidence pertaining to the eucalypts in the context of a recent reformulation of OCBIL theory into 12 evolutionary, ecological and cultural hypotheses and ten conservation management hypotheses. A compelling argument emerges for a new interpretation of the eucalypts evolving out of the OCBILs, rather than out of the rainforests as traditionally interpreted. This calls for a significant reinterpretation of best conservation management of the eucalypts. For example, traditional ideas on application of fire in eucalypt communities regarded as well adapted to this disturbance need to give way to a more nuanced and cautious view. This review of eucalypts seen as evolving out of the OCBILs helps in understanding the group from several new perspectives. Interpretation of other sedentary plant and animal groups as out of the OCBILs is commended for further study.

Divergent lineages in a semi-arid mallee species, Eucalyptus behriana, correspond to a major geographic break in southeastern Australia

AIM

To infer relationships between populations of the semi-arid, mallee eucalypt, Eucalyptus behriana, to build hypotheses regarding evolution of major disjunctions in the species' distribution and to expand understanding of the biogeographical history of southeastern Australia.

LOCATION

Southeastern Australia.

TAXON

Eucalyptus behriana (Myrtaceae, Angiospermae).

METHODS

We developed a large dataset of anonymous genomic loci for 97 samples from 11 populations of E. behriana using double digest restriction site-associated DNA sequencing (ddRAD-seq), to determine genetic relationships between the populations. These relationships, along with species distribution models, were used to construct hypotheses regarding environmental processes that have driven fragmentation of the species' distribution.

RESULTS

Greatest genetic divergence was between populations on either side of the Lower Murray Basin. Populations west of the Basin showed greater genetic divergence between one another than the eastern populations. The most genetically distinct population in the east (Long Forest) was separated from others by the Great Dividing Range. A close relationship was found between the outlying northernmost population (near West Wyalong) and those in the Victorian Goldfields despite a large disjunction between them.

CONCLUSIONS

Patterns of genetic variation are consistent with a history of vicariant differentiation of disjunct populations. We infer that an early disjunction to develop in the species distribution was that across the Lower Murray Basin, an important biogeographical barrier separating many dry sclerophyll plant taxa in southeastern Australia. Additionally, our results suggest that the western populations fragmented earlier than the eastern ones. Fragmentation, both west and east of the Murray Basin, is likely tied to climatic changes associated with glacial-interglacial cycles although it remains possible that major geological events including uplift of the Mount Lofty Ranges and basalt flows in the Newer Volcanics Province also played a role.

Looks can be deceiving: speciation dynamics of co-distributed Angophora (Myrtaceae) species in a varying landscape

Understanding the mechanisms underlying species divergence remains a central goal in evolutionary biology. Landscape genetics can be a powerful tool for examining evolutionary processes. We used genome-wide scans to genotype samples from populations of eight Angophora species. Angophora is a small genus within the eucalypts comprising common and rare species in a heterogeneous landscape, making it an appropriate group to study speciation. We found A. hispida was highly differentiated from the other species. Two subspecies of A. costata (subsp. costata and subsp. euryphylla) formed a group, while the third (subsp. leiocarpa, which is only distinguished by its smooth fruits and provenance) was supported as a distinct pseudocryptic species. Other species that are morphologically distinct could not be genetically differentiated (e.g., A. floribunda and A. subvelutina). Distribution and genetic differentiation within Angophora were strongly influenced by temperature and humidity, as well as biogeographic barriers, particularly rivers and higher elevation regions. While extensive introgression was found between many populations of some species (e.g., A. bakeri and A. floribunda), others only hybridized at certain locations. Overall, our findings suggest multiple mechanisms drove evolutionary diversification in Angophora and highlight how genome-wide analyses of related species in a diverse landscape can provide insights into speciation.

Methods of analysis of chloroplast genomes of C3, Kranz type C4 and Single Cell C4 photosynthetic members of Chenopodiaceae

BACKGROUND

Chloroplast genome information is critical to understanding forms of photosynthesis in the plant kingdom. During the evolutionary process, plants have developed different photosynthetic strategies that are accompanied by complementary biochemical and anatomical features. Members of family Chenopodiaceae have species with C3 photosynthesis, and variations of C4 photosynthesis in which photorespiration is reduced by concentrating CO2 around Rubisco through dual coordinated functioning of dimorphic chloroplasts. Among dicots, the family has the largest number of C4 species, and greatest structural and biochemical diversity in forms of C4 including the canonical dual-cell Kranz anatomy, and the recently identified single cell C4 with the presence of dimorphic chloroplasts separated by a vacuole. This is the first comparative analysis of chloroplast genomes in species representative of photosynthetic types in the family.

RESULTS

Methodology with high throughput sequencing complemented with Sanger sequencing of selected loci provided high quality and complete chloroplast genomes of seven species in the family and one species in the closely related Amaranthaceae family, representing C3, Kranz type C4 and single cell C4 (SSC4) photosynthesis six of the eight chloroplast genomes are new, while two are improved versions of previously published genomes. The depth of coverage obtained using high-throughput sequencing complemented with targeted resequencing of certain loci enabled superior resolution of the border junctions, directionality and repeat region sequences. Comparison of the chloroplast genomes with previously sequenced plastid genomes revealed similar genome organization, gene order and content with a few revisions. High-quality complete chloroplast genome sequences resulted in correcting the orientation the LSC region of the published Bienertia sinuspersici chloroplast genome, identification of stop codons in the rpl23 gene in B. sinuspersici and B. cycloptera, and identifying an instance of IR expansion in the Haloxylon ammodendron inverted repeat sequence. The rare observation of a mitochondria-to-chloroplast inter-organellar gene transfer event was identified in family Chenopodiaceae.

CONCLUSIONS

This study reports complete chloroplast genomes from seven Chenopodiaceae and one Amaranthaceae species. The depth of coverage obtained using high-throughput sequencing complemented with targeted resequencing of certain loci enabled superior resolution of the border junctions, directionality, and repeat region sequences. Therefore, the use of high throughput and Sanger sequencing, in a hybrid method, reaffirms to be rapid, efficient, and reliable for chloroplast genome sequencing.

Extensive Genetic Connectivity and Historical Persistence Are Features of Two Widespread Tree Species in the Ancient Pilbara Region of Western Australia

Phylogeographic studies can be used as a tool to understand the evolutionary history of a landscape, including the major drivers of species distributions and diversity. Extensive research has been conducted on phylogeographic patterns of species found in northern hemisphere landscapes that were affected by glaciations, yet the body of literature for older, unaffected landscapes is still underrepresented. The Pilbara region of north-western Australia is an ancient and vast landscape that is topographically complex, consisting of plateaus, gorges, valleys, and ranges, and experiences extreme meteorological phenomena including seasonal cyclonic activity. These features are expected to influence patterns of genetic structuring throughout the landscape either by promoting or restricting the movement of pollen and seed. Whilst a growing body of literature exists for the fauna endemic to this region, less is known about the forces shaping the evolution of plant taxa. In this study we investigate the phylogeography of two iconic Pilbara tree species, the Hamersley Bloodwood (Corymbia hamersleyana) and Western Gidgee (Acacia pruinocarpa), by assessing patterns of variation and structure in several chloroplast DNA regions and nuclear microsatellite loci developed for each species. Gene flow was found to be extensive in both taxa and there was evidence of long-distance seed dispersal across the region (pollen to seed ratios of 6.67 and 2.96 for C. hamersleyana and A. pruinocarpa, respectively), which may result from flooding and strong wind gusts associated with extreme cyclonic activity. Both species possessed high levels of cpDNA genetic diversity in comparison to those from formerly glaciated landscapes (C. hamersleyana = 14 haplotypes, A. pruinocarpa = 37 haplotypes) and showed evidence of deep lineage diversification occurring from the late Miocene, a time of intensifying aridity in this landscape that appears to be a critical driver of evolution in Pilbara taxa. In contrast to another study, we did not find evidence for topographic features acting as refugia for the widely sampled C. hamersleyana.

Out of Sight, Out of Mind: Widespread Nuclear and Plastid-Nuclear Discordance in the Flowering Plant Genus Polemonium (Polemoniaceae) Suggests Widespread Historical Gene Flow Despite Limited Nuclear Signal

Phylogenomic data from a rapidly increasing number of studies provide new evidence for resolving relationships in recently radiated clades, but they also pose new challenges for inferring evolutionary histories. Most existing methods for reconstructing phylogenetic hypotheses rely solely on algorithms that only consider incomplete lineage sorting (ILS) as a cause of intra- or intergenomic discordance. Here, we utilize a variety of methods, including those to infer phylogenetic networks, to account for both ILS and introgression as a cause for nuclear and cytoplasmic-nuclear discordance using phylogenomic data from the recently radiated flowering plant genus Polemonium (Polemoniaceae), an ecologically diverse genus in Western North America with known and suspected gene flow between species. We find evidence for widespread discordance among nuclear loci that can be explained by both ILS and reticulate evolution in the evolutionary history of Polemonium. Furthermore, the histories of organellar genomes show strong discordance with the inferred species tree from the nuclear genome. Discordance between the nuclear and plastid genome is not completely explained by ILS, and only one case of discordance is explained by detected introgression events. Our results suggest that multiple processes have been involved in the evolutionary history of Polemonium and that the plastid genome does not accurately reflect species relationships. We discuss several potential causes for this cytoplasmic-nuclear discordance, which emerging evidence suggests is more widespread across the Tree of Life than previously thought. [Cyto-nuclear discordance, genomic discordance, phylogenetic networks, plastid capture, Polemoniaceae, Polemonium, reticulations.].

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. A fossil-calibrated chronogram provided a temporal framework for understanding trait transitions. Ancestral state reconstructions and phylogenetic comparative trait correlation analyses provided insights into the evolutionary and ecological drivers associated with Lomandroideae diversification. Lomandroideae diverged from the other Asparagaceae ca. 56.61 million years ago (95% highest posterior density values 70.31-45.34 million years) and the major lineages diversified since the Oligocene. The most recent common ancestor of the clade likely occupied the mesic biome, was hermaphroditic and geophytic. Biome occupancy transitions were correlated with polyploidy and the presence of storage roots. Polyploidy potentially serves as an "enabler" trait, generating novel phenotypes, which may confer tolerance to climatic ranges and soil conditions putatively required for expansion into and occupation of new arid biomes. Storage roots, as a key factor driving biome transitions, may have been associated with fire rather than with aridification events in the Australian flora. This study contributes significantly to our understanding of biome evolution by identifying polyploidy and storage organs as key factors associated with transitions in biome occupancy in this lineage.

Optimisation of a pollen DNA metabarcoding method for diet analysis of flying-foxes (Pteropus spp.)

Determining the diet of flying-foxes can increase understanding of how they function as pollinators and seed dispersers, as well as managing any negative impacts of large roosts. Traditional methods for diet analysis are time consuming, and not feasible to conduct for hundreds of animals. In this study, we optimised a method for diet analysis, based on DNA metabarcoding of environmental DNA (eDNA) from pollen and other plant parts in the faeces. We found that existing eDNA metabarcoding protocols are suitable, with the most useful results being obtained using a commercial food DNA extraction kit, and sequencing 350–450 base pairs of a DNA barcode from the internally transcribed spacer region (ITS2), with ~550 base pairs of the chloroplast rubisco large subunit (rbcL) as a secondary DNA barcode. A list of forage plants was generated for the little red flying-fox (Pteropus scapulatus), the black flying-fox (Pteropus alecto) and the spectacled flying-fox (Pteropus conspicillatus) from our collection sites across Queensland. The diets were determined to comprise predominantly Myrtaceae species, particularly those in the genera Eucalyptus, Melaleuca and Corymbia. With more plant genomes becoming publicly available in the future, there are likely to be further applications of eDNA methods in understanding the role of flying-foxes as pollinators and seed dispersers.

The complete chloroplast genome sequence of the Australian Mirbelioid pea Platylobium obtusangulum Hook. (Leguminosae: subf. Papilionoideae, tribe Bossiaeeae)

We sequenced and assembled the whole chloroplast genome of the Australian-endemic shrub Platylobium obtusangulum. The total size of the genome is 150,090 base pairs (bp), including two inverted repeat regions of 25,511 bp each, one large single copy region of 80,567 bp and a small single copy region of 18,501 bp. The genome has a GC content of 36.7% and includes 127 annotated genes (83 protein coding, 36 tRNA genes and eight rRNA genes). Phylogenetic analysis of chloroplast genomes placed the Platylobium obtusangulum genome in the expected position of the Mirbelioid clade in the legume family (Leguminosae: Papilionoideae).

Identifying genetic markers for a range of phylogenetic utility-From species to family level

Resolving the phylogenetic relationships of closely related species using a small set of loci is challenging as sufficient information may not be captured from a limited sample of the genome. Relying on few loci can also be problematic when conflict between gene-trees arises from incomplete lineage sorting and/or ongoing hybridization, problems especially likely in recently diverged lineages. Here, we developed a method using limited genomic resources that allows identification of many low copy candidate loci from across the nuclear and chloroplast genomes, design probes for target capture and sequence the captured loci. To validate our method we present data from Eucalyptus and Melaleuca, two large and phylogenetically problematic genera within the Myrtaceae family. With one annotated genome, one transcriptome and two whole-genome shotgun sequences of one Eucalyptus and four Melaleuca species, respectively, we identified 212 loci representing 263 kbp for targeted sequence capture and sequencing. Of these, 209 were successfully tested from 47 samples across five related genera of Myrtaceae. The average percentage of reads mapped back to the reference was 57.6% with coverage of more than 20 reads per position across 83.5% of the data. The methods developed here should be applicable across a large range of taxa across all kingdoms. The core methods are very flexible, providing a platform for various genomic resource availabilities and are useful from shallow to deep phylogenies.

Chloroplast genome analysis of box-ironbark Eucalyptus

Eucalyptus L'Hérit. (Myrtaceae) is a taxonomically complex and highly speciose genus that dominates much of Australia's woody vegetation. However, very little information is available about the molecular biology and chloroplast diversity of certain groups, such as Eucalyptus section Adnataria, which is found in many woodland habitats of eastern Australia. We report four new complete chloroplast genomes of Eucalyptus, including three genomes from species previously lacking any chloroplast reference sequences. Plastomes of E. albens, E. conica, E. crebra and E. melliodora assembled using a de novo approach were shown to be largely identical to each other, and similar in size and structure to previously published chloroplast genomes from Eucalyptus. A total of 132 genes (114 single-copy genes and 18 duplicated genes in the IR regions) were identified, and shown to be highly conserved in terms of gene order, content and organization. Slightly higher divergence in the intergenic spacers was identified through comparative genomic analyses. Chloroplast sequences of 35 additional individuals representing 12 species were assembled using a reference guided approach. Rates of nucleotide substitution varied among the protein coding genes, with 17 genes under possible positive selection, and 29 invariant genes. Phylogenetic analysis of either the whole reconstructed plastome sequences or the individual genes revealed extreme discordance with expected species boundaries or higher-level relationships. Plastome relationships were better predicted by geography than by nuclear DNA or taxonomic relationships, suggesting a substantial influence of gene flow over and above the effects of incomplete lineage sorting. These results provide resources for future research and valuable insights into the prevalence of interspecific gene flow among Eucalyptus species.

Rooting of eucalypt cuttings as a problem-solving oriented model in plant biology

Species of Eucalyptus are some of the most planted trees in the world, providing fiber, cellulose, energy, and wood for construction and furniture in renewable fashion, with the added advantage of fixing large amounts of atmospheric carbon. The efficiency of eucalypts in forestry relies mostly on the clonal propagation of selected genotypes both as pure species and interspecific hybrids. The formation of new roots from cambium tissues at the base of cuttings, referred to as adventitious rooting (AR), is essential for accomplishing clonal propagation successfully. AR is a highly complex, multi-level regulated developmental process, affected by a number of endogenous and environmental factors. In several cases, highly desirable genotypes from an industrial point of view carry along the undesirable trait of difficulty-to-root (recalcitrance). Understanding the bases of this phenotype is needed to identify ways to overcome recalcitrance and allow efficient clonal propagation. Herein, an overview of the state-of-the-art on the basis of AR recalcitrance in eucalypts addressed at various levels of regulation (transcript, protein, metabolite and phenotype), and OMICs techniques is presented. In addition, a focus is also provided on the gaps that need to be filled in order to advance in this strategic biological problem for global forestry industry relying on eucalypts.

Evolution of pollination by frugivorous birds in Neotropical Myrtaceae

Bird pollination is relatively common in the tropics, and especially in the Americas. In the predominantly Neotropical tribe Myrteae (Myrtaceae), species of two genera, Acca and Myrrhinium, offer fleshy, sugary petals to the consumption of birds that otherwise eat fruits, thus pollinating the plants in an unusual plant-animal interaction. The phylogenetic position of these genera has been problematic, and therefore, so was the understanding of the evolution of this interaction. Here we include new sequences of Myrrhinium atropurpureum in a comprehensive molecular phylogeny based on a balanced sample of two plastid and two nuclear markers, with the aim of providing the historical framework of pollination by frugivorous birds in Myrteae. We developed 13 flower and inflorescence characters that comprehensively depict the macroscopic morphological components of this interaction. Bayesian and parsimony phylogenies concur in placing both Acca and Myrrhinium in a clade with Psidium species; with Myrrhinium sister to Psidium. Mapping of morphological characters indicated some degree of convergence (e.g., fleshy petals, purplish display) but also considerable divergence in key characters that point to rather opposing pollination strategies and also different degrees of specialization in Acca versus Myrrhinium. Pollination by frugivorous birds represents a special case of mutualism that highlights the evolutionary complexities of plant-animal interactions.

The complete chloroplast genome sequence of Spyridium parvifolium var. parvifolium (family Rhamnaceae; tribe Pomaderreae)

We assembled the complete chloroplast genome of the Australian shrub Spyridium parvifolium var. parvifolium. The genome was 161,012 bp in length, with a pair of inverted repeats (IRs) of 26,515 bp, separated by a large single copy (LSC) region of 88,814 bp and a small single copy region (SCC) of 19,168 bp. The GC content was 36.9%. In total, 130 genes were annotated, including 86 protein coding genes, 36 tRNA genes and 8 rRNA genes. Phylogenetic analysis of 56 chloroplast genes placed this genome of S. parvifolium var. parvifolium within the family Rhamnaceae.