Capparis comprises ~145 species, of which ~21 occur in Australia; however, the relationships and taxonomic status of Australian Capparis taxa remain to be tested. We present phylogenies of all Australian Capparis taxa by analysing Angiosperms353 loci using coalescent and concatenated approaches. All trees resolve Capparis as monophyletic, with a whole-genome duplication (WGD) event detected at the crown. Capparis sect. Capparis and sect. Busbeckea are monophyletic but sect. Monostichocalyx is non-monophyletic. The relationships of species within sect. Busbeckea are poorly supported due to rapid radiation following ancient WGD. The relationships of taxa within sect. Capparis and the clades of sect. Monostichocalyx are well supported, with some incomplete lineage sorting. Capparis spinosa is geographically, morphologically and phylogenetically structured across northern Australia. Based on these results, we describe five new species and two new subspecies of Capparis, bringing the total number of species in Australia to 26. Capparis xylocarpa, C. megacarpa, C. loxophleba and C. splendidissima are newly described. Capparis loranthifolia var. bancroftii is raised to species level as C. bancroftii. Capparis spinosa subsp. nummularia is re-circumscribed, and two new subspecies, C. spinosa subsp. formicosa and C. spinosa subsp. insularis are described. We provide a key for all Australian taxa.
Dinckleria opaca M.A.M.Renner & M.Paulsen is described from Anglesea amber for fossils previously reported in the literature as an undetermined liverwort of the family Plagiochilaceae. The fossils are fragmentary and critical character systems are not preserved, complicating generic attribution. Membership in Dinckleria is supported by the ovate-elliptic and nearly symmetrical leaf shape, the trilobed leaf apex, and the vestigial, unlobed, triangular underleaves. Fossil preservation is poor, with no evident impregnation of plant material by resins, such that the fossil comprises the amber-air interface capturing the volume of the included plant material, that in turn contains highly degraded and disaggregated remnants of the plant itself. The amber-air interface has trace impressions of internal cell walls standing proud above the collapsed and concave external walls, typical of dehydrated plant material, and appears to have experienced minor deformation and distortion during amber formation, such that these leaf cell impressions and leaf cell surfaces are incompletely preserved. The age of the fossil, at 42 Ma, contrasts with the shallow phylogenetic divergences within D. pleurata, the species currently extant in Victoria and also south-east Queensland and New Zealand, suggesting a complex biogeographic history for the Dinckleria lineage in south-east Australia involving extinction and recolonisation by long-distance dispersal.
Several species of the genus Erigeron (Asteraceae) have become established as weeds in Australia, some of these becoming invasive. Uncertainty remains about the identity and taxonomy of some species formerly placed in Conyza. Australian floras and checklists recognise Erigeron bilbaoanus, but taxonomists in other countries consider the name a synonym of Erigeron floribundus. Likewise, the Australian Plant Census (and the Flora of North America) treats Erigeron pusillus as a synonym of Erigeron canadensis, but some Australian state and territory checklists recognise this as a distinct species. We use target capture data to infer species limits and the genetic relatedness of lineages in 'Conyza' introduced to Australia. Results indicate that Erigeron pusillus and Erigeron canadensis in Australia are more genetically differentiated than the other related and widely accepted species of the genus. Therefore, these taxa should be accepted as distinct at the species level. The species currently recognised as Erigeron bilbaoanus in Australia matches the lectotype of Conyza floribunda, and Australian taxonomy should be updated accordingly. At least in Australia, Erigeron floribundus shows the largest degree of genetic admixture of the five study species. To support accurate identification and further research, we provide an updated identification key to Erigeron of Australia.
The phylogenetic positions of two species from Lord Howe Island assigned to the genus Grammitis, G. nudicarpa and G. pulchella, and two small Australian grammitid fern genera, Aenigmatogrammitis and Howeogrammitis, were investigated through phylogenetic analyses of atpB, rbcL, rps4-trnS, trnG-trnR and trnL-trnF chloroplast sequences. Grammitis nudicarpa and G. pulchella were shown to be misplaced in Grammitis, being placed in a clade comprising Archigrammitis, Oreogrammitis and Prosaptia instead. A new genus, Phaneroloma, is described to accommodate these two species. Descriptions of both Phaneroloma species and an identification key to the species are provided. The phylogenetic positions of Aenigmatogrammitis stenophylla and Howeogrammitis diminuta previously reported with fewer chloroplast markers were here confirmed, and the large divergences separating them from their closest relatives support their continued recognition as separate genera.
The poorly known Western Australian species of the red algal genera Callithamnion Lyngb. and Corynospora J.Agardh (Ceramiales) described by William Henry Harvey in his seminal 1855 paper are reassessed based on morphological and molecular analyses of original and recent collections. Several generic reassignments are proposed, including Desikacharyella australis (Harv.) Huisman, Verbr. & G.W.Saunders (for Corynospora australis Harv.), Guiryella gracilis (Harv.) Huisman, Verbr. & G.W.Saunders (for Corynospora gracilis Harv.), Anotrichium flabelligerum (Harv.) Huisman, Verbr. & G.W.Saunders (for Callithamnion flabelligerum Harv.), Pleonosporium perpusillum (P.C.Silva) Huisman, Verbr. & G.W.Saunders and Pleonosporium crispulum (Harv.) Huisman, Verbr. & G.W.Saunders (for Callithamnion perpusillum P.C.Silva and Callithamnion crispulum Harv.), Aglaothamnion scopula (Harv.) Huisman, Verbr. & G.W.Saunders (for Callithamnion scopula Harv.) and the elevation of Anotrichium thyrsigerum (Harv.) Huisman, Verbr. & G.W.Saunders (for Callithamnion thyrsigerum Harv., previously treated as a variety or synonym of Anotrichium tenue (C.Agardh) Nägeli) to species level. In addition, Callithamnion cliftonii Huisman, Verbr. & G.W.Saunders is proposed as a replacement name for the illegitimate Callithamnion multifidum Harv. and this, and Callithamnion debile Harv., are retained in the genus. Two new species, Ptilothamnion harveyanum Huisman, Verbr. & G.W.Saunders and Seirospora decipiens Huisman, Verbr. & G.W.Saunders, are described from recent collections.
Spatial phylogenetics complement existing biodiversity metrics of species richness and endemism by incorporating evolutionary information from phylogenies with spatial distribution data. These complementary metrics of phylogenetic diversity (PD), phylogenetic endemism (PE), and categorical analysis of neo- and paleo-endemism (CANAPE) have largely been obtained from phylogenies constructed with a few genetic markers from different genomic datasets. Incongruent topologies may affect subsequent spatial phylogenetic results, leading to uncertainty for conservation outcomes. Here, we examined the effects of topological conflicts between plastid and nuclear phylogenies of two Australian plant genera – Isopogon R.Br. ex Knight and Petrophile R.Br. ex Knight (Proteaceae). We constructed the first densely sampled and generally well-resolved nuclear and plastid phylogenies of the two genera using a hybrid capture high throughput sequencing approach. We show that incongruent phylogenies from different molecular datasets have an important effect on downstream spatial phylogenetic analyses. Significant areas of PD and PE and neo- and paleo-endemism for Isopogon and Petrophile include south-west Western Australia, Kangaroo Island and the Sydney Basin. These areas are located along the mesic fringes of the Australian continent, congruent with the peripheral vicariance hypothesis in biogeography. However, these significant areas differ depending on whether the analyses were made with a nuclear or plastid topology. We caution against combining different datasets as is commonly done without detailed assessment of potential incongruence between datasets.
Reproductive systems in Lamiaceae typically consist of bilabiate zygomorphic flowers and dry mericarp fruit, therefore examining deviations from this strategy contributes to our understanding of evolution. Teucrium L. (Lamiaceae: Ajugoideae) is easily recognised by the unilabiate flower. The genus is cosmopolitan but most speciose in the Mediterranean region. Previous phylogenetic analysis showing three segregate genera nested within Teucrium raises questions about the taxon's dispersal throughout the region and the distinctive morphological changes. We conducted phylogenomic analyses of nuclear genes sequenced by targeted enrichment (Angiosperms353) for all Australasian species, phrase names and outgroups (39 total). Results show high support for most species clades and unequivocally place most 'unknowns' in context with other described taxa. Australasian Teucrium constitute at least two distantly related clades. The most speciose, with a crown age of 10.2-14.8 Ma, is widespread across Australia and includes an arid-adapted lineage that evolved actinomorphic corollas and fleshy fruits. The second clade of three eastern Australian species has a crown age of 5.9-12.2 Ma that corresponds best with dispersal associated with the Sunda-Sahul collision. Our results highlight repeated colonisation of Teucrium in Australia and corresponding shifts towards animal dispersal that took place as early as c. 9.2 Ma.
The circumscription and application of Prostanthera ovalifolia R.Br. appears to have been based largely on leaf shape, leading to a geographically and morphologically diverse concept of the species. This approach has completely or partially subsumed other species (namely P. atriplicifolia A.Cunn. ex Benth., P. latifolia (Benth.) Domin, P. lanceolata Domin and P. cineolifera R.T.Baker & H.G.Sm.), and included considerable variation hypothesised by some authors as distinct species (viz. P. sp. Hawkesbury (B.J. Conn 2591), P. sp. Olney State Forest (R.L. Palsson 166) and P. sp. Oxley Wild Rivers National Park (J.B. Williams s.n. NE 91044)). Morphological and molecular data, supported by phytochemical data, are used to partially resolve the taxonomy of this group. The circumscription of Prostanthera cineolifera is clarified and the name lectotypified. Three new species from New South Wales are recognised: Prostanthera dyarubbin Palsson & R.T.Mill., P. faucicola Palsson & I.Telford and P. milleri Palsson & J.J.Bruhl. Prostanthera milleri fits the criteria of Critically Endangered. We also lectotypify Prostanthera ovalifolia.
The angiosperm order Santalales comprises more than 2500 species, most of which are hemi- or holoparasitic on other plants, and derive water and nutrients via specialised structures that attach to host roots or stems. The parasitic lifestyle has affected the morphology and genomes of these plants, and classification of the order has been difficult, with outstanding questions about membership of and relationships between families in the order. We chose to focus on improving phylogenetic sampling in the broadly circumscribed Santalaceae sens. lat., with emphasis on Australasian members of Amphorogynaceae and Viscaceae as part of the Genomics for Australian Plants Initiative. We used target capture with the Angiosperms353 bait set to generate a dataset of 318 nuclear loci × 195 samples, including publicly available data from other Santalales families. Phylogenetic inferences using maximum likelihood concatenation and a summary coalescent approach were largely congruent and resolved relationships between most families, agreeing with much of the previous work on the order. Some relationships that have been difficult to resolve remained so, such as branching order among some families in Olacaceae sens. lat. and Santalaceae sens. lat. Denser sampling in Amphorogynaceae and Viscaceae provided new insights into species-level relationships in genera such as Leptomeria and Choretrum, and allowed testing of recent phylogenetic work in Korthalsella. Our new phylogenetic hypothesis is consistent with one origin of root hemiparasitism, two origins of holoparasitism and five origins of aerial parasitism in the order. Although Angiosperms353 was successful, some phylogenetic bias in gene recovery suggests that future studies may benefit from more specific baits and deeper sequencing, especially for Viscaceae.
Recent phylogenetic studies have demonstrated that Hibiscus L. as traditionally defined is grossly polyphyletic. In a major step towards making Hibiscus monophyletic, the genus Sabdariffa (DC.) Kostel. is here reinstated for Hibiscus section Furcaria DC. In total, 123 new combinations are provided (for 117 species and 6 subspecies). Numerous lectotypes are designated. Sabdariffa has a pantropical distribution, with high species diversity in tropical Africa, tropical America and northern Australia. False roselle (Sabdariffa acetosella (Welw. ex Hiern) M.M.Hanes & R.L.Barrett), kenaf (Sabdariffa cannabina (L.) M.M.Hanes & R.L.Barrett) and roselle (Sabdariffa gossypiifolia (Mill.) M.M.Hanes & R.L.Barrett) are all of global economic significance. Ma‘o hau hele (Sabdariffa brackenridgei (A.Gray) M.M.Hanes & R.L.Barrett) is the official state flower of Hawai’i. Full synonymy and type details are included, along with distributions and references to existing descriptions for all species. A series of regional keys to species is presented here with current names in Sabdariffa.
The genus Melichrus R.Br. has received very little taxonomic attention and treatments have largely disagreed on species delimitation. The eastern Australian clade of Melichrus was last revised in 1958. Over 60 years later we present new, in-depth evidence for species delimitation. A morphological dataset (90 individuals from 68 populations, scored for 26 characters) was analysed using NMDS ordination with Bayesian Inference cluster modelling (mclust) and UPGMA hierarchical clustering to detect morphological discontinuities in the genus that may indicate species boundaries. Discontinuities in the morphological analyses were compared with those apparent in clustering (principal component analysis, SplitsTree Neighbour-Net, STRUCTURE and conStruct) and statistical analyses (HE, HO, FIS and FST) of a DArTseq SNP dataset of 548 samples from 110 populations of Melichrus. These new lines of evidence form the basis of detailed recommendations for a revised species taxonomy of Melichrus including the description of eight new species, recircumscription of previously described species and the correction of a longstanding nomenclatural misapplication.
The Dicranemataceae was monographed morphotaxonomically by Kraft in 1977, to which the four genera Dicranema Sond., Peltasta J.Agardh., Reptataxis Kraft and Tylotus J.Agardh were attributed. All, save for a species of Tylotus J.Agardh (from east Asia), were endemic to Australia. Additions (in 2006 and 2014 respectively) were the genus Pinnatiphycus N’Yeurt, Payri & P.W.Gabrielson from New Caledonia and Fiji and a new species of Tylotus from Hawaii. General features emphasised by Kraft were similarities of apical and internal structure, zonate tetrasporangia, monoecious gametophytes and placentate cystocarps. The genera did not show uniformity in regard to thallus habits and especially carposporophytes, however, the major differences of which were not accorded any family-level significance. Two later studies, N’Yeurt et al. in 2006 and Kraft et al. in 2014, presented limited molecular data but did not treat the family as a whole or fully resolve relationships between all of the taxa, leaving Kraft’s assumption that the family was monophyletic unchallenged. We address all of the genera, both anatomically and molecularly, and support proposal of two new families, the Peltastaceae and Tylotaceae, in addition to a monogeneric Dicranemataceae. A new genus and species of Peltastaceae, Peltastanomala virantra G.W.Saunders & Kraft, has unique axial and spermatangial anatomies and an unexpected family association with Peltasta. Two additional new genera and species (Chambersius thyrsus G.W.Saunders & Kraft and Huismanophycus marinus G.W.Saunders & Kraft) are even more dissimilar to Peltasta in habit and structure but weakly allied to the Peltastaceae on molecular evidence. Both are therefore regarded as incertae sedis.
Zieria obcordata A.Cunn. (Rutaceae), an endangered species endemic to central New South Wales, Australia, faces significant conservation challenges due to limited occurrence in two small, isolated populations. Using genome-wide SNPs (DArTseq), we examine genetic relationships and diversity within and between these populations, and make comparisons with other Zieria species. Our results confirm that Z. obcordata is a distinct species, with the Bathurst and Wellington populations showing sufficient genetic divergence to warrant recognition as two subspecies: Z. obcordata subsp. obcordata and Z. obcordata subsp. wuuluman (formally described here). Minor morphological differences further support this classification. Genomic analyses reveal minimal gene flow between the subspecies, along with extremely low heterozygosity and high inbreeding coefficients within each. Compared to other Zieria species, including Z. covenyi, Z. cytisoides, Z. laevigata, Z. odorifera and Z. smithii, both subspecies exhibit exceptionally low genetic diversity, likely due to geographic isolation, genetic drift and inbreeding. We provide conservation assessments for both subspecies and conclude that each qualifies to be listed as Critically Endangered under the New South Wales Biodiversity Conservation Act 2016. We recommend strategies to facilitate gene flow between the subspecies to improve genetic diversity and enhance fitness.
Leaf fossils collected in 1908 from the Arauco-Concepci & oacute;n Coal Measures of Chile (the Lota-Coronel flora) during a Swedish expedition to southern South America are formally assigned to the important Gondwanan family Proteaceae as Proteaceaefolia araucoensis R.J.Carp. & McLoughlin gen. nov., sp. nov. This is the oldest South American record of macrofossils that can be assigned to Proteaceae with confidence due to the likelihood of the age dating to the latest Paleocene. The fossils lack cuticle but the large, lobed and minutely toothed form is consistent only with extant species of the subfamily Grevilleoideae (notably, Orites excelsus R.Br.) that are confined to eastern Australian rainforests. A new assessment of the Swedish Lota-Coronel collection and review of previous palynological and macrofossil studies, also provide evidence of the strong biogeographic connection that existed between southern South America and Australasia during the early Paleogene, and contradict a traditional view that several Chilean floras of this age consist wholly or largely of Neotropical taxa. Notable austral taxa include Casuarinaceae (as abundant pollen), diverse Podocarpaceae (as both foliage and pollen) and likely Cunoniaceae (leaves). No taxa with clearly Neotropical nearest living relatives have been found to date, but previous conclusions for a warm and very wet early Paleogene climate are supported.
Drosera (Droseraceae) is one of the largest carnivorous plant genera globally, with Australia considered a nexus for the evolution of the genus. We present the most densely sampled phylogenomic analyses for Australian Drosera to date. As part of the Genomics for Australian Plants Initiative Stage II, 92 Drosera samples representing all major clades within Australia and key extra-Australian taxa were newly sequenced using Angiosperm353 and OzBaits nuclear bait sets, and the OzBaits plastid bait set. In total, 380 nuclear and 57 plastid loci were included in our final analyses. Our findings are broadly in congruence with conclusions of previous morphological studies that were informed by molecular data regarding the major lineages within Drosera. Incongruencies between the results from plastid and nuclear sequence data sets were primarily restricted to within-clade relationships, with high discordance noted in two closely affiliated species groups with centres of diversity across northern Australia and south-west Western Australia. Potential drivers of this phylogenetic discordance are investigated using Quartet Sampling and are discussed. An important outcome of these data is to highlight the diversity of novel evolutionary lineages within Australia for this group of plants that exhibit highly modified traits to survive in arid Australian environments.
Analysis of ITS and 28S regions of Subulispora and related taxa supports the placement of the genus within the family Phlogicylindriaceae, Amphisphaeriales. Two new species, S. chlamydospora M.G.A.Primo & Gusmão and S. grandiae M.G.A.Primo & Gusmão are described, and two new combinations, Dactylaria argentina (Aramb. & Mengasc.) M.G.A.Primo & Gusmão and D. malaysiana (Nawawi & Kuthub.) M.G.A.Primo & Gusmão are proposed. A taxonomic key, comparison table for the nine accepted species of Subulispora and illustrations of all studied taxa are provided.
Hibbertia is the largest genus in Dilleniaceae and one of the largest Australian plant genera, with ~350 current and more than 100 known undescribed species in Australia. We present the first published phylogeny based on rigorous sampling of Hibbertia. As part of Genomics for Australian Plants Stage II, 95 Hibbertia species were newly sequenced using Angiosperm353, OzBaits nuclear and OzBaits plastid bait sets, resulting in 402 nuclear and 79 plastid loci that were subsampled to retain the most phylogenetically useful 300 and 60 loci respectively. Nuclear and plastid phylogenies were reconstructed using concatenation and coalescent approaches, and further analysed using Quartet Sampling. We found that Hibbertia and the four subgenera within the genus are robustly supported as monophyletic and recovered 14 major clades, supported in both datasets, within the two largest subgenera (subg. Hemistemma and subg. Hibbertia). However, many relationships between these major clades are unresolved and discordant. Some incongruence was also detected between the plastid and nuclear trees. Discordance was particularly high in the largest eastern Australian clade of subg. Hemistemma. Possible causes of this discordance, and relationships between and within these major clades, are discussed.
Taxonomic uncertainty in Coronidium has existed since its original circumscription. Recent molecular phylogenetic analyses inferred Coronidium to be non-monophyletic and composed of four distinct clades, leading to the erection of Leucozoma and the confirmation that C. scorpioides (Labill.) Paul G.Wilson and related species are more closely related to other Australian Gnaphalieae. The present study focused on the delimitation of those species inferred to be part of Coronidium, Leucozoma and the closely related Helichrysum leucopsideum DC. We gathered DArTseq single-nucleotide polymorphism data and tested species limits by examining genotypic differences, ancestry, and morphological characters observed on herbarium specimens and living collections. Results support the recognition of four new narrowly endemic species, namely, C. batianoffii T.L.Collins & I.Telford, C. bruhlii T.L.Collins, L. alexandri T.L.Collins and L. wollumbin T.L.Collins. Results indicated that the narrow endemic C. fulvidum Paul G.Wilson is a variable hybrid between C. newcastlianum (Domin) Paul G.Wilson and C. rupicola (DC.) Paul G. Wilson, and subspecies of C. oxylepis (F.Muell.) Paul G.Wilson to be a polymorphic aggregate or ochlospecies, the subject of ongoing study. We lectotypify H. elatum A.Cunn ex DC. and Helipterum glutinosum Hook. and provide revised descriptions of all taxa in the genera, their conservation status, a dichotomous key, tables distinguishing closely related taxa and distribution maps.
Chamelaucieae is a diverse tribe in Myrtaceae with ~800 species in 37 genera distributed across Australia. We applied target capture sequencing using the Angiosperms353 probe set for 131 taxa as part of the Genomics for Australian Plants initiative. Sampling all genera (36) from 10 of 11 named subtribes, we present a phylogenomic analysis for the tribe. This phylogenomic approach has allowed us to better resolve subtribal relationships across the tribe, resulting in an updated classification and additional subtribe (total of 12 subtribes including Triplarininae). Despite these advances, the phylogenetic placements of Stenostegiinae, Astarteinae, and Micromyrtinae remain equivocal and resolution of these relationships should be a focus of future research. We constructed a dated phylogeny from this genomic dataset to investigate the tribe’s biogeographic history and diversification dynamics. We estimate that the crown radiation occurred in the Eocene (c. 42 Ma), with the ancestral area of origin in Australia unresolved. Subsequent divergence and origin of subtribes mostly occurred in south-west Western Australia with frequent dispersals from there into the semi-arid and arid interior since the Miocene (20 Ma). Dispersals out of northern and eastern Australia were limited and confined to dispersal events into the arid interior. Using paleoenvironmental diversification models we show that after the initial radiation, diversification in Chamelaucieae declined rapidly until the Eocene–Oligocene boundary extinction pulse event and subsequently more slowly to the present, with a modest increase during the Middle Miocene Climatic Optimum. No significant diversification rate shifts were detected within clades except within the subtribe Chamelauciinae. There was no significant geographic-dependent diversification in the tribe. Our results add to the growing literature revealing that high plant diversity in south-west Western Australia is due to more time for species accumulation attributed to long-term climatic stability rather than elevated diversification rates.
