Biology subjects

Crayn, D. M.

Publications and source records attributed to Crayn, D. M..

5 recordsLinked to original sources

bioRxiv2025

The complex evolutionary history of Capparis L. (Capparaceae Juss.) in Australia, and the description of five new species and two new subspecies

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 split into three subspecies: subsp. formicosa, subsp. insularis, and subsp. nummularia. We provide a key for all Australian taxa.

evolutionary biology↗

bioRxiv2024

Nuclear phylogenomics of grasses (Poaceae) supports current classification and reveals repeated reticulation

O_LIGrasses (Poaceae) comprise around 11,800 species and are central for human livelihoods and terrestrial ecosystems. Knowing their relationships and evolutionary history is key to comparative research and crop breeding. Advances in genome-scale sequencing allow for increased breadth and depth of phylogenomic analyses, making it possible to infer a new reference species tree of the family. C_LIO_LIWe inferred a comprehensive species tree of grasses by combining new and published sequences for 331 nuclear genes from genome, transcriptome, target enrichment and shotgun data. Our 1,153-tip tree covers 79% of grass genera (including 21 genera sequenced for the first time) and all but two small tribes. We compared it to a 910-tip plastome tree. C_LIO_LIThe nuclear phylogeny matches that of the plastome at most deep branches, with only a few instances of incongruence. Gene tree-species tree reconciliation suggests that reticulation events occurred repeatedly in the history of grasses. C_LIO_LIWe provide a robust framework for the grass tree of life to support research on grass evolution, including modes of reticulation, and genetic diversity for sustainable agriculture. C_LI

plant biology↗

bioRxiv2024

Plastid phylogenomics reveals evolutionary relationships in the mycoheterotrophic orchid genus Dipodium and provides insights into plastid gene degeneration

The orchid genus Dipodium R.Br. (Epidendroideae) comprises leafy autotrophic and leafless mycoheterotrophic species, the latter confined to sect. Dipodium. This study examined plastome degeneration in Dipodium in a phylogenomic and temporal context. Whole plastomes were reconstructed and annotated for 24 Dipodium samples representing 14 species and two putatively new species, encompassing over 80% of species diversity in sect. Dipodium. Phylogenomic analysis based on 68 plastid loci including a broad outgroup sampling across Orchidaceae found sect. Leopardanthus as sister lineage to sect. Dipodium. Dipodium ensifolium, the only leafy autotrophic species in sect. Dipodium was found sister to all leafless, mycoheterotrophic species, supporting a single evolutionary origin of mycoheterotrophy in the genus. Divergence time estimations found that Dipodium arose ca. 33.3 Ma near the lower boundary of the Oligocene and crown diversification commenced in the late Miocene, ca. 11.3 Ma. Mycoheterotrophy in the genus was estimated to have evolved in the late Miocene, ca. 7.3 Ma, in sect. Dipodium. The comparative assessment of plastome structure and gene degradation in Dipodium revealed that plastid ndh genes were pseudogenised or physically lost in all Dipodium species, including in leafy autotrophic species of both Dipodium sections. Levels of plastid ndh gene degradation were found to vary among species as well as within species, providing evidence of relaxed selection for retention of the NADH dehydrogenase complex within the genus. Dipodium exhibits an early stage of plastid genome degradation as all species were found to have retained a full set of functional photosynthesis-related genes and housekeeping genes. This study provides important insights into plastid genome degradation along the transition from autotrophy to mycoheterotrophy in a phylogenomic and temporal context.

evolutionary biology↗

bioRxiv2023

Global analysis of Poales diversification - parallel evolution in space and time into open and closed habitats

O_LIPoales are one of the most species-rich, ecologically and economically important orders of plants and often characterise open habitats, enabled by unique suites of traits. We test the hypotheses that Poales species are assembled into distinct phyloregions, with centres of high phylogenetic diversity and endemism clustered in tropical regions, and that cosmopolitan families show parallel transitions into open and closed habitats at different times. C_LIO_LIWe sampled 42% of Poales species and obtained taxonomic and biogeographic data from the World Checklist of Vascular Plants database, which was combined with open/closed habitat data scored by taxonomic experts. A dated supertree of Poales was constructed. We integrated spatial phylogenetics with regionalization analyses, historical biogeography, ancestral state estimations, and models of contingent evolution. C_LIO_LIDiversification in Poales and assembly of open and closed habitats result from dynamic evolutionary processes that vary across lineages, time, space, and traits, most prominently in tropical and southern latitudes. Our results reveal parallel and recurrent patterns of habitat and trait transitions in the species-rich families Poaceae and Cyperaceae, yet other smaller families display unique evolutionary trajectories. C_LIO_LIThe Poales have achieved global dominance via parallel evolution in open habitats, with notable, spatially and phylogenetically restricted divergences into strictly closed habitats. C_LI

ecology↗

bioRxiv2022

Plastid phylogenomics clarifies broad-level relationships in Bulbophyllum (Orchidaceae) and provides insights into range evolution of Australasian section Adelopetalum

The hyper diverse orchid genus Bulbophyllum is the second largest genus of flowering plants and exhibits a pantropical distribution with a center of diversity in tropical Asia. The only Bulbophyllum section with a center of diversity in Australasia is sect. Adelopetalum. However, phylogenetic placement, interspecific relationships, and spatio-temporal evolution of the section have remained largely unclear. To infer broad-level relationships within Bulbophyllum and interspecific relationships within sect. Adelopetalum, a genome skimming dataset was generated for 89 samples, yielding 70 plastid coding regions and the nuclear ribosomal DNA cistron. For 18 additional samples, Sanger data from two plastid loci (matK, ycf1) and nuclear ITS were added using a supermatrix approach. The study provided new insights into broad-level relationships in Bulbophyllum, including phylogenetic evidence for the non-monophyly of sections Beccariana, Brachyantha, Brachypus, Cirrhopetaloides, Cirrhopetalum, Desmosanthes, Minutissima, Oxysepala, Polymeres and Sestochilos. Section Adelopetalum and sect. Minutissima s.s. formed a highly supported clade that was resolved in sister group position to the remainder of the genus. Divergence time estimations based on a relaxed molecular clock model placed the origin of Bulbophyllum in the early Oligocene (ca. 33.2 Ma) and of sect. Adelopetalum in the late Oligocene (ca. 23.6 Ma). Ancestral range estimations based on a BAYAREALIKE model identified the Australian continent as ancestral area of sect. Adelopetalum. The section underwent crown diversification during the mid-Miocene to the late Pleistocene, predominantly in continental Australia. At least two independent long-distance dispersal events were inferred eastwards from the Australian continent to New Zealand, and New Caledonia from the early Pliocene onwards, likely mediated by the predominantly westerly winds of the southern hemisphere. Retraction and fragmentation of eastern Australian rainforests from the early Miocene onwards are discussed as likely drivers of lineage divergence within sect. Adelopetalum, facilitating allopatric speciation.

evolutionary biology↗