Marsileaceaephyllum, a new genus for marsileaceous macrofossils: leaf remains from the Early Cretaceous (Albian) of southern Gondwana

Three new taxa from Albian, Early Cretaceous assemblages in Gondwana (Australia and Antarctica) and two previously described fossils from the Late Cretaceous and Eocene of North America are attributable to the heterosporous semi-aquatic fern family Marsileaceae. They are assigned to Marsileaceaephyllum, a morphotaxon erected here for sterile remains (whole plants, and isolated leaves and leaflets) of Marsileaceae. The Gondwanan taxa, Marsileaceaephyllum lobatum and Marsileaceaephyllum spp. B-C, have either a cruciform leaflet arrangement or dichotomous and anastomosing venation characteristic of modern Marsileaceae. Two previously established taxa, Marsilea johnhallii and Marsilea sp., which represent sterile Marsileaceae, are also transferred to the new genus (now Marsileaceaephyllum johnhallii and Marsileaceaephyllum sp. A, respectively). Examination of all fossil venation patterns reveals four new venation types not present in extant taxa, suggesting that most fossil Marsileaceae (leaves) are distinct from extant genera, and are likely members of extinct lineages. This is further supported by the absence of modern megaspore types in the Early Cretaceous.     

Conservation genomics of an Australian cycad Cycas calcicola,and the Absence of Key Genotypes in Botanic Gardens

Understanding the genetic diversity of wild populations is fundamental to conserving species in-situ and ex-situ. To aid conservation plans and to inform ex-situ conservation, we examined the genetic diversity of the cycad Cycas calcicola (Cycadaceae). Samples were collected from wild populations in the Litchfield National Park and Katherine regions in the Northern Territory, Australia. Additional samples were obtained from botanic garden plants that were originally collected in the Katherine region, Daly River and Spirit Hills in the Northern Territory, Australia. Using RADseq we recovered 2271 informative genome-wide SNPs, revealing low to moderate levels of gene diversity (uH_e?=?0.037 to 0.135), very low levels of gene flow, and significant levels of inbreeding (mean F_IS?=?0.491). Population structure and multivariate analysis showed that populations fall into two genetic groups (Katherine vs Litchfield?+?Daly River?+?Spirit Hills). Genetic differentiation was twice as high between populations of the Katherine and Litchfield regions (F_ST?~?0.1) compared to within these two regions (F_ST?~?0.05). Increasing population fragmentation together with high levels of inbreeding and very little gene flow are concerning for the future adaptability of this species. The results indicated that the ex-situ collections (1) had significantly lower genetic diversity than the wild populations, and (2) only partly capture the genetic diversity present, particularly because the Litchfield National Park populations are not represented. We recommend that ex-situ collections be expanded to incorporate the genetic diversity found in Litchfield National Park and to increase the number of representatives from Daly River/Spirit Hills, and that in-situ populations from the Katherine and Greater Litchfield regions be conserved as separate management units.

     

RADseq as a valuable tool for plants with large genomes—A case study in cycads

Full genome sequencing of organisms with large and complex genomes is intractable and cost ineffective under most research budgets. Cycads (Cycadales) represent one of the oldest lineages of the extant seed plants and, partly due to their age, have incredibly large genomes up to ~60 Gbp. Restriction site‐associated DNA sequencing (RADseq) offers an approach to find genome‐wide informative markers and has proven to be effective with both model and nonmodel organisms. We tested the application of RADseq using ezRAD across all 10 genera of the Cycadales including an example data set of Cycas calcicola representing 72 samples from natural populations. Using previously available plastid and mitochondrial genomes as references, reads were mapped recovering plastid and mitochondrial genome regions and nuclear markers for all of the genera. De novo assembly generated up to 138,407 high‐depth clusters and up to 1,705 phylogenetically informative loci for the genera, and 4,421 loci for the example assembly of C. calcicola. The number of loci recovered by de novo assembly was lower than previous RADseq studies, yet still sufficient for downstream analysis. However, the number of markers could be increased by relaxing our assembly parameters, especially for the C. calcicola data set. Our results demonstrate the successful application of RADseq across the Cycadales to generate a large number of markers for all genomic compartments, despite the large number of plastids present in a typical plant cell. Our modified protocol was adapted to be applied to cycads and other organisms with large genomes to yield many informative genome‐wide markers.