The population genetics of two temperate rainforest trees, Lagarostrobos franklinii (Hook f.) Quinn (Huon pine), and Atherosperma moschatum Labill. (Sassafras)

The population genetics of two temperate rainforest tree species endemic to south eastern Australia were studied. Both species are long-lived and members of ancient families. There are parallels between the two species even though one was a gymnosperm and the other an angiosperm. For example, both species reproduce both vegetatively and sexually. Lagarostrobos franklinii (Huon pine) (Podocarpaceae) is mostly dioecious and wind pollinated, while Atherosperma moschatum (sassafras) (Monimiaceae), is monoecious or dioecious and insect pollinated. Both have potential for long distance seed dispersal, L.franklinii by water and A. moschatum by wind. The population genetics of both species was studied from stands throughout their geographic range using isozyme analysis. Most genetic diversity was found within rather than among sites. Genetic diversity among sites was low but generally consistent with expectations for each species (Hamrick and Godt 1979). Atherosperma moschatum had much more diversity among sites than Huon pine, with its mainland sites differentiating significantly from its Tasmanian ones. In Huon pine, most differentiation was found in isolated sites. Diversity within sites was also low in Huon pine but was much greater in sassafras. The structure of genotypes within stands was examined using spatial autocorrelation. In both species trees of like genotypes were found to be clustered at short distances. This genetic substructuring was found regardless of population size, density, distance from other stands, level of inbreeding, history, etc. Most sites deviated from Hardy-Weinberg expectations with deficiencies of heterozygotes, and high levels of allelic fixation, and were effectively inbred. The size structure and floristics within stands were investigated and used to assist in the interpretation of the patterns of genetic variation, inbreeding and stand dynamics found in each species. There was much variation in size structures and regeneration modes between sites in both species and neither appeared to require large scale disturbances for regeneration. The two species varied in the relationships between site environmental/ecological similarity and genetic similarity. In both species there was as much diversity in genetic variability and size structure in small isolated stands as there was in stands within larger assemblages. The proportion of trees contributing to the reproductive population, as well as the proportion of each gender type within that population, were estimated for Huon pine stands. On average thirty percent of Huon pine trees greater than one metre tall were reproductively active in the mast year recorded, and overall there were equal proportions of male and female trees. The relationships between reproduction and gender expression, with size structure, density, floristics, inbreeding and genotypes were investigated. Stands were also compared to identify if there were geographical or climatic trends in the distribution of these characteristics. Reproduction was found to increase with increasing tree size and also with more open canopies. Sites with similar proportions of females were found to also have similar species compositions. The distribution of reproductive trees and gender types within stands was investigated using spatial autocorrelation. The results were compared with genotypic distributions within the same stands. Although there was no direct correlation between gender type and genotype, both genotype and gender type were clustered at the same spatial scale, suggesting that such clustering may have a strong vegetative component. Huon pine seed production was estimated at one site and seed dispersal was investigated. Very large quantities of seed were shed. Seed dispersal laterally was negligible, but potential for dispersal down water courses was great as it stayed afloat for extended periods. Huon pine seed germination was investigated both in the field and under experimental conditions. Germination generally was slow, and with a low success rate. However seed in the field germinated at particular daylengths (regardless of temperature) in two consecutive seasons. Both species showed evidence that vegetative reproduction and localised pollen and seed dispersal have led to the development of family clusters, leading to inbreeding, and local fixation of allelic proportions. However infrequent long distance gene flow has probably reduced population differentiation. The population viability of each species was discussed

Population modelling and genetics of a critically endangered Madagascan palm Tahina spectabilis.

Madagascar is home to 208 indigenous palm species, almost all of them endemic and >80% of which are endangered. We undertook complete population census and sampling for genetic analysis of a relatively recently discovered giant fan palm, the Critically Endangered Tahina spectablis in 2008 and 2016. Our 2016 study included newly discovered populations and added to our genetic study. We incorporated these new populations into species distribution niche model (SDM) and projected these onto maps of the region. We developed population matrix models based on observed demographic data to model population change and predict the species vulnerability to extinction by undertaking population viability analysis (PVA). We investigated the potential conservation value of reintroduced planted populations within the species potential suitable habitat. We found that the population studied in 2008 had grown in size due to seedling regeneration but had declined in the number of reproductively mature plants, and we were able to estimate that the species reproduces and dies after approximately 70 years. Our models suggest that if the habitat where it resides continues to be protected the species is unlikely to go extinct due to inherent population decline and that it will likely experience significant population growth after approximately 80 years due to the reproductive and life cycle attributes of the species. The newly discovered populations contain more genetic diversity than the first discovered southern population which is genetically depauperate. The species appears to demonstrate a pattern of dispersal leading to isolated founder plants which may eventually lead to population development depending on local establishment opportunities. The conservation efforts currently put in place including the reintroduction of plants within the species potential suitable habitat if maintained are thought likely to enable the species to sustain itself but it remains vulnerable to anthropogenic impacts

Advancing DNA barcoding and metabarcoding applications for plants requires systematic analysis of herbarium collections-an Australian perspective

Building DNA barcode databases for plants has historically been ad hoc, and often with a relatively narrow taxonomic focus. To realize the full potential of DNA barcoding for plants, and particularly its application to metabarcoding for mixed-species environmental samples, systematic sequencing of reference collections is required using an augmented set of DNA barcode loci, applied according to agreed data generation and analysis standards. The largest and most complete reference collections of plants are held in herbaria. Australia has a globally significant flora that is well sampled and expertly curated by its herbaria, coordinated through the Council of Heads of Australasian Herbaria. There exists a tremendous opportunity to provide a comprehensive and taxonomically robust reference database for plant DNA barcoding applications by undertaking coordinated and systematic sequencing of the entire flora of Australia utilizing existing herbarium material. In this paper, we review the development of DNA barcoding and metabarcoding and consider the requirements for a robust and comprehensive system. We analyzed the current availability of DNA barcode reference data for Australian plants, recommend priority taxa for database inclusion, and highlight future applications of a comprehensive metabarcoding system. We urge that large-scale and coordinated analysis of herbarium collections be undertaken to realize the promise of DNA barcoding and metabarcoding, and propose that the generation and curation of reference data should become a national investment priority

Conservation genetics and ecology of the endangered rainforest shrub, Triunia robusta, from the Sunshine Coast, Australia

Triunia robusta, which until recently was thought to be extinct, is now classified nationally as endangered. It is an understorey species restricted to the subcoastal rainforests in a small region of the Sunshine Coast, Queensland. The project involved sampling the genetic variation and measuring the population size and size distribution of T. robusta and its geographically closest congener T. youngiana, which occurs further south and has a wider geographic distribution. A total of 877 T. robusta plants were recorded across the 11 populations, approximately half (56.8%) of these were juveniles less than 1 m tall, whereas in T. youngiana only about 36.4% of a population was composed of juveniles. Genetic diversity was similar but significantly higher for T. robusta than T. youngiana if the very small T. robusta populations (2 or 3 plants) were excluded from analysis (P less than 0.05). The mean percentage of polymorphic loci among populations was high for both species. Triunia robusta is not, on average, more inbred than the more common T. youngiana. There was more differentiation between the T. robusta populations, which were in close proximity, than between the more geographically separated T. youngiana populations. Thus, there is evidence of more gene flow between populations of T. youngiana than between those of T. robusta. However, there was no geographic relationship between genetic similarity and geographic proximity in T. robusta

Genetic and ecological variation in Atherosperma moschatum and the implications for conservation of its biodiversity

Population genetics and ecology of Atherosperma moschatum Labill. (sassafras), a major canopy tree of Australian temperate rainforests, were examined and used to identify priorities and strategies for conservation of its genetic diversity. The genetic diversity among populations was fairly low, but higher than average for long-lived late successional or wind dispersed species (Hamrick and Godt 1989). Genetic distances between populations were correlated with geographic distances and climatic differences. The major genetic differentiation was between the mainland populations and those in Tasmania, with the New South Wales populations being quite genetically distinct. Most genetic variation was found within populations, however, most populations were inbred. This is likely to be due to selfing and spatial genetic substructure resulting from vegetative spread and local dispersal. There was evidence of regeneration in all populations, however no consistent regeneration patterns emerged. Population density was inexplicably correlated with genetic distance. There was as much diversity in all variables (ecological and genetic) measured in small isolated populations as there was in stands within larger assemblages; therefore, population size does not appear to be a major factor affecting viability. Genetic variation was spread throughout the distribution of A. moschatum. Therefore, populations from throughout its range would need to be conserved to retain the genetic diversity within this species

Conservation and genetics in the fragmented monsoon rainforest in the Northern Territory, Australia: a case study of three frugivore-dispersed species

Monsoon rainforest in the Northern Territory exists as an archipelago of tiny patches thought to be previously more continuous but having had retracted to a fragmented state by the Pleistocene. However, there is evidence of some more recent rainforest expansion, and many species have seeds that are dipsersed by small frugivores (birds and bats). Carpentaria acuminata and Ptychosperma bleeseri are endemic to the Northern Territory and Syzygium nervosum is endemic to the Northern Territory within its Australian distribution. Carpentaria acuminata and S. nervosum are common through moist rainforest, but P. bleeseri is rare, found in eight locations near Darwin. All have frugivore-dispersed seeds. The three species were surveyed across their geographic range to compare their population genetics. The results from C. acuminata and S. nervosum were analysed to investigate the distribution of allelic diversity, the effect of patch size and isolation on genetic diversity, and the effectiveness of seed dispersal by vagile frugivores. Genetic diversity (expected heterozygosity) was correlated with mean annual rainfall in both S. nervosum and C. acuminata. Genetic diversity (alleles per locus, percentage of polymorphic loci, expected heterozygosity) was also negatively correlated with population isolation but not patch size in C. acuminata. There was significant heterogeneity and low gene flow among C. acuminata populations (FST 0.379, Nm = 0.39) but not among S. nervosum populations, which had substantial evidence of gene flow (FST 0.118, Nm = 1.67). The distribution of rare alleles in C. acuminata was consistent with the theory of Pleistocene retraction to refugia. Ptychosperma bleeseri was genetically uniform across all sites. Only four individuals differed in their genotypes. The results suggest that the present populations originated from a single founder population rather than having independently contracted from a more extensive distribution. All three species had evidence of some more recent population expansion

Investigating the Relationship between Fire Severity and Post-Fire Vegetation Regeneration and Subsequent Fire Vulnerability

The Australian 2019–2020 wildfires impacted the subtropical rainforest with a variety of burn severities, making them vulnerable to another burn. Rainforest post-fire regenerated vegetation could be highly flammable, containing fire-promoting species such as Lantana camara and fire-suppressing species such as Phytolacca octandra. This study investigated whether early post-fire regeneration may make rainforests more flammable and if this varies with fire severity. This study sampled three national parks where rainforest burnt in 2019–2020 across different fire severities to test if there were consistent patterns in post-fire regeneration flammability. We found that flammable species increased in the regions where fire severity was higher

Data from: Characterization of microsatellite primers in the endangered orchid Phaius australis and cross-amplification to P. bernaysii (Orchidaceae)

Premise of the study: The swamp orchid, Phaius australis (Orchidaceae), is nationally endangered due to illegal collection and habitat loss and fragmentation, resulting in a disjunct distribution in spring and coastal wetland ecotones along Australia's east coast. Polymorphic microsatellite markers were developed to study genetic diversity and population structure for conservation and restoration purposes. Methods and Results: Illumina HiSeq high-throughput sequencing was used to develop 15 nuclear microsatellite markers, including 10 polymorphic markers for P. australis. Polymorphism at each marker was evaluated using 90 individuals from four natural populations. The number of alleles per locus ranged from one to three, and the observed and expected heterozygosity varied from 0.036 to 0.944 and from 0.035 to 0.611, respectively. These markers transferred successfully to congener P. bernaysii. Conclusions: The microsatellite markers will be useful for revealing levels of genetic diversity and gene flow for P. australis and may inform future conservation efforts