Pervasive admixture between eucalypt species has consequences for conservation and assisted migration

Abstract

Conservation management often uses information on genetic population structure to assess the importance of local provenancing for ecological restoration and reintroduction programs. For species that do not exhibit complete reproductive isolation, the estimation of population genetic parameters may be influenced by the extent of admixture. Therefore, to avoid perverse outcomes for conservation, genetically informed management strategies must determine whether hybridization between species is relevant, and the extent to which observed population genetic patterns are shaped by interspecific versus intraspecific gene flow. We used genotyping by sequencing to identify over 2,400 informative single nucleotide polymorphisms across 18 populations of Eucalyptus regnans F. Muell., a foundation tree species of montane forests in south‐eastern Australia. We used these data to determine the extent of hybridization with another species, Eucalyptus obliqua L'Hér., and investigate how admixture influences genetic diversity parameters, by estimating metrics of genetic diversity and examining population genetic structure in datasets with and without admixed individuals. We found hybrid individuals at all sites and two highly introgressed populations. Hybrid individuals were not distributed evenly across environmental gradients, with logistic regression identifying hybrids as being associated with temperature. Removal of hybrids resulted in increases in genetic differentiation ( F ST ), expected heterozygosity, observed heterozygosity and the inbreeding coefficient, and different patterns of isolation by distance. After removal of hybrids and introgressed populations, mountain ash showed very little population genetic structure, with a small effect of isolation by distance, and very low global F ST (0.03). Our study shows that, in plants, decisions around provenancing of individuals for restoration depend on knowledge of whether hybridization is influencing population genetic structure. For species in which most genetic variation is held within populations, there may be little benefit in planning conservation strategies around environmental adaptation of seed sources. The possibility for adaptive introgression may also be relevant when species regularly hybridize.

Scale‐dependent signatures of local adaptation in a foundation tree species

“…The remaining samples were collected from across the VCH, with variable distances between samples and at a range of elevations and topographic conditions (Figure 1b). As messmate ( Eucalyptus obliqua ) commonly hybridises with mountain ash, we collected 20 messmate samples to allow for the calculation of ancestry coefficients and exclusion of admixed individuals from the data set (as per von Takach Dukai et al, 2019). All samples were placed in individual brown paper bags for air‐drying and then stored at 4°C prior to DNA extraction.…”

“…Library preparation for genotyping‐by‐sequencing was conducted as per von Takach Dukai et al, (2019), and included (1) digestion of 400 ng of genomic DNA of each sample using PstI restriction enzyme digestion (New England BioLabs Inc.), (2) fragment ligation with a unique barcode adapter pair, (3) purification and PCR amplification using two GBS primers (Integrated DNA Technologies; Elshire et al, 2011), (4) post‐purification quantification using microfluidic capillary electrophoresis (PerkinElmer Labchip GX‐II), (5) equimolar pooling using an automated robotic liquid handling machine (PerkinElmer NGS Express), and (6) purification using a Genelute PCR Clean‐Up Kit (Sigma‐Aldrich). The pooled samples were then size fractionated and a 250–450 bp gel cutout was performed, with sequencing conducted on multiple lanes of an Illumina HiSeq 2500 platform (along with hundreds of additional mountain ash samples used for separate projects) using a 100‐base paired‐end read.…”

“…Importantly, the Bass Strait separates the Victorian and Tasmanian parts of the species range, with a distance of at least 200 km probably preventing any gene flow between these regions for at least ten thousand years (Duncan et al, 2016; Lambeck et al, 2014). Within each region, the distribution of the species is further divided by inhospitable low‐lying habitats, which have led to levels of genetic differentiation among parts of Victoria that are approximately equal to that between Tasmania and the mainland (von Takach Dukai et al, 2019). Forests dominated by mountain ash are also considered critically endangered ecosystems, with wildfire and logging causing substantial changes to the age structure and structural characteristics of the forest (Burns et al, 2015; Lindenmayer et al, 2015; von Takach Dukai et al, 2018).…”

Ten years on – a decade of intensive biodiversity research after the 2009 Black Saturday wildfires in Victoria’s Mountain Ash forest

“…The key threat to the population of Mountain Ash trees in the Central Highlands of Victoria relates to the shortening of inter-fire intervals and the time required for Mountain Ash to mature and produce viable seed. Recent published work shows the minimum period between disturbances before Mountain Ash have sufficient seed in the canopy to regenerate is ~20 years, although there is some environmentally-associated intraspecific variation (von Takach Dukai et al 2018). Like many eucalypts, Mountain Ash hybridises readily with other species including Messmate (Eucalyptus obliqua) and Red Stringybark (Eucalyptus macrorhyncha) (Ashton and Sandiford 1988).…”

Investigating the role of urbanisation, wetlands and climatic conditions in nematode parasitism in a large Australian elapid snake

“…It is possible that a small number of wetlands have been lost or created over this time, however we believe that these are unlikely to have a substantial impact on the results of the study. The location (coordinates in decimal degrees) of all 80 adult snakes were uploaded into the Atlas of Living Australia's (ALA) Spatial Portal (https://spatial.ala.org.au/#), and five environmental variables at each point were extracted: mean annual precipitation (RAIN), topographic wetness index (TWI), mean annual maximum temperature (MAXTEMP), mean annual temperature (MEANTEMP) and mean annual minimum temperature (MINTEMP) (von Takach Dukai et al, 2019). Variables extracted from the ALA have been derived from various sources, and are based on an average of 50 years of climate data centred on 1990 (Williams et al, 2010; Xu and Hutchinson, 2013).…”