Habitat fragmentation imperils the persistence of many functionally important species, with climate change a new threat to local persistence due to climate-niche mismatching. Predicting the evolutionary trajectory of species essential to ecosystem function under future climates is challenging but necessary for prioritizing conservation investments. We use a combination of population genetics and niche suitability models to assess the trajectory of a functionally important, but highly fragmented, plant species from south-eastern Australia (Banksia marginata, Proteaceae). We demonstrate significant genetic structuring among, and high level of relatedness within, fragmented remnant populations, highlighting imminent risks of inbreeding. Population simulations, controlling for effective population size (Ne), suggest that many remnant populations will suffer rapid declines in genetic diversity due to drift in the absence of intervention. Simulations were used to demonstrate how inbreeding and drift processes might be suppressed by assisted migration and population mixing approaches that enhance the size and connectivity of remnant populations. These analyses were complemented by niche suitability models that predicted substantial reductions of suitable habitat by 2080; ~ 30% of the current distribution of the species climate niche overlaps with the projected distribution of the species climate niche in the geographic region by the 2080s. Our study highlights the importance of conserving remnant populations and establishing new populations in areas likely to support B. marginata in the future, and adopting seed sourcing strategies that can help populations overcome the risks of inbreeding and maladaptation. We also argue that ecological replacement of B. marginata using climatically-suited plant species might be needed in the future to maintain ecosystem processes where B. marginata cannot persist. We recommend the need for progressive revegetation policies and practices to prevent further deterioration of species such as B. marginata and the ecosystems they support. 

Genomic DNA was extracted from 30 mg tissue samples for individual specimens using the NucleoSpin® 96 Plant II protocol (Machery-Nagel Inc., Düren, KO, GER) and DNA quantitation was performed as per the QuantiFluor® dsDNA System (Promega Inc, Madison, NY, USA).Banksia marginataDNA samples were genotyped at 10 microsatellite loci using a composite of genetic markers developed by He et al. 2013 and Fatemi et al. 2014, and additional markers developed in the present study using the approach outlined in Miller et al. 2019) (Table 2). In order to distinguish PCR products upon capillary separation, primers for the ten microsatellite markers were tagged with a unique fluorescent label during PCR using the method outlined in Blacket et al. (2012). Reaction matrices for PCR amplification consisted of 5 ml Qiagen multiplex mix (Qiagen, Chadstone, Victoria, Australia), 4 ml of primer mix (0.2 mM of each primer) and 2 ml of template DNA. PCR conditions consisted of an initial 15 min denaturing step at 94 °C, followed by 40 cycles of 94 °C for 30 s, 59 °C for 1:30 min, and 72 °C for 1:00 min, with a final extension step of 60 °C for 30 min. Genotyping was subsequently performed using an Applied Biosystems 3730 capillary analyser and product lengths were determined relative to a GS500LIZ_3730 size standard. Fragment analyses were conducted using an ABI3730 XL DNA analyser. Microsatellite profiles were examined and scored manually and assessed for polymorphisms using GeneMapper version 4.0 (Applied Biosystems).