Ecological genomics and adaptation of rosewoods Dalbergia cochinchinensis and D. oliveri for conservation and restoration

Global biodiversity, in particular tropical forests, is decreasing under both environmental change and anthropogenic disturbance. Environmental change alters species’ adaptability to their current habitat, leading to loss of fitness and range shift, while anthropogenic disturbance reduces their adaptive capacity. Conserving and restoring threatened species and ecosystems thus become a grand challenge for the 21st century. This thesis studies two threatened rosewood species, Dalbergia cochinchinensis and D. oliveri, which are illegally exploited for their valuable timber in the Greater Mekong Subregion. They became the world’s most trafficked wild product between 2005 and 2014, amounting to ~40% of the total global trade. Conservation efforts grew in the last decade to tackle the range-wide challenge, aiming to improve the species’ survival, amplify the production of genetic materials, and designate more conservation units. However, a sustainable supply of genetic materials can meet several challenges that compromise the effectiveness of a restoration programme, namely the genetic bottlenecks, maladaptation, and climate change. While knowledge of adaptation can predict and mitigate these risks, standard study approaches such as common garden experiments have become impractical due to the acute threats of illegal logging in these two species, which are lacking in a priori knowledge.
This thesis aims to increase the knowledge of genetic and physiological underpinning of adaptation in the two Dalbergia species with relevance to application in conservation and restoration strategies. This thesis presents a rich body of genomic resources such as chromosome-scale genomes and reference transcriptomes, which advance the progress in less-represented angiosperm tree genomes and woody legume genomes and enable studies in genetic diversity. Comparative genomic studies revealed insight into the evolution and potential adaptive role of of certain gene families in tropical Dalbergia species. The landscape genomic study provides a comprehensive scan of adaptive signals and reports significant differences of the adaptive variation between the two species, where D. cochinchinensis is driven by temperature variability and D. oliveri by precipitation variability. The controlled stress experiment provides a physiological understanding of how the two species regulate their water relations and photosynthetic apparatus to respond to drought differently, where D. cochinchinensis has a more anisohydric behaviour than D. oliveri. These contrasting patterns of adaptation indicate how the two species may differentiate their niches, while co-occurring in some habitats.
The knowledge of adaptive variation identifies hotspots of local adaptation and vulnerability towards climate change, and thus are expected to help conservation practitioners delineate conservation units, compare provenances for assisted germplasm transfer, and prioritise conservation actions. It also opens new avenues for future research, including combining common garden experiments and genomic approaches to more fully unravel genotype-phenotype-environment relationships.

Advisor: MacKay, J
Boshier, D