Genomic drivers of early-life fitness in Picea rubens

Forest genomics in the Caucasus through the lens of its dominant tree species - Fagus orientalis

The last glacial period is known to have greatly influenced the demographic history of temperate forest trees, with important range contractions and post-glacial expansions that led to the formation of multiple genetic lineages and secondary contact zones in the Northern Hemisphere. These dynamics have been extensively studied for European and North American species but are still poorly understood in other temperate regions of rich biodiversity such as the Caucasus. Our study helps filling that gap by deciphering the genomic landscapes of F. orientalis across the South Caucasus. The use of genome-wide data confirmed a past demographic history strongly influenced by the Last Glacial Maximum, revealing two disjunct glacial refugia in the Colchis and Hyrcanian regions. The resulting patterns of genetic diversity, load and differentiation are not always concordant across the region, with genetic load pinpointing the location of the glacial refugia more efficiently than genetic diversity alone. The Hyrcanian forests show depleted genetic diversity and substantial isolation, even if long-distance gene flow is still present with the main centre of diversity in the Greater Caucasus. Finally, we characterize a strong heterogeneity of genetic diversity and differentiation along the species chromosomes, with noticeably a first chromosome showing low diversity and weak differentiation.

Bringing genomics to the field: An integrative approach to seed sourcing for forest restoration

Premise

Global anthropogenic change threatens the health and productivity of forest ecosystems. Assisted migration and reforestation are tools to help mitigate these impacts. However, questions remain about how to approach sourcing seeds to ensure high establishment and future adaptability.

Methods

Using exome-capture sequencing, we demonstrate a computational approach to finding the best n-sets from a candidate list of seed sources that collectively achieve high genetic diversity (GD) and minimal genetic load (GL), while also increasing evolvability in quantitative traits. The benefits of this three-part strategy (diversity-load-evolvability) are to increase near-term establishment success while also boosting evolutionary potential to respond to future stressors. Members of The Nature Conservancy and the Central Appalachian Spruce Restoration Initiative planted 58,000 seedlings across 255 acres. A subset of seedlings was monitored for establishment success and variation in growth.

Results

The results show gains in GD relative to GL and increases in quantitative genetic variation in seedling growth for pooled vs. single-source restoration. No single "super source" was observed across planting sites; rather, monitoring results demonstrate that pooling of multiple sources helps achieve higher GD:GL and evolvability.

Discussion

Our study shows the potential for integrating genomics into local-scale restoration and the importance of building partnerships between academic researchers and applied conservation managers.

Postglacial phylogeography, admixture, and evolution of red spruce (Picea rubens Sarg.) in Eastern North America

Climate change is a major evolutionary force that can affect the structure of forest ecosystems worldwide. Red spruce (Picea rubens Sarg.) has recently faced a considerable decline in the Southern Appalachians due to rapid environmental change, which includes historical land use, and atmospheric pollution. In the northern part of its range, red spruce is sympatric with closely related black spruce (Picea mariana (Mill.) B.S.P.), where introgressive hybridization commonly occurs. We investigated range-wide population genetic diversity and structure and inferred postglacial migration patterns and evolution of red spruce using nuclear microsatellites. Moderate genetic diversity and differentiation were observed in red spruce. Genetic distance, maximum likelihood and Bayesian analyses identified two distinct population clusters: southern glacial populations, and the evolutionarily younger northern populations. Approximate Bayesian computation suggests that patterns of admixture are the result of divergence of red spruce and black spruce from a common ancestor and then introgressive hybridization during post-glacial migration. Genetic diversity, effective population size (Ne) and genetic differentiation were higher in the northern than in the southern populations. Our results along with previously available fossil data suggest that Picea rubens and Picea mariana occupied separate southern refugia during the last glaciation. After initial expansion in the early Holocene, these two species faced a period of recession and formed a secondary coastal refugium, where introgressive hybridization occurred, and then both species migrated northward. As a result, various levels of black spruce alleles are present in the sympatric red spruce populations. Allopatric populations of P. rubens and P. mariana have many species-specific alleles and much fewer alleles from common ancestry. The pure southern red spruce populations may become critically endangered under projected climate change conditions as their ecological niche may disappear.

Seed Germination and Seedling Growth Influenced by Genetic Features and Drought Tolerance in a Critically Endangered Maple

Understanding the adaptation of plant species will help us develop effective breeding programs, guide the collection of germplasm, and improve the success of population restoration projects for threatened species. Genetic features correlate with species adaptation. Acer yangbiense is a critically endangered plant species with extremely small populations (PSESP). However, no information was available on its seed germination and seedling growth in populations with different genetic characteristics. In this study, we investigated seed germination and compared the performance of 566 seedlings in 10 maternal half-sib families cultivated in Kunming Botanical Garden. The results showed that A. yangbiense seeds required an average of 44 days to start germinating, with a 50% germination rate estimated to take about 47-76 days, indicating slow and irregular germination. There is a trade-off between the growth and survival in A. yangbiense seedlings, with fast growth coming at the cost of low survival. Groups that were able to recover from a recent bottleneck consistently had higher relative growth rates. High genetic diversity and low levels of inbreeding are likely to be responsible for their improved survival during drought conditions and rapid growth under optimal environmental conditions. Our results suggest that maternal genetic traits might be used as indicators for conservation and population restoration. These findings provide us with new information that could be applied to support ex situ conservation and reintroduction of threatened species.

Genotypic variation and plasticity in climate-adaptive traits after range expansion and fragmentation of red spruce (Picea rubens Sarg.)

Shifting range limits are predicted for many species as the climate warms. However, the rapid pace of climate change will challenge the natural dispersal capacity of long-lived, sessile organisms such as forest trees. Adaptive responses of populations will, therefore, depend on levels of genetic variation and plasticity for climate-responsive traits, which likely vary across the range due to expansion history and current patterns of selection. Here, we study levels of genetic and plastic variation for phenology and growth traits in populations of red spruce (Picea rubens), from the range core to the highly fragmented trailing edge. We measured more than 5000 offspring sampled from three genetically distinct regions (core, margin and edge) grown in three common gardens replicated along a latitudinal gradient. Genetic variation in phenology and growth showed low to moderate heritability and differentiation among regions, suggesting some potential to respond to selection. Phenology traits were highly plastic, but this plasticity was generally neutral or maladaptive in the effect on growth, revealing a potential liability under warmer climates. These results suggest future climate adaptation will depend on the regional availability of genetic variation in red spruce and provide a resource for the design and management of assisted gene flow. This article is part of the theme issue 'Species' ranges in the face of changing environments (Part II)'.