Larix species range dynamics in Siberia since the Last Glacial captured from sedimentary ancient DNA

Biological Processes Underlying Genetic Adaptation of Larches to Cold and Dry Winter Conditions in Eastern Siberia

The boreal forests of central and eastern Siberia, dominated by larches, are challenged by increasingly harsher continental conditions and more frequent droughts. Despite the crucial ecosystem services provided by these Siberian boreal forests, the major stressors driving the selective factors as well as the genetic adaptation mechanisms of larches are still unknown. Here we present a landscape genomics study on 243 individuals of the dominant larch tree species, Larix gmelinii and L. cajanderi. We assessed genotype-environment associations (GEAs) between genetic variation of individual markers based on genotyping-by-sequencing (GBS) data and bioclimatic variables recorded at the sampling locations. We find that the cold and dry winter conditions of eastern Siberia are likely the main selective factor driving the genetic adaptation of larches. Gene ontology (GO) enrichment analysis identified metabolic, transmembrane transport, and homeostatic, as well as developmental processes among the main biological processes underlying genetic adaptation driven by cold and dry winter conditions.

Phylogenomic analyses shed new light on the spatiotemporal evolution of global larches: Implications for the dynamics of boreal forests

As the Earth warms, understanding the long-term dynamics of forest ecosystems is essential for guiding forest management and biodiversity conservation. Insights from past dynamics may provide valuable lessons for managing today's forests. Here, we investigated the spatiotemporal evolution of global larches to gain further insights into how boreal forests change over time. We first reconstructed a highly resolved and robust phylogeny of Larix covering all widely recognized species, using both transcriptome-based 1,301 orthologous genes (OGs) and plastid genomes. In sharp contrast to previous studies, an unexpected deep split between the circumboreal and Qinghai-Tibetan Plateau (QTP) larches was revealed in our study. Within each lineage, two geographically distinct clades were further resolved. Biogeographical analyses suggest that Larix might have an origin of Eocene in high-latitude uplands, and during the Miocene, all extant species have appeared. Cenozoic climate- and orogeny-triggered vicariance likely played a major role in the divergence of global larches. Our results also demonstrate that the proto-boreal forest biome may have a relatively old origin back to the early Miocene, and significant winnowing and species alteration would have occurred as the climate shifted to much colder and drier conditions during the Neogene. Ecological niche analyses show various responses of the circumboreal and QTP larches under different climate scenarios, but both lineages are negatively impacted by warming climates. These findings have important conservation implications given the sensitivity of boreal forests in the face of global warming. Our work further emphasizes the importance of a solid phylogenetic framework for evolutionary and biogeographical inferences.

Special Issue on "Plant Biology and Biotechnology: Focus on Genomics and Bioinformatics 2.0"

The analysis of molecular mechanisms underlying plant adaptation to environmental changes and stress response is crucial for plant biotechnology [...].

Phylogeography of Toona ciliata (Meliaceae) Complex in China Inferred from Cytonuclear Markers

Toona ciliata is an important timber species but is recognized as an endangered species at level II in China. Its genetic conservation is of increasing concern. Provenance trials and other breeding programs were conducted to develop seed transfer rules and multiplications. Here, we investigated twenty-nine populations sampled across the natural distribution of the T. ciliata complex using mtDNA and nrDNA ITS (ribosomal internal transcribed spacer) markers. Haplotype diversity was h = 0.190 ± 0.202 and nucleotide diversity was π = 0.000383 ± 0.000536 for mtDNA marker. Nucleotide diversity for ITS sequences was 0.00837 ± 0.000783. Haplotypes exhibited phylogeographic structure in spatial distribution. The extent of genetic differentiation was significant (Fst = 0.6994 ± 0.0079 for ITS and 0.8870 ± 0.0077 for mtDNA marker). Isolation by distance (IBD) and by elevation (IBE) occurred among populations. Phylogenetic relationships from mtDNA marker indicated three genetically distinct regions, each without IBD effects. Compared with pollen flow, seed flow was strongly impeded in the western region, but extensive in the central region, and less impeded in the eastern region. Most populations did not exhibit expansion, with only a few populations showing expansion after bottleneck effects. We discussed a strategy of region-based genetic conservation and proposed to conserve multiple populations in the western and eastern regions and a few populations in the central region.