Genomic clines across the species boundary between a hybrid pine and its progenitor in the eastern Tibetan Plateau

Hybrid zones in the European Alps impact the phylogeography of alpine vicariant willow species (Salix L.)

Introduction

In the European Alps, Pleistocene climate oscillations resulted in geographical range expansions and restrictions of species. Postglacial recolonizations often result in secondary contact hybridization of vicariant species, thereby creating hybrid zones with patterns of introgression. Here, we compare the genetic structure of two secondary contact hybrid zones between two vicariant willow species pairs occurring in the European Alpine System. Supplemented by morphological and ecological data, we try to understand the factors shaping the hybrid zones and their influence on geographical range filling patterns.

Methods

RAD sequencing and morphometric data were used to characterize biogeographical history, genetic diversity and the hybrid zone of each species pair. Vegetation relevés and species distribution models provided ecological context and support.

Key results

Results suggest that recolonization of the Alps happened from peripheral glacial refugia, resulting in broad secondary contact zones in the Eastern Alps in both species pairs. Both hybrid zones show introgression, but differ in symmetry and intensity of gene flow, in the type of introgressed loci, and in the geographical range. Habitat preferences and species distribution models do not indicate ecological barriers to recolonization.

Conclusions

Hybrid zones do not only affect the genetic structure of species by gene flow and introgression, but also appear to impact the biogeographical patterns of species.

Evolutionary radiation of the Eurasian Pinus species under pervasive gene flow

Evolutionary radiation, a pivotal aspect of macroevolution, offers valuable insights into evolutionary processes. The genus Pinus is the largest genus in conifers withc . $$ c. $$ 90% of the extant species emerged in the Miocene, which signifies a case of rapid diversification. Despite this remarkable history, our understanding of the mechanisms driving radiation within this expansive genus has remained limited. Using exome capture sequencing and a fossil-calibrated phylogeny, we investigated the divergence history, niche diversification, and introgression among 13 closely related Eurasian species spanning climate zones from the tropics to the boreal Arctic. We detected complex introgression among lineages in subsection Pinus at all stages of the phylogeny. Despite this widespread gene exchange, each species maintained its genetic identity and showed clear niche differentiation. Demographic analysis unveiled distinct population histories among these species, which further influenced the nucleotide diversity and efficacy of purifying and positive selection in each species. Our findings suggest that radiation in the Eurasian pines was likely fueled by interspecific recombination and further reinforced by their adaptation to distinct environments. Our study highlights the constraints and opportunities for evolutionary change, and the expectations of future adaptation in response to environmental changes in different lineages.

The chromosome-level genome assembly of an endangered herb Bergenia scopulosa provides insights into local adaptation and genomic vulnerability under climate change

BACKGROUND

Global climate change poses severe threats to biodiversity and ecosystem stability. Rapid climate oscillations potentially lead to species geographic range shifts, population declines, and even extinctions. The rare and endangered species, being critical components of regional biodiversity, hold the key to understanding local adaptation and evolutionary processes shaping species distributions. Therefore, assessing the evolutionary mechanisms of local adaptation and population vulnerability under climate change is crucial for developing conservation strategies of endangered species.

RESULTS

In this study, we assembled a high-quality, chromosome-level genome of the rare and endangered herb Bergenia scopulosa in the Qinling Mountains in East Asia and resequenced 37 individual genomes spanning its entire geographic distributional ranges. By integrating population genetics, landscape genomics, and climate datasets, a substantial number of adaptive single-nucleotide polymorphism loci associated with climate variables were identified. The genotype-environment association analysis showed that some cold-tolerant genes have played pivotal roles in cold environmental adaptation of B. scopulosa. These findings are further corroborated through evolutionary analysis of gene family and quantitative PCR validation. Population genomic analysis revealed 2 distinct genetic lineages in B. scopulosa. The western lineage showed higher genomic vulnerability and more rare cold-tolerance alleles, suggesting its heightened sensitivity to impending climate shifts, and should be given priority conservation in the management practices.

CONCLUSIONS

These findings provide novel insights into local adaptation and genomic vulnerability of B. scopulosa under climate change in the Qinling Mountains in East Asia. Additionally, the study also offers valuable guidance for formulating conservation strategies for the rare and endangered plants.