Abstract
The genus Caragana (Fabaceae), comprising predominantly xerophytic shrubs, is ecologically important in arid ecosystems across Asia and Eastern Europe. Hybridization is increasingly recognized as a critical evolutionary mechanism, yet its role in arid adaptation and lineage diversification remains underexplored. Here, we test the hypothesis that ancient hybridization-facilitated ecological expansion and diversification in Caragana. We generated a chromosome-level genome assembly for Caragana arborescens and conducted genome-wide resequencing of 98 individuals across 73 species, representing the full taxonomic breadth of the genus. Phylogenomic reconstructions and reticulation analyses (QuIBL, HyDe, PhyloNet, and TreeMix) uncovered pervasive ancient hybridization, particularly between sections Caragana and Calophaca, which gave rise to five descendant lineages. These hybridization events coincided with late Oligocene aridification and were temporally associated with sharp increases in diversification rates. Introgressed genomic regions were significantly enriched for genes involved in drought tolerance, including those regulating root development, osmoregulation, and hormone signaling. Key gene families, such as late embryogenesis abundant (LEA), sulfate transporters (SULTR), NAM-ATAF-CUC (NAC), and nitrate transporter 1 / peptide transporter family (NPF), exhibited duplications and evolutionary rate shifts in hybrid lineages. Furthermore, Aridity Index data confirmed that hybrid lineages occupy more arid habitats than either parent, highlighting a link between introgression and ecological breadth. Our findings demonstrate that ancient hybridization served as a catalyst for adaptive innovation and diversification in Caragana, offering a genomic mechanism for rapid radiation in response to climatic aridification. This study underscores the evolutionary significance of hybridization in enabling plant lineages to colonize and thrive in extreme environments.
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Claims 8
Claim · model-written summary
Pervasive ancient hybridization occurred in Caragana, particularly between sections Caragana and Calophaca.
CaraganaOrganisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Phylogenomic reconstructions and reticulation analyses (QuIBL, HyDe, PhyloNet, and TreeMix) uncovered pervasive ancient hybridization, particularly between sections Caragana and Calophaca, which gave rise to five descendant lineages”
Claim · model-written summary
The hybridization events coincided with late Oligocene aridification.
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Phylogenomic reconstructions and reticulation analyses (QuIBL, HyDe, PhyloNet, and TreeMix) uncovered pervasive ancient hybridization, particularly between sections Caragana and Calophaca, which gave rise to five descendant lineages”
e1“These hybridization events coincided with late Oligocene aridification and were temporally associated with sharp increases in diversification rates”
Claim · model-written summary
The hybridization events were temporally associated with sharp increases in diversification rates.
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Phylogenomic reconstructions and reticulation analyses (QuIBL, HyDe, PhyloNet, and TreeMix) uncovered pervasive ancient hybridization, particularly between sections Caragana and Calophaca, which gave rise to five descendant lineages”
e1“These hybridization events coincided with late Oligocene aridification and were temporally associated with sharp increases in diversification rates”
Claim · model-written summary
Introgressed genomic regions were significantly enriched for genes involved in drought tolerance.
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Phylogenomic reconstructions and reticulation analyses (QuIBL, HyDe, PhyloNet, and TreeMix) uncovered pervasive ancient hybridization, particularly between sections Caragana and Calophaca, which gave rise to five descendant lineages”
e2“Introgressed genomic regions were significantly enriched for genes involved in drought tolerance, including those regulating root development, osmoregulation, and hormone signaling”
Claim · model-written summary
The LEA, SULTR and NAC gene families showed duplications and evolutionary rate shifts in hybrid lineages.
- Gene
- late embryogenesis abundant (LEA), sulfate transporters (SULTR), NAM-ATAF-CUC (NAC)e3
- Outcome
- duplications and evolutionary rate shiftse3
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Phylogenomic reconstructions and reticulation analyses (QuIBL, HyDe, PhyloNet, and TreeMix) uncovered pervasive ancient hybridization, particularly between sections Caragana and Calophaca, which gave rise to five descendant lineages”
e3“Key gene families, such as late embryogenesis abundant (LEA), sulfate transporters (SULTR), NAM-ATAF-CUC (NAC), and nitrate transporter 1 / peptide transporter family (NPF), exhibited duplications and evolutionary rate shifts in hybrid lineages”
Claim · model-written summary
The NPF gene family showed duplications and evolutionary rate shifts in hybrid lineages.
- Gene
- nitrate transporter 1 / peptide transporter family (NPF)e3
- Outcome
- duplications and evolutionary rate shiftse3
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Phylogenomic reconstructions and reticulation analyses (QuIBL, HyDe, PhyloNet, and TreeMix) uncovered pervasive ancient hybridization, particularly between sections Caragana and Calophaca, which gave rise to five descendant lineages”
e3“Key gene families, such as late embryogenesis abundant (LEA), sulfate transporters (SULTR), NAM-ATAF-CUC (NAC), and nitrate transporter 1 / peptide transporter family (NPF), exhibited duplications and evolutionary rate shifts in hybrid lineages”
Claim · model-written summary
Hybrid lineages occupy more arid habitats than either parent.
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Phylogenomic reconstructions and reticulation analyses (QuIBL, HyDe, PhyloNet, and TreeMix) uncovered pervasive ancient hybridization, particularly between sections Caragana and Calophaca, which gave rise to five descendant lineages”
e4“Furthermore, Aridity Index data confirmed that hybrid lineages occupy more arid habitats than either parent”
Claim · model-written summary
A chromosome-level genome assembly was generated for Caragana arborescens.
- Taxon
- Caragana arborescens
Caragana arborescense5 - Outcome
- chromosome-level genome assemblye5
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e5“We generated a chromosome-level genome assembly for Caragana arborescens”