Multiple paternally inherited chloroplast capture events associated with
Taxus speciation in the Hengduan Mountains
- Han-Tao Qin,
- Michael Moeller,
- Richard Milne,
- Ya-Huang Luo,
- Guang-Fu Zhu,
- De-Zhu Li,
- Jie Liu,
- Lianming Gao
Richard Milne
The University of Edinburgh School of Biological Sciences
Author ProfileYa-Huang Luo
Kunming Institute of Botany Chinese Academy of Sciences
Author ProfileGuang-Fu Zhu
Kunming Institute of Botany Chinese Academy of Sciences
Author ProfileDe-Zhu Li
Kunming Institute of Botany Chinese Academy of Sciences
Author ProfileJie Liu
Kunming Institute of Botany Chinese Academy of Sciences
Author ProfileLianming Gao
Kunming Institute of Botany Chinese Academy of Sciences
Author ProfileAbstract
Mountainous regions can promote complex speciation scenarios, including
hybridization leading to chloroplast capture, revealed by incongruent
phylogenetic trees. Four allopatric Taxus lineages from the Hengduan
Mountains, southwestern China, exhibit cytonuclear phylogenetic
discordance. We use multi-omic data at the population level to
investigate their historical speciation processes. Transcriptome data
consistently showed that T. florinii and the Emei type, which are the
focus of cytonuclear discordance, originated in the Late Miocene.
Population genomic analysis based on ddRAD-seq data revealed limited
contemporary inter-specific gene flow. However, neither taxon exhibited
the mosaic nuclear genomes that usually characterized hybrids. Taxus
florinii appears to have originated when a lineage of T. wallichiana
captured the T. chinensis plastid type, whereas plastid introgression in
the opposite direction generated the Emei Type. All four species have
distinct ecological niches, and introgression might have contributed to,
or even initiated, their ecological divergence. We propose that these
speciation events represent very rare examples of chloroplast capture
events despite the paternal cpDNA inheritance of Gymnosperms. These
events might have been triggered by orogenic activities of the Hengduan
Mountains and the intensification of the Asian monsoon in the late
Miocene, and may represent a scenario more common in these mountains
than presently known.