Genomic divergence and introgression among three Populus species

Zhang, Han; Zhang, Xu; Wu, Guangxin; Dong, Congcong; Liu, Jianquan; Li, Minjie

doi:10.1016/j.ympev.2022.107686

Cited by 10 publications

(5 citation statements)

References 92 publications

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“…The population demographic history analyses showed the effective population size sharply declined about 1 Mya (Fig. 4 ), which is consistent with analyses of other temperate forests trees such as Asian butternut (Juglans section Cardiocaryon) [ 33 ] and Populus species [ 41 ]. During the Quaternary Period, global climatic changes influenced the demography and distribution of most plant species.…”

Section: Discussionsupporting

confidence: 83%

Genomic divergence and demographic history of Quercus aliena populations

Han,

Tong,

Zhang

et al. 2024

BMC Plant Biol

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Background Quercus aliena is a major montane tree species of subtropical and temperate forests in China, with important ecological and economic value. In order to reveal the species’ population dynamics, genetic diversity, genetic structure, and association with mountain habitats during the evolutionary process, we re-sequenced the genomes of 72 Q. aliena individuals. Results The whole chloroplast and nuclear genomes were used for this study. Phylogenetic analysis using the chloroplast genome dataset supported four clades of Q. aliena, while the nuclear dataset supported three major clades. Sex-biased dispersal had a critical role in causing discordance between the chloroplast and nuclear genomes. Population structure analysis showed two groups in Q. aliena. The effective population size sharply declined 1 Mya, coinciding with the Poyang Glaciation in Eastern China. Using genotype–climate association analyses, we found a positive correlation between allele frequency variation in SNPs and temperature, suggesting the species has the capacity to adapt to changing temperatures. Conclusion Overall, this study illustrates the genetic divergence, genomic variation, and evolutionary processes behind the demographic history of Q. aliena.

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Section: Discussionsupporting

confidence: 83%

Genomic divergence and demographic history of Quercus aliena populations

Han,

Tong,

Zhang

et al. 2024

BMC Plant Biol

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“…In detail, 7X-SLR of S. dunnii , 15X-SLR of S. arbutifolia , and 15W-SLR of S. purpurea accumulated more repeat sequences compared to their homologous Y- or Z-SLR, and inversions were identified on the X-Y and Z-W pairs (Wang et al, unpublished). In Salicaceae, Salix ’s sister genus Populus has relatively small SLRs in species with known SDSs (0.08–2 Mb, Wang et al, 2023 ), which probably facilitates hybridizations between species with ZW and XY systems, e.g., P. alba ZW × P. tremula XY = P. × canescens , which is fully fertile ( Meikle, 1984 ; Zhang et al, 2023 ). In Salix , hybridization between different clades ( Salix and Vetrix ) is less common ( Mosseler, 1990 ), which may be due to the long SLRs and the heteromorphic chromosomes (see above).…”

Section: Discussionmentioning

confidence: 99%

Sex chromosome turnover plays an important role in the maintenance of barriers to post-speciation introgression in willows

Xue,

Applequist,

Hörandl

et al. 2024

Evolution Letters

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Almost all species in the genus Salix (willow) are dioecious and willows have variable sex-determining systems, the role of this variation in maintaining species barriers is relatively untested. We first analyzed the sex determination systems (SDS) of two species, Salix cardiophylla and Salix interior, whose positions in the Salix phylogeny make them important for understanding a sex chromosome turnover that has been detected in their relatives, and that changed the system from male (XX/XY) to female (ZW/ZZ) heterogamety. We show that both species have male heterogamety, with sex-linked regions (SLRs) on chromosome 15 (termed a 15XY system). The SLRs occupy 21.3% and 22.8% of the entire reference chromosome, respectively. By constructing phylogenetic trees, we determined the phylogenetic positions of all the species with known SDSs. Reconstruction of ancestral SDS character states revealed that the 15XY system is likely the ancestral state in willows. Turnovers of 15XY to 15ZW and 15XY to 7XY likely contributed to early speciation in Salix and gave rise to major groups of the Vetrix and Salix clades. Finally, we tested introgression among species in the phylogenetic trees based on both autosomes and SLRs separately. Frequent introgression was observed among species with 15XY, 15ZW, and 7XY on autosomes, in contrast to the SLR datasets, which showed less introgression, and in particular no gene flow between 15ZW and 7XY species. We argue that, although SDS turnovers in willow speciation may not create complete reproductive barriers, the evolution of SLRs plays important roles in preventing introgression and maintaining species boundaries.

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“…The heteromorphic sex chromosomes play important roles in hybrid sterility/inviability (Drosophila, Ferree & Barbash, 2009) and in reducing introgression of sex chromosome compared with the autosomes in Heliconius butterflies (Martin et al, 2013) and Ficedula flycatchers (Ellegren et al, 2012), while the homomorphic fish species didn’t show X-autosome introgression differences (Schumer et al, 2014). In Salicaceae, the sister genus Populus with the small size of the SDS in species with known SDSs (0.08 to 2 Mb, Wang et al, 2023a) and a single-locus system with epigenetic control (Müller et al, 2020), which probably facilitate hybridizations between species with ZW and XY systems, e.g., P. alba ZW x P. tremula XY = P. x canescens , an abundant hybrid species which is fully fertile (Meikle, 1984; Zhang et al, 2023). In Salix , the hybridization between different clades ( Salix and Vetrix ) of Salix is less common (Mosseler, 1990), which may contribute from the long sex-linked regions and the micro-heteromorphic chromosomes since sex-linked regions can accumulate more non-random sex specific or the incompatible recessive genes.…”

Section: Discussionmentioning

confidence: 99%

Sex determination system turnovers play important roles in the willows speciation

Xue,

Applequist,

Hörandl

et al. 2023

Preprint

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Almost all species in the genus Salix (willow) are dioecious, but some have male and some female heterogamety, and the chromosomal location of the sex-linked regions (termed SDSs) differs between different species. We first analyzed the SDSs of two species, Salix cardiophylla and S. interior, whose positions in the Salix phylogeny make them important species for understanding a sex chromosome turnover that has been detected in their relatives, and that changed the system from male to female heterogamety. We show that both species have male heterogamety, with XY-linked regions on chromosome 15 (termed a 15XY system). The sex-linked regions occupy 21.3% and 22.8% of the entire reference chromosome, respectively. By constructing phylogenetic trees of species with known SDSs, we determined the phylogenetic positions of all the species. Reconstruction of SDSs revealed that 15XY system is likely the ancestral of willows. Finally, we tested for both current and ancestral gene flow between different species with the same or different sex-determining systems, as the sex chromosomes can play important roles in reproductive isolation between species. We inferred lower gene flow between species with XY on chromosome 7 (7XY) and ZW on chromosome 15 (15ZW) systems, compared with gene flow either between species with XY on chromosome 15 (15XY) and 15ZW systems or between species with 7XY and 15XY systems. We argue that, although sex chromosomes turnovers in willows may not create complete reproductive barriers, gene flow may be reduced between species with different SDSs.

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Genomic divergence and introgression among three Populus species

Cited by 10 publications

References 92 publications

Genomic divergence and demographic history of Quercus aliena populations

Genomic divergence and demographic history of Quercus aliena populations

Sex chromosome turnover plays an important role in the maintenance of barriers to post-speciation introgression in willows

Sex determination system turnovers play important roles in the willows speciation

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