Comparative genomics and transcriptomics analysis reveals evolution patterns of selection in the Salix phylogeny

Zhao, Yanjie; Liu, Xinyi; Guo, Ruifeng; Hu, Kunrong; Cao, Yong; Dai, Fei

doi:10.1186/s12864-019-5627-z

Cited by 11 publications

(8 citation statements)

References 58 publications

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“…Salix and Vetrix. Similar clade formations have also been reported for the Japanese (Azuma et al, 2000), Chinese (Chen et al, 2010;Zhao et al, 2019) and American Salix species in respected subgenera (Lauren-Moreau et al, 2015). However, the species of subgenera Chamaetia and Vetrix ended up in the same group with moderately high posterior probability and bootstrap values (0.87/76) in the ITS phylogenetic tree of the current study.…”

Section: Phylogenetic Implicationssupporting

confidence: 88%

Molecular phylogenetic analysis resolving the taxonomic discrepancies among Salix L. species naturally found in Turkey

Acar¹,

Değirmenci²,

Duman³

et al. 2022

Dendrobiology

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Detailed phylogenetic relationships and molecular dating are still quite rare for the complex and diverse genus Salix L. Here we focus on the taxonomic status and phylogeny of twenty-six Salix taxa naturally found in Turkey using the chloroplast DNA regions (trn T-F, matK, and rbcL) to unravel the relationship among them. The status of Salix species was also checked in the phylogenetic tree constructed with the data from Internal Transcribed Spacer (ITS) region of nuclear gene, including 158 accessions from the GenBank and 126 newly generated sequences of 26 Salix taxa (24 species) naturally found in Turkey. The phylogenetic analysis of the sequence data from both the chloroplast (cpDNA) and nuclear (nrDNA) DNA regions enabled a reliable classification of the genus at the subgeneric level (Salix and Vetrix) with high posterior probability/ bootstrap values as 1/100. The study provides important information on the Salix phylogenetic placements and diverging times of S. pentandroides, S.apoda, S. armenorossica, S. pseudomedemii, S. pedicellata subsp. pedicellata, S. pseudodepressa, S. amplexicaulis, two subspecies of S.triandra, and two endemic species of Turkey (S. purpurea subsp. leucodermis and S. rizeensis) for the first time. Taxonomically, S. amplexicaulis and S. rizeensis previously classified under the subgenus Vetrix were clustered phylogenetically under the subgenus Salix. Subgenera Salix species appears to be diverged from the subg. Vetrix in Eocene (ca. 45.1 Mya) while the estimated divergence times of subg. Salix and subg. Vetrix dated back to 23.1 and 21.65 Mya, respectively. However, divergence times among species within Salix and Vetrix subgenera of Turkey seem to be around the Pliocene period. Molecular phylogenetic relationship between Salix species native to Turkey and Salix species from the world were mainly associated with taxonomic hierarchy, rather than geographic proximity.

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Section: Phylogenetic Implicationssupporting

confidence: 88%

Molecular phylogenetic analysis resolving the taxonomic discrepancies among Salix L. species naturally found in Turkey

Acar¹,

Değirmenci²,

Duman³

et al. 2022

Dendrobiology

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“…Molecular studies to date for the Chamaetia‐Vetrix clade of willows have either failed to resolve relationships within the Chamaetia ‐ Vetrix clade (Chen et al, 2010; Barkalov & Kozyrenko, 2014; Percy et al, 2014; Lauron‐Moreau et al, 2015; Wu et al, 2015), or included only a few species of this clade (Zhang et al, 2018b; Zhao et al, 2019). A well‐resolved phylogeny of European species did not include, or included only one, Salix species from the HDM and adjacent areas (Wagner et al, 2018, 2019).…”

Section: Discussionmentioning

confidence: 99%

Restriction‐site associated DNA sequencing data reveal a radiation of willow species (SalixL., Salicaceae) in the Hengduan Mountains and adjacent areas

Wagner

Hörandl

2020

J of Sytematics Evolution

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The Hengduan Mountains (HDM) in China are an important hotspot of plant diversity and endemism, and are considered to be a secondary diversification center for the woody plant genus Salix L. (Salicaceae). Here we aimed to reconstruct the spatiotemporal evolution of the Salix Chamaetia‐Vetrix clade in the HDM and to test for the occurrence of a local radiation. We inferred phylogenetic relationships based on more than 34 000 restriction‐site associated DNA loci from 27 species. Phylogenetic analyses recovered a well‐resolved tree topology with two major clades, the Eurasian clade and the HDM clade, with a divergence time of ca. 23.9 Ma. Species in the HDM clade originated in the northern part of the range and adjacent areas, and then dispersed into the southern HDM, westwards to the Himalayas and eastwards to the Qinling Mountains. Niche modelling analyses reveal that range contractions occurred in the northern areas during the last glacial maximum, while southward expansions resulted in range overlaps. Reconstructions of character evolution related to plant height, inflorescence, and flower morphology suggest that adaptations to altitudinal distribution contributed to the diversification of the HDM willows. Our data support the occurrence of a radiation in the HDM within the Salix Chamaetia‐Vetrix clade. Dispersal within the mountain system, and to adjacent regions, in addition to survival in glacial refugia shaped the biogeographical history of the clade, while adaptations of the HDM willows along an altitudinal gradient could be important ecological factors explaining the high species diversity of Salix in this area.

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“…So far, molecular studies of the Chamaetia-Vetrix clade either failed to resolve relationships within the Chamaetia - Vetrix clade (Chen et al, 2010; Barkalov & Kozyrenko, 2014; Lauron-Moreau et al, 2015; Wu et al, 2015), or included only a few species of this clade (Zhang et al, 2018a; Zhao et al, 2019). A well-resolved phylogeny of European species did not include Salix species from the HDM and adjacent areas (Wagner et al, 2018).…”

Section: Discussionmentioning

confidence: 99%

RAD sequencing data reveal a radiation of willow species (SalixL., Salicaceae) in the Hengduan Mountains and adjacent areas

Wagner

Hoerandl

2020

Preprint

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AbstractThe Hengduan Mountains (HDM) in South West China are an important hotspot of plant diversity and endemism and considered to be a secondary diversification center for the woody plant genus Salix (Salicaceae). This study aimed to reconstruct the spatio-temporal evolution of the Salix Chamaetia-Vetrix clade in the HDM and to test for the occurrence of a radiation. We inferred phylogenetic relationships based on more than 34,000 RAD loci of 27 species. Phylogenetic analyses recovered a well-resolved tree topology with two major clades, the Eurasian and the HDM clade and a divergence time of c. 23.9 Ma. The HDM clade comprises two subclades. The species of the HDM clade originated in north HDM and adjacent areas and then dispersed into the south HDM, westwards to the Himalayas and eastwards to the Qinling Mountains. Niche modelling analyses revealed that during the last glacial maximum, range contractions were observed in the northern areas, while southward expansions resulted in range overlaps. The reconstruction of putative adaptive character evolution of plant height, inflorescence and flower morphology indicate that adaptations to altitudinal distribution contributed to the diversification of the HDM willows. Our data indicate that a radiation occurred in HDM within the Salix Chamaetia-Vetrix clade. Dispersal within the mountain system and to adjacent regions as well as survival in glacial refugia have shaped the biogeographical history of the clade. Differentiation along altitudinal zonation concomitant to morphological adaptations to colder climates may be important ecological factors for the high species diversity of Salix in this area.

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Comparative genomics and transcriptomics analysis reveals evolution patterns of selection in the Salix phylogeny

Cited by 11 publications

References 58 publications

Molecular phylogenetic analysis resolving the taxonomic discrepancies among Salix L. species naturally found in Turkey

Molecular phylogenetic analysis resolving the taxonomic discrepancies among Salix L. species naturally found in Turkey

Restriction‐site associated DNA sequencing data reveal a radiation of willow species (SalixL., Salicaceae) in the Hengduan Mountains and adjacent areas

RAD sequencing data reveal a radiation of willow species (SalixL., Salicaceae) in the Hengduan Mountains and adjacent areas

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