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A plastid phylogenomic framework for the palm family (Arecaceae) - PubMed

  • ️Sun Jan 01 2023

A plastid phylogenomic framework for the palm family (Arecaceae)

Gang Yao et al. BMC Biol. 2023.

Abstract

Background: Over the past decade, phylogenomics has greatly advanced our knowledge of angiosperm evolution. However, phylogenomic studies of large angiosperm families with complete species or genus-level sampling are still lacking. The palms, Arecaceae, are a large family with ca. 181 genera and 2600 species and are important components of tropical rainforests bearing great cultural and economic significance. Taxonomy and phylogeny of the family have been extensively investigated by a series of molecular phylogenetic studies in the last two decades. Nevertheless, some phylogenetic relationships within the family are not yet well-resolved, especially at the tribal and generic levels, with consequent impacts for downstream research.

Results: Plastomes of 182 palm species representing 111 genera were newly sequenced. Combining these with previously published plastid DNA data, we were able to sample 98% of palm genera and conduct a plastid phylogenomic investigation of the family. Maximum likelihood analyses yielded a robustly supported phylogenetic hypothesis. Phylogenetic relationships among all five palm subfamilies and 28 tribes were well-resolved, and most inter-generic phylogenetic relationships were also resolved with strong support.

Conclusions: The inclusion of nearly complete generic-level sampling coupled with nearly complete plastid genomes strengthened our understanding of plastid-based relationships of the palms. This comprehensive plastid genome dataset complements a growing body of nuclear genomic data. Together, these datasets form a novel phylogenomic baseline for the palms and an increasingly robust framework for future comparative biological studies of this exceptionally important plant family.

Keywords: Arecaceae; Nuclear-plastid discordance; Palmae; Phylogenomics; Plastome.

© 2023. The Author(s).

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1

Maximum likelihood (ML) phylogenetic tree of Arecaceae inferred from the incomplete-105 regions matrix. Bootstrap support (BS) values inferior to 100% are shown, with dashes denoting a support inferior to 50%. Numbers in brackets indicate the BS values obtained from the analyses of the complete-coding/complete-105 matrices. Taxon names are followed by their GenBank accession numbers (sequences downloaded from NCBI) or voucher specimen information (plastomes newly obtained). For the 49 genera with a large proportion of missing data and for which individual plastid regions had to be retrieved from NCBI (see the “Methods” section), only the genus name is provided, but detailed sequence accession numbers can be found in Additional file 2: Table S2

Fig. 1
Fig. 1

Maximum likelihood (ML) phylogenetic tree of Arecaceae inferred from the incomplete-105 regions matrix. Bootstrap support (BS) values inferior to 100% are shown, with dashes denoting a support inferior to 50%. Numbers in brackets indicate the BS values obtained from the analyses of the complete-coding/complete-105 matrices. Taxon names are followed by their GenBank accession numbers (sequences downloaded from NCBI) or voucher specimen information (plastomes newly obtained). For the 49 genera with a large proportion of missing data and for which individual plastid regions had to be retrieved from NCBI (see the “Methods” section), only the genus name is provided, but detailed sequence accession numbers can be found in Additional file 2: Table S2

Fig. 2
Fig. 2

Comparison between the palm topologies derived from nuclear and plastome data. a‒c Tribal relationships in Arecoideae, the arrowhead indicates the crown of the core arecoids; d, e tribal and subtribal relationships in Calamoideae; f, g tribal relationships in Ceroxyloideae; h, i subtribal relationships in Trachycarpeae (Coryphoideae); NT nuclear topology, PT plastome topology; NT were obtained a from the maximum likelihood analysis of Comer et al. [39]; b, h from the multispecies coalescent analysis of KTLE [60] (KTLE tree); d from the multispecies coalescent analysis of Kuhnhäuser et al. [49]; and f from the maximum parsimony analysis of Baker et al. [66]; PT of c, e, g, and i were all obtained from the present study

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