Exploration of Plastid Phylogenomic Conflict Yields New Insights into the Deep Relationships of Leguminosae

Abstract

Phylogenomic analyses have helped resolve many recalcitrant relationships in the angiosperm tree of life, yet phylogenetic resolution of the backbone of the Leguminosae, one of the largest and most economically and ecologically important families, remains poor due to generally limited molecular data and incomplete taxon sampling of previous studies. Here, we resolve many of the Leguminosae’s thorniest nodes through comprehensive analysis of plastome-scale data using multiple modified coding and noncoding data sets of 187 species representing almost all major clades of the family. Additionally, we thoroughly characterize conflicting phylogenomic signal across the plastome in light of the family’s complex history of plastome evolution. Most analyses produced largely congruent topologies with strong statistical support and provided strong support for resolution of some long-controversial deep relationships among the early diverging lineages of the subfamilies Caesalpinioideae and Papilionoideae. The robust phylogenetic backbone reconstructed in this study establishes a framework for future studies on legume classification, evolution, and diversification. However, conflicting phylogenetic signal was detected and quantified at several key nodes that prevent the confident resolution of these nodes using plastome data alone. [Leguminosae; maximum likelihood; phylogenetic conflict; plastome; recalcitrant relationships; stochasticity; systematic error.]

Analysis of paralogs in target enrichment data pinpoints multiple ancient polyploidy events inAlchemillas.l. (Rosaceae)

“…We estimated an ML tree of the plastome alignment with RAxML using a partition by coding (CDS) and noncoding regions (introns and intergenic spacers) scheme, with a GTRGAMMA model for each partition and clade support assessed with 100 rapid BS replicates and QS using 1,000 replicates, to detect potential plastome conflict in the backbone of Alchemilla s.l. as recently reported in other groups (e.g., Gonçalves et al 2019;Walker et al 2019;Morales-Briones et al 2020;Zhang et al 2020).…”

New Insights Into the Plastome Evolution of the Millettioid/Phaseoloid Clade (Papilionoideae, Leguminosae)

“…For this study, we used a total of plastomes of 43 species from the MP clade including one plastome from NCBI, seven plastomes from Zhang et al (2020)'s phylogenetic study of the whole family, and newly sequenced plastomes of 35 species from 35 genera ( Supplementary Table S1). These species were selected based on the availability of tissues for sampling and their representation of previously recognized tribes in the clade (LPWG, 2013).…”

Comparative Genomics and Phylogenetic Analyses of Christia vespertilionis and Urariopsis brevissima in the Tribe Desmodieae (Fabaceae: Papilionoideae) Based on Complete Chloroplast Genomes

“…Phylogenetic analyses based on relatively few genetic markers [ 5 , 9 ] have helped to elucidate phylogenetic relationships within the Desmodieae, but some intergeneric and interspecific relationships were poorly resolved due to insufficient polymorphic sites. Chloroplast genomes with sufficient informative sites can clarify difficult phylogenetic relationships and have been successfully used to resolve phylogenetic relationships at almost any taxonomic level [ 20 , 30 , 31 ]. In our study, phylogenetic trees inferred from different methods based on the complete cp genomes, LSC, SSC, IR, and PCGs showed an identical topology, with high resolution at each node, which indicates that these datasets taken collectively are useful for reconstructing phylogenetic relationships among the Desmodieae.…”

“…With the development of next-generation sequencing (NGS), complete plastome sequencing has increased dramatically. In recent years, phylogenomic studies of cp genomes have provided new insights into subfamilial relationships and species diversification within Fabaceae [ 18 , 19 , 20 ]. In Desmodieae, cp genomes of 10 species representing seven genera have been published [ 20 , 21 ], but the cp genomes of Christia and Urariopsis species are still unknown.…”