Plastid Phylogenomics And Biogeographic Study Of The Eastern Africa Endemic Genus Dendrosenecio(Asteraceae)

The giant senecios(Dendrosenecio,Asteraceae),comprising of 11 species and five subspecies,are among the most conspicuous alpine plant groups in the world.The group is endemic to the tropical mountains of Eastern Africa(afro-mountains),where they are intriguingly distributed,with each except 3 being confined to a single mountain.Despite attracting significant attention from researchers,the radiation patterns,and infrageneric phylogenetic relationships have been considerably controversial,and based on the long taxonomic history,Dendrosenecio stands out as a problematic genus.This has further been augmented by inadequacy of informative molecular resources for use to divulge well resolved relationships within the genus.Besides,the Eastern Africa region is a biodiversity hotspot,which is characterized by isolated mountains and a huge number of endemic species.In situ radiation of the afro-mountain flora is less understood as there are limited studies based on explicit models and fossil-calibrated molecular clocks.Therefore,the distinctive distribution of the giant senecios provide an ideal model to comprehensively investigate the divergence history and the colonization patterns of the Eastern African mountains.In this study,whole chloroplast genome(plastome)sequences of 46 individuals,including all taxa(11 species and five subspecies)of Dendrosenecio,were sequenced,assembled and characterized.Plastome genome comparative analyses were conducted within the genus,and against other available plastome genomes of the Senecioneae tribe.The entire plastome sequences,without one IR region,were employed to reconstruct the phylogeny of the giant senecios using the Maximum Likelihood and Bayesian Inference methods.Additionally,divergence times were estimated using fossil calibrations,and the ancestral areas were reconstructed in order to infer their biogeographic history.The plastomes were circular DNA molecules of sizes ranging from 150,454 base pairs(bp)to 150,606 bp.A quadripartite structure was exhibited with a Large Single Copy(83,401-83,465),Small Single Copy(17,605-17,775 bp),and a pair of Inverted Repeat regions(24,686-24,691 bp).Whole genome characterization revealed a high degree of similarity particularly in the organization,gene content,repetitive sequence composition and codon usage.The plastomes encoded an identical number(113)of unique genes out of which 79 were protein-coding genes,30 transfer ribonucleic acid and four ribosomal ribonucleic acid genes.Among the 79 shared protein coding genes,only 33 exhibited polymorphism,of which a majority was due to single nucleotide mutations.Insertions/deletions were detected in genes psbT,rpoC2,and ycf1.Gene evolutionary analysis showed that most genes are under neutral selection.In addition,76 unique microsatellites,and 65 long dispersed repeats were identified within the genus.The phylogenomic analyses yielded two robustly supported clades.One clade included species sampled from Tanzania,while the other clade included species from Kenya and Uganda.A strong correlation between phylogenetic relationships and geographic proximity was evidenced.Non-monophyly was detected in certain species which is due to potential ancient hybridization.Divergence time estimations indicated that the giant senecios likely originated at approximately 2.3 million years ago(highest posterior density 95%;0.77,4.40).However,rapid radiations happened recently.Ancestral area reconstructions shows ambiguous ancestral area at the root node,although Mt.Kilimanjaro is highly favored.Mt.Kenya and Mt.Muhavura are suggested as the probable ancestral ranges for sub-clades I and II,respectively.The complete plastome for each of the giant senecios was reported here for the first time,allowing for a comprehensive genus-wide comparative analysis.Little sequence variation was detected among the plastomes,although potential cpDNA markers,mainly the repetitive sequences were identified for population genetic investigations,and specific,and intra-specific identification.A few of the markers were region-specific indicating potential for use in future biogeographical and evolutionary studies.This study provided improved phylogenetic resolution,emphasizing the significance of investigating more loci in resolving phylogenetic relationships,and also highlighting the potential of whole plastome sequences as super DNA barcodes.Pliopleistocene climate oscillations and geologic events seem to have initiated the diversification of Dendrosenecio.However,multiple long-distance dispersals,and vicariance episodes,followed by allopatric speciation(geographic and/or altitudinal)appeared to be the main drivers of the recent radiation of giant senecios.The results presented here shed light on the evolution of this famous afro-alpine group.It also lays the baseline for future research on the factors that shaped the distribution of the afro-mountain flora.