Comparative Phvlogeographic Study Of Smilax Rotundi-Folia And S.walteri In North America

Smilax rotundifolia and Smilax walteri are an important lineage of the North American Smilax.Although they are sister species with similar morphological characters,they occupy different habitats.S.rotundifolia has a wide distribution and is an important understory component of temperate forests in eastern North America;while S.walteri is mostly found in wetlands of southeastern USA.Most of the previous studies about S.rotundifolia and S.walteri focused on physiological traits and/or their interactions with fungi.Yet studies related to phylogeny and phylogeography of these two species have not been reported.In this study,we used microsatellite markers and complete chloroplast genome data,combined with ecological niche modeling(ENM)to explore the genetic diversity,genetic structure,population dynamic history model and distribution change of S.rotundifolia and S.walteri.The results are as follows:1)Population genetic study based on microsatellite markers:6,153 simple sequences repeats were obtained for microsatellite primers development using transcriptome data of the S.rotundifolia.Then,130 pairs of microsatellite primers were synthesized.After screening,24 pairs were finally determined for subsequent analysis.Genetic diversity,genetic structure,phylogenetic relationship,and phylogeographic pattern were analyzed for 466 individuals from 60 populations of S.rotundifolia and S.walteri based on these microsatellite markers.The expected heterozygosity of S.rotundifolia ranged 0.207 to 0.690 with an average of 0.471,the observed heterozygosity ranged from 0.195 to 0.925 with an average of 0.550,and polymorphism information content(PIC)values ranged from 0.366 to 0.835,the average was 0.550;For S.walteri,the expected heterozygosity and observed heterozygosity was ranged 0?0.660 and 0?1,respectively(the average was 0.332 and 0.422).And the range of PIC was 0?0.829,the average was 0.394.PCoA analysis based on Nei's distance showed that S.rotundifolia and S.walteri belong to two main clusters;STRUCTURE cluster analyses based on Bayesian algorithm found that S.rotundifolia had two gene pools in east and west of its own with an explicit separate with S.walteri;Population from two gene pools of the S.rotundifolia in the PCoA indicated two conspicuous clusters of indicating two lineages,while some mixtures also detected.The gene flow between the two lineages of S.rotundifolia was strong and the gene flow between S.walteri and the two lineages of S.rotundifolia was weakly detected.DIY-ABC analyses based on the approximate Bayesian theory speculated that S.walteri may differentiated from the common ancestor population at a certain time,then expanded alone;and the two lineages of S.rotundifolia divided after,then expand independently.Indicated that S.rotundifolia and S.walteri are two genetically distinct species.2)Phylogenetics and divergence time estimation based on complete chloroplast genomes:Two individuals from different lineages of S.rotundifolia and two S.walteri individuals from different regions were selected for complete chloroplast genome sequencing.After assemble,four chloroplast genomes were compared in length,gene composition,and gene size.And we found slight differences among them.Polymorphic site analysis of different fragments,complete sequence simple repeats and repeated structural analysis,and codon usage bias analysis revealed that a total of 31 mutations were found in the alignment of the four chloroplast genomes,including 12 base substitutions and 19 indels,with PI values ranging from 0.00012 to 0.0067.The forward,reverse,complementary,and palindromes repeats appeared to be similar in the four chloroplast genomes.A total of 117 repeating structures were found,of which 54 were present in all four individuals.The parameters of codon usage bias and the number of synonymous codons in the four chloroplast genomes were similar.The results of the divergence time estimation using six chloroplast fragments showed that S.rotundifolia and S.walteri probably began to differentiate at 5.36 Ma,and the intraspecific differentiation within S.rotundifolia was about 1.59 Ma.3)Ecological niche modeling:587 distribution sites of S.rotundifolia and 98 distribution sites of S.walteri was extracted from the major plant specimens or museum websites and used for ecological niche modeling.The past(LGM),current(Present,1950-2000)and the future(Future,2050)climate layer,and 19 possible related climatic factors were downloaded for the simulation analysis of the potential distribution areas of S.rotundifolia and S.walteri in different periods.The results show that the potential distribution areas of S.rotundifolia and S.walteri were basically consistent with the current actual distribution area.During the LGM period,the distribution areas of S.rotundifolia and S.walteri were significantly smaller than the current distribution area.Compared with the current period,the distribution area of S.rotundifolia was compressed on the both sides of Appalachian Mountains,with a most appropriate area in the east and west;and the distribution area of S.walteri in the LGM is compressed to the southern part of the Gulf Coast,the closer to the coast,the more suitable habitat.Comparing with the current distribution area,the future distribution of S.rotundifolia showed no significant change,while the future distribution of S.walteri showed comparable expansion.In the estimation of the accuracy of the distribution models of S.rotundifolia and S.walteri,the AUG values were all greater than 0.9,indicating a well model fit.