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Additional file 1.

Additional file 2 : Figure S1. Plastome maps for the 20 Medicago, Trigonella, and Melilotus species. Genes shown outside the circle are transcribed clockwise and those inside are transcribed counter clockwise. Genes belonging to different functional groups are color-coded. The dark gray area in the inner circle indicates GC content and the thick black line shows the extent of different regions. LSC: large single copy; SSC: small single copy; IRA: inverted repeat A; IRB: inverted repeat B. The two areas enclosed by red boxes in (d) indicate small IRs in Medicago lupulina. In (k), red arrows No. 1 and 2 outside the circle point to the breakpoints of the inverted region involving all genes from ycf1 to rpl20. Gene order in the M. truncatula 02 ptDNA between the arrows is in the reverse orientation and its length is ~ 44-kb (44,228 bp). Below the map are shown the alignments of 24-bp incomplete inverted repeats in the inversion endpoints in the M. truncatula 02 and cognate sequences in M. truncatula 01. Figure S2. IRs alignment within the four Melilotus dentata individuals and the repetitive elements of indel regions in Melilotus dentata 02 and Melilotus dentata 03. Yellow bar represents protein coding gene; red bar represents rRNA gene; pink bar represents tRNA gene. Numerals above indicate nucleotide positions within the repeat alignment indicate the length of an indel within the IR. Mismatches are indicated by colored blocks and identical bases are gray. Mean pairwise identity over all pairs in each alignment column is indicated by the histogram: green 100%. IRA: inverted repeat A, IRB: inverted repeat B. Different repetitive elements were marked with different colored boxes. Figure S3. Mauve (Multiple Alignment of Conserved Genomic Sequence with Rearrangements) alignment of the plastomes of the 20 species using plastome of Wisteria floribunda as a reference. Figure S4. Confirmation of tRNA duplication in five species. Plastome sequences were mapped to themselves which contain all copies of the replicated tRNA (lower) and plastome sequences which contain a single copy of the replicated tRNA (upper). The scale at the left reports the depth of sequences, which is indicated graphically by the blue histogram. Figure S5. The degree of genomic rearrangements shows significant positive correlation with (a) dispersed repeats and (b) tandem repeats. Figure S6. The mechanism of tRNA duplication detected in five species. Both (a) and (b) contain a tandem repeat and two forward repeats that duplicate trnV-GAC twice. The three species in (c) contain a tandem repeat that duplicates the trnN-GUU gene. Thick black lines represent double stranded DNA. Pink boxes represent gene sequences, red and blue boxes represent tandem repeats, green boxes represent forward repeats and numbers indicate the length of repeats. Figure S7. Repeats around endpoints of all inversions. Red boxes represent regions of inversion, orange boxes represent protein-coding genes, and pink boxes represent tRNA genes. Black lines above double stranded DNA represent tandem repeats. Black lines below double stranded DNA represent dispersed repeats. The palindromic repeats are indicated by red lines. Figure S8. Repetitive DNA in the acquired introns. Yellow boxes represent exons. The lines between the yellow boxes represent acquired introns. The red content represents repetitive sequences. Figure S9. Comparison of the 20 plastomes using the annotation of Medicago falcata as a reference. The vertical scale indicates the percentage of identity, ranging from 50 to 100%. The horizontal axis indicates the coordinates within the plastomes. Genomic regions are color-coded as conserved non-coding sequences (CNS), exons, and tRNA or rRNA. Figure S10. Significance test for nonsynonymous (dN) (upper) and synonymous (dS) (lower) substitution rates of clpP, accD, and ycf1 compared to rbcL for all the comparisons within both IRLC taxa we have found (left) and our own 20 species (right). ****, P

Understanding the relative roles of geography and ecology in driving speciation, population divergence and population dynamics is a longstanding goal in ecology and evolutionary biology. This is especially true for organisms inhabiting in mountains that usually harbor extremely high species richness and endemism. In this thesis, I combine macro-evolutionary approaches and population genomic analyses at multiple evolutionary timescales to investigate how historically geological and climatic events affected diversification, speciation and demography of Primula section Armerina in the Qinghai-Tibet Plateau (QTP). At macro-evolutionary level, I reconstruct phylogenetic trees of the section and discuss the factors accounting for the incongruence between the chloroplast and nuclear trees that mainly occur among closely related species. I demonstrate that the section originated from the Himalayas and the recent uplift of the QTP has probably triggered its diversification. I also show that niche evolution affects biogeographic patterns of three closely related species in this section. Then, I use population genomic data to examine the interspecific divergence and maintenance of species cohesion between these three closely related species. I successfully obtain a clear relationship among the three species and provide a strong evidence for an origin of the three species in the Himalayas. The following divergences between them coincide with the uplift of the Hengduan Mountains and the Northeast QTP, which highlights the important roles played by past geological events in triggering initial interspecific divergence. After a long period of divergence, the three species came into secondary contact triggered by past climatic changes but with no significant hybridization. I further show that spatial and environmental factors may play an important role in the maintenance of species cohesion. In the final two chapters, I investigate demographic histories of two of the three closely related species that are endemic to the QTP and evaluate the effects of the Quaternary climatic oscillations on their demography. I demonstrate that only the ancestral populations of the two species could survive in different refugia during the largest glaciation that occurred in the QTP. Most of the genetic lineages identified by the population genomic analyses diverged from their ancestral populations only after this glaciation event. The last glacial maximum (LGM) had littler effects on these genetic lineages. Moreover, the response to climatic changes of populations of a species depends on its specific ecological preferences. Finally, all the historical, spatial and environmental factors act as drivers of population differentiation in these alpine plant species. Overall, this work contributes to a significant advance to our understanding of the mechanisms of the interplay between geological and ecological factors in driving speciation and evolution in mountains. -- Comprendre de quelle manière la géographie et l'écologie contribuent au processus de spéciation, à la divergence et la dynamique des populations est un des objectifs majeurs de l'écologie et de la biologie évolutive. Cet intérêt est particulièrement fort pour les régions montagneuses qui présentent une grande diversité d'espèces et un fort taux d'endémisme. Dans cette thèse, j'intègre des approches macro-évolutive avec des analyses de génomique des populations à différentes échelles de temps pour étudier comment les évènements géologiques et climatiques passés ont affecté la diversification, la spéciation et la démographie des espèces de la section Armenia du genre Primula du plateau Tibétain. Au niveau macro-évolutif, j'ai reconstruit l'arbre phylogénétique du groupe et émis des hypothèses pour expliquer l'incongruence observée pour les espèces proches entre les arbres phylogénétiques basés sur des marqueurs nucléaires et chloroplastiques. J'ai démontré que la section Armenia est originaire de l'Himalaya et que la récente orogenèse de cette chaine de montagne a probablement été le facteur déclencheur de sa diversification. J'ai aussi montré que l'évolution de la niche a influencé la biogéographie de trois espèces proches de cette section dont j'ai pu établir avec précision les relations de parenté et leur origine dans l'Himalaya. La divergence entre ces trois espèces coincide avec l'orogenèse des monts Hengduan et le Nord-Est du plateau Tibétain, ce qui démontre l'importance des évènements géologiques passés dans la divergence inter-spécifique. Après une longue période d'isolation les trois espèces, des changements climatiques ont par le passé induit un contact secondaire mais sans que cela entraine une hybridisation significative. J'ai ensuite montré que les facteurs spatiaux et environnementaux pourraient jouer un rôle important dans le maintien de la cohésion des espèces. Dans les deux derniers chapitres, j'étudie l'histoire démographique de deux des trois espèces proches endémiques du plateau Tibétain et j'évalue les effets des oscillations climatiques du Quaternaire sur leur démographie. Je démontre que les populations ancestrales des deux espèces ont pu survivre dans différents refuges au cours de la plus longue glaciation du plateau Tibétain. La plupart des lignées génétiques identifiées par les analyses de génomique des populations ont divergé de ces populations ancestrales suite à cet évènement de glaciation. Le dernier maximum glaciaire n'a eu que peu d'effet sur ces lignées. D'autre part, la réponse des populations d'une espèce aux changements climatiques dépend de ses préférences écologiques spécifiques. Enfin, l'ensemble des facteurs historiques, spatiaux et environnementaux agissent comme des moteurs de la différenciation de ces espèces montagneuses. Dans l'ensemble ce travail contribue de manière significative à la compréhension des méchanismes de l'interaction entre les facteurs géologiques et écologiques dans la formation et l'évolution des espèces au sein des massifs montagneux.