Folium Anthochlamys multinervis100 56 65 82Suaeda maritima Suaeda crassifolia Suaeda altissima Suaeda physophora Suaeda microphylla Bienertia cycloptera Allenrolfea occidentalis79 54 62 76Halostachys belangeriana Halopeplis amplexicaulis Kalidium cuspidatum Kalidium caspicum Kalidium foliatum Arthrocnemum macrostachyum Sarcocornia utahensis Salicornia europaea Tecticornia disarticulata Sclerostegia moniliformis Tecticornia australasica Pachycornia triandra Salicornia dolichostachya Halosarcia indica Halocharis hispida96 96 51 89 96Salsola vermiculata Salsola implicata Salsola micranthera Salsola orientalis Salsola dshungarica Petrosimonia sibirica91 94 100 93Petrosimonia nigdeensis Petrosimonia glaucescens Petrosimonia squarrosa Salsola affinis Climacoptera brachiata Halimocnemis villosa Halimocnemis karelinii Climacoptera lanata94 100 93Salsola sukaczevii Salsola ferganica Salsola heptapotamica Nanophyton erinaceum Salsola genistoides Salsola arbuscula Salsola kali100Salsola praecox Salsola pellucida Salsola paulsenii Salsola chinghaiensisSalsola zaidamica Salsola collina Salsola komarovii Salsola ruthenicaKochia americana Bassia diffusa Bassia 
dasyphylla83 74 64Maireana brevifolia Sclerolaena obliquicuspis Roycea divaricata Dissocarpus paradoxus97 83Bassia sedoides Camphorosma monspeliaca Kochia densiflora Chenoleoides tomentosaBassia prostrata Panderia pilosa Sympegma regelii Halothamnus bottae Salsola laricifolia54Salsola arbusculiformis Rhaphidophyton regelii94Ofaiston monandrum Salsola rosacea Noaea mucronata Anabasis brevifolia Anabasis truncata Anabasis eriopoda94 84 85 92 94Anabasis aphylla Anabasis salsa Anabasis elatior Salsola foliosa Girgensohnia oppositifloraHalogeton glomeratus100Haloxylon ammodendron 1317923 Haloxylon persicum Iljinia regelii Haloxylon tamariscifolium Horaninovia ulicina Halogeton arachnoideusRubisco Evolution in C4 EudicotsFigure 1. Maximum likelihood phylogram based on rbcL sequences of 179 Amaranthaceae species. Numbers above the Autophagy branches are ML bootstrap support percentages. Filled orange circles of the first, second and third columns after species names indicate presence of C4 photosynthesis, serine at the position 281 and isoleucine at the position 309, respectively. The figure was composed using iTOL program [62]. doi:10.1371/journal.pone.0052974.gacid sites. The tree length value obtained from the model M0 was compared with tree length values obtained from other models to control for consistency among models. We performed two LRTs to compare null models which assume the same selective pressure along all branches of a phylogeny and do not allow positive selection (dN/dS .1) with nested models which do allow it [33]. The first LRT, M1a-M2a, compares the M1a model (Nearly Neutral) which allows 0# dN/dS #1 with the M2a model (Selection model; same as the M1a model plus an extra class under positive selection with dN/dS .1). The second LRT, M8aM8, compares the M8a model which assumes a 12926553 discrete beta distribution for dN/dS, which is constrained between 0 and 1 Epigenetics including a class with dN/dS = 1 with the M8 model which allows the same distribution as M8a but an extra class under positive selection with dN/dS .1. Finally, we performed two branch-site tests of positive selection along prespecified foreground branches [33,34,35]. The first was the A model for basal C4 branches only where positive selection was allowed only on branches leading to C4 clades. The second was the A model for all C4 branches where positiv.Folium Anthochlamys multinervis100 56 65 82Suaeda maritima Suaeda crassifolia Suaeda altissima Suaeda physophora Suaeda microphylla Bienertia cycloptera Allenrolfea occidentalis79 54 62 76Halostachys belangeriana Halopeplis amplexicaulis Kalidium cuspidatum Kalidium caspicum Kalidium foliatum Arthrocnemum macrostachyum Sarcocornia utahensis Salicornia europaea Tecticornia disarticulata Sclerostegia moniliformis Tecticornia australasica Pachycornia triandra Salicornia dolichostachya Halosarcia indica Halocharis hispida96 96 51 89 96Salsola vermiculata Salsola implicata Salsola micranthera Salsola orientalis Salsola dshungarica Petrosimonia sibirica91 94 100 93Petrosimonia nigdeensis Petrosimonia glaucescens Petrosimonia squarrosa Salsola affinis Climacoptera brachiata Halimocnemis villosa Halimocnemis karelinii Climacoptera lanata94 100 93Salsola sukaczevii Salsola ferganica Salsola heptapotamica Nanophyton erinaceum Salsola genistoides Salsola arbuscula Salsola kali100Salsola praecox Salsola pellucida Salsola paulsenii Salsola chinghaiensisSalsola zaidamica Salsola collina Salsola komarovii Salsola ruthenicaKochia americana Bassia diffusa Bassia dasyphylla83 74 64Maireana brevifolia Sclerolaena obliquicuspis Roycea divaricata Dissocarpus paradoxus97 83Bassia sedoides Camphorosma monspeliaca Kochia densiflora Chenoleoides tomentosaBassia prostrata Panderia pilosa Sympegma regelii Halothamnus bottae Salsola laricifolia54Salsola arbusculiformis Rhaphidophyton regelii94Ofaiston monandrum Salsola rosacea Noaea mucronata Anabasis brevifolia Anabasis truncata Anabasis eriopoda94 84 85 92 94Anabasis aphylla Anabasis salsa Anabasis elatior Salsola foliosa Girgensohnia oppositifloraHalogeton glomeratus100Haloxylon ammodendron 1317923 Haloxylon persicum Iljinia regelii Haloxylon tamariscifolium Horaninovia ulicina Halogeton arachnoideusRubisco Evolution in C4 EudicotsFigure 1. Maximum likelihood phylogram based on rbcL sequences of 179 Amaranthaceae species. Numbers above the branches are ML bootstrap support percentages. Filled orange circles of the first, second and third columns after species names indicate presence of C4 photosynthesis, serine at the position 281 and isoleucine at the position 309, respectively. The figure was composed using iTOL program [62]. doi:10.1371/journal.pone.0052974.gacid sites. The tree length value obtained from the model M0 was compared with tree length values obtained from other models to control for consistency among models. We performed two LRTs to compare null models which assume the same selective pressure along all branches of a phylogeny and do not allow positive selection (dN/dS .1) with nested models which do allow it [33]. The first LRT, M1a-M2a, compares the M1a model (Nearly Neutral) which allows 0# dN/dS #1 with the M2a model (Selection model; same as the M1a model plus an extra class under positive selection with dN/dS .1). The second LRT, M8aM8, compares the M8a model which assumes a 12926553 discrete beta distribution for dN/dS, which is constrained between 0 and 1 including a class with dN/dS = 1 with the M8 model which allows the same distribution as M8a but an extra class under positive selection with dN/dS .1. Finally, we performed two branch-site tests of positive selection along prespecified foreground branches [33,34,35]. The first was the A model for basal C4 branches only where positive selection was allowed only on branches leading to C4 clades. The 
second was the A model for all C4 branches where positiv.