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Angiosperms evolved from gymnosperms and, until recently, some scientists argued that the two angiosperm branches, the monocotyledons and dicotyledons, had arisen independently. If this were true, the angiosperms would be polyphyletic. The evidence, however, supports a single (monophyletic) point of origin: there are many angiosperm features that are unlikely to have evolved more than once. The claim that angiosperms as a whole were monophyletic was validated by molecular phylogenetic analyses in 1999, and further revealed that the two categories of monocots and dicots were not entirely correct. Dicots apparently evolved in fragmented groups from different ancestors both before and after the split with the monocots, therefore making up a polyphyletic unit. Monocots, on the other hand, appear to be monophyletic. Molecular analyses show increasing support for a pre-Cretaceous separation between angiosperms and gymnosperms. A study in 1989 by Martin et al. puts the split between monocots and dicots at 300 million years ago in the late Carboniferous, suggesting that the angiosperms split from the gymnosperms before then. A comparable study in the same year by Li et al. on the DNA of chloroplast sequences estimates the monocot separation from the rest of the angiosperms at 250-220 million years; there is therefore a 100 million year discrepancy between the two dates.

Critics point out that these studies are based on the erroneous phylogeny treating monocots and dicots as two monophyletic lineages. The studies also assume that molecular evolution has progressed at a steady rate through geological time, which appears not to be the case. A larger study in 1999 by Qui et al., analysing the three cellular genomes – the mitochondrial, the nuclear and the chloroplast gene sequences – thus avoiding the problems of the previous single-genome analyses, has placed the split between angiosperms and gymnosperms as early as the late Carboniferous, 290 million years ago. There is, however, no fossil evidence to back this estimate.

Several molecular phylogenetic analyses in living plants of the three cellular genomes, especially concentrating on duplicated genes and genes with high substitution rates, have all reached similar conclusions on the plant groups that are the closest to the common ancestor of all angiosperms. Many multiple gene sequence comparisons have placed Amborella, a woody vesselless shrub found only in New Caledonia and represented by a single species, on the first branch of the of the phylogenetic tree since 1999, suggesting that it is probably the species representative of one of the oldest flowering plant lineages, which separated from the common ancestor first. The second group to branch off were the Nymphaeales, the water lilies. Some phylogenies place the water lilies on the first branch with Amborella. The third branch comprises Austrobaileya - another single species group found only in Australia, Trimenia and Illicium species which include the star anise.

Above these basal lineages, which are termed ANITA lineages from the initials of the groups, the remaining angiosperms fall into eight well-supported monophyletic categories, of which the relationships have not yet been determined. Monocots are increasingly presented by molecular studies as the next branch, leaving the remaining angiosperms to fall into seven groups: the eudicots and the category eumagnoliids containing four of the groups (Piperaceae, Magnoliales, Winteraceae and Laureales), with two further groups (Chloranthaceae and Ceratophyllum) occupying unresolved positions as sister-groups of monocots or eudicots depending on the genes investigated.

Amborella, the most primitive extant angiosperm? http://www.ucalgary.ca/~laidlaw/amborella/amborella_web.html

Understanding the relationships between extant groups can help reconstruct a common ancestor from the basal lineages. However, because angiosperms are so diverse in their morphology and ecology, the appreciation of the ancestral characteristics depends strongly on the relationships recognized in the analysis. What's more, there is no insurance that the traits present in the basal groups are ancestral. If what have been identified as the basal lineages did indeed separate from the common ancestor near the start of the angiosperm radiation, they have had over 130 million years to evolve different characters to the ancestor as a result of environmental challenges such as climate change or the changes in plant community structure resulting from the radiation of angiosperms. Furthermore, what are considered as the basal lineages might, even before separation from the ancestor, already be derived compared to the very first angiosperms. Indeed, based on molecular clock analyses, the basal extant generic diversifications appear to be younger than Early Cretaceous.