However, their assignment to nodes in the tree of living species of crown group.)To overcome these calibration problems, we decided to employ additional constraints from well-dated fossils of conifers, cycads, and flowering plants.
This required a relaxed clock approach (i.e., modeling substitution rate change along branches) because the larger data matrix rejected the clock assumption and added the problem of the uncertain phylogenetic placement of Gnetales among seed plants (above).
These conserved gene regions will often be uninformative in the group of interest.
Species relationships within Asian cannot be resolved with the highly conserved gene regions required for seed plant-wide analyses and dating.
The changing hierarchical relationships among seed plants (and accordingly changing placements of distant fossils) resulted in small changes of within-Age estimation from molecular sequences has emerged as a powerful tool for inferring the time it took a plant lineage to radiate in a particular area.
Analytical methods now try to model change in substitution rates along individual branches of a phylogeny by combining molecular data with multiple simultaneous time constraints, usually from fossils (Thorne et al., 1998; Rambaut and Bromham, 1998; Kishino et al., 2001; Thorne and Kishino, 2002; Aris-Brosou and Yang, 2002; Sanderson, 2002; Drummond and Rambaut, 2005).
Instead, we relied on a six-locus data set that includes nuclear, mitochondrial, and chloroplast genes, spacers, and introns.
The accepted hypothesis has long been that the pantropical range of , today restricted to the Namib dessert, is known from a 110-My-old seedling from the Lower Cretaceous (Aptian) Crato Formation in northeastern Brazil (Rydin et al., 2003).
We explored the effects of resolved and polytomous input topologies in a rate-heterogeneous sequence data set for has 10 species in South America, 1 in tropical West Africa, and 20 to 25 in tropical Asia, and explanations for the ages of these disjunctions involve long-distance dispersal and/or the breakup of Gondwana. Relationships among Gnetales and the other seed plant lineages are still unresolved, and we therefore used differently resolved topologies, including one that contained a basal polytomy among gymnosperms.