Abstract
With the growing number of phylogenetic studies that use length variable DNA sequences, incorporating information from length-mutational events into phylogenetic analysis is becoming increasingly important. A new method, modified complex indel coding is described that aims at maximizing the phylogenetic information retained from unambiguously aligned sequence regions or regions where the principal relative position of gaps to one another can be safely established. An algorithm is described that allows application of the method to all theoretically possible gap-nucleotide patterns. A platform-independent computer program is introduced that automates the new method as well as several previously published coding schemes. Differences to previously published indel coding approaches as well as to the integration of ambiguously aligned regions into phylogenetic analysis are discussed.
Highlights
Woody perennial plants have repeatedly evolved from herbaceous ancestors in isolated situations, such as islands and mountaintops (Bohle, Hilger, & Martin, 1996; Carlquist, 1974)
The remaining 16 named species form a clade within Euphorbia subgenus Chamaesyce section Anisophyllum, hereafter referred to as Hawaiian Euphorbia (Yang & Berry, 2011)
A prior phylogenetic study with taxon sampling throughout section Anisophyllum suggested that Hawaiian Euphorbia originated following allopolyploidy, with their closest relatives being small herbs occurring in dry, warm, and exposed habitats in southern United States, northern Mexico, and the Caribbean, including E. cinerascens, E. leucantha, E. mendezii, E. stictospora, and E. velleriflora (Figure 1f; Yang & Berry, 2011)
Summary
Woody perennial plants have repeatedly evolved from herbaceous ancestors in isolated situations, such as islands and mountaintops (Bohle, Hilger, & Martin, 1996; Carlquist, 1974). A prior phylogenetic study with taxon sampling throughout section Anisophyllum suggested that Hawaiian Euphorbia originated following allopolyploidy, with their closest relatives being small herbs occurring in dry, warm, and exposed habitats in southern United States, northern Mexico, and the Caribbean, including E. cinerascens, E. leucantha, E. mendezii, E. stictospora, and E. velleriflora (Figure 1f; Yang & Berry, 2011). The long- distance dispersal most likely occurred via the tiny seeds (typically 1–2 mm long) that adhere to birds with their mucilaginous seed coat (Carlquist, 1966, 1980; Price & Wagner, 2004) Following their arrival on the Hawaiian Islands, Hawaiian Euphorbia became woody, and some species lost the mucilaginous seed coat and developed larger seeds (Carlquist, 1966). We tested whether Hawaiian Euphorbia moved into forest understory a single time and dispersed among islands, or if they moved into forest understory independently on different islands
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