Phylogenetic Relationships of Monocots Based on the Highly Informative Plastid Gene ndhF

Abstract

We used ndhF sequence variation to reconstruct relationships across 282 taxa representing 78 monocot families and all 12 orders. The resulting tree is highly resolved and places commelinids sister to Asparagales, with both sister to Liliales-Pandanales in the strict consensus; Pandanales are sister to Dioscoreales in the bootstrap majority-rule tree, just above Petrosaviales. Acorales are sister to all other monocots, with Alismatales sister to all but Acorales. Relationships among the four major clades of commelinids remain unresolved. Relationships within orders are consistent with those based on rbcL, alone or in combination with atpB and 18S nrDNA, and generally better supported: ndhF contributes more than twice as many informative characters as rbcL, and nearly as many as rbcL, atpB, and 18S nrDNA combined. Based on functional arguments, we hypothesized that net venation and fleshy fruits should both evolve-and thus undergo concerted convergence-in shaded habitats, and revert to parallel venation and dry, passively dispersed fruits in open, sunny habitats. Our data show that net venation arose at least 26 times and disappeared 9 times, whereas fleshy fruits arose 22 times and disappeared 11 times. Both traits arose together at least 15 times and disappeared together 5 times. They thus show a highly significant pattern of concerted convergence (P < I0-9 ) and are each even more strongly associated with shaded habitats (P < I0-10 to I0-23 ); net venation is also associated, as predicted, with broad-leaved aquatic plants. Exceptions to this pattern illustrate the importance of other selective constraints and phylogenetic inertia.

Phylogeny, Genome Size, and Chromosome Evolution of Asparagales

“…and even some Iridaceae . Similarly, Behniaceae, Blandfordiaceae, Ruscaceae, Tecophilaeaceae, and some Agavaceae (e.g., Hosta) possess net-veined leaves that are associated with mesic, forest-understory environments (see Givnish et al 2006 on concerted evolution of net-veined leaves and fleshy fruits in monocots). Given these morphological parallelisms, it can often be difficult to assign macromorphological characters to separate two families for taxonomic keys, as illustrated by African taxa of Anthericaceae and Asphodelaceae (Stedje and Nordal 1994).…”

“…Polyploidization and chromosomal rearrangements are thought to generate reproductive isolation or prevent recombination in linkage groups that contain ecologically important loci, thereby playing a role in speciation (Riese berg 2001 ; Lonnig and Saedler 2002). Fluctuations in chromosome number and genome size have also been correlated with a number of morphological and environmental variables in plants, which can generate novel phenotypes that lead to habitat divergence (Levin 1983;Bennett 1987;Grime 1998;Ohri et al 1998;Watanabe et al 1999;Bennett et al 2000;Givnish et al 2000;Gregory 2002;Osborn et al 2003).…”

“…GenBank numbers for rbcL, atpB, and trnL-F have been previously published Pireset al 2004). GenBank numbers for matK, ndhF, and atp1 are in press or will be presented in forthcoming publications and will not be provided here (see Davis et al 2004;Chase et al 2006;Givnish et al 2006;Petersen et al 2006). This analysis focuses on only 79 taxa of Asparagales and outgroups, but we are preparing a future analysis of ca.…”

“…2003), across Poaceae (Kellogg 2000(Kellogg , 2001Gaut 2002;Levy and Feldman 2002;Choffnes Inada et a!. 2003;Guo and Moose 2003), among commelinids (e.g., Givnish et a!. 2000), and finally, comparisons of gene and genome duplication events across the monocot/magnoliid-eudicot divide (e.g., Dias et a!.…”

Systematics of Bromelioideae (Bromeliaceae)—Evidence from Molecular and Anatomical Studies

“…Marker Genera/species of Bromeliaceae Ranker et al (1990) Givnish et al (1990 Clark and Clegg (1990) Clark et al (1993 restriction sites (cp) restriction sites (cp) rbcL rbcL rbcL 9/10 (T: 4/5, P: 3/3, B: 2/2) 7/7 3/3 7/7 7/7 (T: 3/3, P: 2/2, B: 2/2) Terry and Brown (1996) Givnish et al (1997) Terry et al (1997a) Terry et al (1997b) Horres et al (2000) ndhF restriction sites (nr ϩ cp) ndhF ndhF trnL intron 30/51 (T: 7/28, P: 8/8, B: 15/15) 4/19 (mostly Brocchinia; P: 4/19) 29/30 (T: 6/7, P: 8/8, B: 15/15) 9/28 (mostly Tillandsioideae) 32/62 (T: 7/23, P: 9/19, B: 16/20) Behnke et al (2000) Crayn et al (2000) rbcL matK 11/11 (T: 2/2, P: 5/5, B: 4/4) 15/40 (mostly Pitcairnioideae; T: 3/3, P: 11/36, B: 1/1) Reinert et al (2003) matK 11/35 (analysis of data by Crayn et al 2000, P: 11/35) Crayn et al (2004) Givnish et al (2005) matK & rps16 intron ndhF 24/51 (T: 7/10, P: 9/33, B: 8/8) 25/35 (T: 5/5, P: 14/24, B: 6/6) ter to a branch with Poaceae, Anarthriaceae, Restionaceae, Flagellariaceae, Xyridaceae, Cyperaceae, Juncaceae, Thurniaceae, and Mayacaceae (Chase et al 2000). In a study of ndhF cpDNA data analysis, Givnish et al (2006) found that members of Typhaceae are sister to Bromeliaceae at the base of the order Poales sensu APG II (2003), with Rapateaceae next divergent.…”