Showing papers by "Michael F. Fay published in 2006"

Multigene Analyses of Monocot Relationships

Abstract: We present an analysis of supra-familial relationships of monocots based on a combined matrix of nuclear 18S and partial 26S rDNA, plastid atpB, matK, ndhF, and rbcL, and mitochondrial atpl DNA sequences. Results are highly congruent with previous analyses and provide higher bootstrap support for nearly all relationships than in previously published analyses. Important changes to the results of previous work are a well-supported position of Petrosaviaceae as sister to all monocots above Acorales and Alismatales and much higher support for the commelinid clade. For the first time, the spine of the monocot tree has some bootstrap support, although support for paraphyly of liliids is still only low to moderate (79-82%). Dioscoreales and Pandanales are sister taxa (moderately supported, 87-92%), and Asparagales are weakly supported (79%) as sister to the commelinids. Analysis of just the four plastid genes reveals that addition of data from the other two genomes contributes to generally better support for most clades, particularly along the spine. A new collection reveals that previous material of Petermannia was misidentified, and now Petermanniaceae should no longer be considered a synonym of Colchicaceae. Arachnitis (Corsiaceae) falls into Liliales, but its exact position is not well supported. Sciaphila (Triuridaceae) falls with Pandanales. Trithuria (Hydatellaceae) falls in Poales near Eriocaulaceae, Mayacaceae, and Xyridaceae, but until a complete set of genes are produced for this taxon, its placement will remain problematic. Within the commelinid clade, Dasypogonaceae are sister to Poales and Arecales sister to the rest of the commelinids, but these relationships are only weakly supported.

Absence of phylogenetic signal in the niche structure of meadow plant communities

Abstract: A significant proportion of the global diversity of flowering plants has evolved in recent geological time, probably through adaptive radiation into new niches. However, rapid evolution is at odds with recent research which has suggested that plant ecological traits, including the β- (or habitat) niche, evolve only slowly. We have quantified traits that determine within-habitat α diversity (α niches) in two communities in which species segregate on hydrological gradients. Molecular phylogenetic analysis of these data shows practically no evidence of a correlation between the ecological and evolutionary distances separating species, indicating that hydrological α niches are evolutionarily labile. We propose that contrasting patterns of evolutionary conservatism for α- and β-niches is a general phenomenon necessitated by the hierarchical filtering of species during community assembly. This determines that species must have similar β niches in order to occupy the same habitat, but different α niches in order to coexist.

Phylogeny, Genome Size, and Chromosome Evolution of Asparagales

Abstract: Asparagales are a diverse monophyletic order that has numerous species (ca. 50% of monocots) including important crop plants such as Allium, Asparagus, and Vanilla, and a host of ornamentals such as irises, hyacinths, and orchids. Historically, Asparagales have been of interest partly because of their fascinating chromosomal evolution. We examine the evolutionary dynamics of Asparagales genomes in an updated phylogenetic framework that combines analyses of seven gene regions (atp1, atpB, matK, ndhF, rbcL, trnL intron, and trnL-F intergenic spacer) for 79 taxa of Asparagales and outgroups. Asparagales genomes are evolutionarily labile for many characters, including chromosome number and genome size. The history and causes of variation in chromosome number and genome size remain unclear, primarily because of the lack of data in small clades in the phylogenetic tree and the lack of comparative genetic maps, apart from Allium and Asparagus. Genomic tools such as bacterial artificial chromosome (BAC) libraries should be developed, as both molecular cytogenetic markers and a source of nuclear genes that can be widely used by evolutionary biologists and plant breeders alike to decipher mechanisms of chromosomal evolution.

Genetic diversity and ecological differentiation in the endangered fen orchid (Liparis loeselii)

Abstract: Liparis loeselii is a rare and endangered orchid occurring in Europe and north-east America. Genetic diversity and structure of this species in north-west France and the United Kingdom were investigated using amplified fragment length polymorphisms (AFLPs). Although clonality and autogamy are common in L. loeselii, we found moderate to important variability within populations. We observed a significant genetic differentiation between populations occurring in dune slacks and fens. This may be correlated with leaf shape as dune slack individuals are sometimes treated as the distinct variety L. loeselii var. ovata. Genetic differentiation between populations was generally low suggesting that gene flow can occur over long distances and possibly across the English Channel. These results show that populations from dune slacks and fens should be managed separately and that geographically distant populations may be equivalent.

Phylogenetics of Lilliales

Abstract: In order to investigate interfamilial relationships of Liliales we analyzed a combined matrix of plastid rbcL, trnL intron, trnL-F intergenic spacer, matK, and ndhF, and mitochondrial atpl DNA sequences. The results are generally congruent with previous broad analyses and provide higher bootstrap support for many relationships. Important changes relative to previous studies are the recognition of Petermanniaceae distinct from Colchicaceae and the tentative inclusion of Corsiaceae in the order. This brings the number of families in the order from nine to eleven. The additional data presented here strengthen the case for including Uvulariaceae in Colchicaceae and Calochortaceae in Liliaceae.

Molecular Studies of Subfamily Gilliesioideae (Alliaceae)

Abstract: We present an analysis of relationships in Gilliesioideae (Alliaceae) based on a combined matrix of plastid rbcL, the trnL intron, the trnL-F intergenic spacer, and the rpsl6 intron and nuclear ITS ribosomal DNA sequences. The results are generally congruent with previous analyses, indicating two well-supported groups: Ipheion plus allied genera ("Ipheieae" ined.) and Gilliesieae. They also provide higher bootstrap support for many patterns of relationships. Polyphyly of Ipheion and Nothoscordum is confirmed. Increased taxon sampling (particularly in Gilliesieae) and additional molecular data would be desirable to provide further resolution and to allow an appropriate taxonomic revision to be made.

Little genetic differentiation across Europe between early‐flowering and late‐flowering populations of the rapidly declining orchid Neotinea ustulata

Abstract: Amplified fragment length polymorphism (AFLP) was used to characterize genetic diversity of the endangered Burnt Orchid, Neotinea (formerly Orchis) ustulata. Fingerprinting of Estonian and British populations revealed surprisingly little genetic differentiation between populations but larger amounts of diversity within populations, especially in Britain. The resulting mean Fst value of 0.51 is unusually high for an orchid species. Much of the variation follows a west–east cline across Europe, whereas the much-discussed early- and late-flowering taxa of N. ustulata are considered insufficiently distinct to be viewed as separate subspecies. The later flowering N. ustulata var. aestivalis probably evolved independently on two or three occasions, each time diverging from the earlier flowering nominate race. The identity of the genes underpinning phenology in the species, and the potential selective advantages of phenological divergence, merit further study. Overall genetic diversity within populations is sufficiently high to render impoverishment an unlikely cause of their recent, precipitous decline. © 2006 The Linnean Society of London, Biological Journal of the Linnean Society, 2006, 87, 13–25.

A molecular phylogenetic study of generic and subgeneric relationships in the southwest Australian endemics Conostylis and Blancoa (Haemodoraceae)

Abstract: We sequenced the plastid gene matK and the nuclear ribosomal spacer ITS for 39 of the 47+ species of Conostylis as well as its monotypic sister genus Blancoa, which some authors have included within Conostylis. Conostylis received 99% bootstrap support as monophyletic, with 100% support that Blancoa is its sister. Within Conostylis, the study provides strong support for two large sister clades, which we refer to as clades A (100%) and B (99%). Clade A consists of C. subgen. Conostylis plus the recently discovered C. glabra of C. subgen. Pendula sect. Divaricata (100%), and C. subgen. Pendula sect. Appendicula (100%). Clade B consists of species mostly placed within the remainder of C. subgen. Pendula but also contains members of the other small subgenera. Subgenus Pendula can be recircumscribed as monophyletic by excluding sect. Appendicula, Conostylis phathyrantha, and C. glabra and including subgen. Androstemma and subgen. Greenia. The status of the other two minor subgenera-C. subgen. Brachycaulon and C. subgen. Bicolorata-requires further investigation. Conostylis sect. Divaricata is polyphyletic. Ancient vicariance events are postulated for Conostylis involving separation of major clades in the northern and southern kwongan regions of southwestern Australia. The phylogenetic pattern in Conostylis is consistent across several lineages with the prolonged persistence of relictual taxa combined with explosive more recent speciation, the latter pronounced in the northern kwongan. There is evidence of significant divergence in major speciation mechanisms and chromosome number change among the three most species-rich subgenera/sections (dysploidy in Pendula and Appendicula vs. diploid speciation in Conostylis). Further investigation is needed to evaluate these ideas and elucidate the patterns of speciation in this most diverse genus of Haemodoraceae.

Simple phylogenetic tree searches easily "succeed" with large matrices of single genes

Abstract: Here we show with both extensive real and simulated data that rigorous and time-intensive approaches, including parsimony, maximum likelihood and Bayesian methods, to reconstructing large phylogenetic trees are unwarranted with small amounts of data (i.e., single or small numbers, 2-3 genes) because they actually produce trees with scores that are shorter or otherwise less optimal than the model tree or trees produced with larger amounts of data. Furthermore they also fail to obtain consistently more correct groups than simple parsimony methods, leaving the latter to be preferred. When numbers of variable sites are limited relative to numbers of taxa sampled, simpler swapping strategies perform as well as much more rigorous methods. We caution against confidence in any results based on small data sets, even if (or especially if) there have been thorough analyses. Analyses of such data sets for exploratory purposes should rely on simple search strategies and not use excessive branch swapping or time.