Elizabeth A. Zimmer

The earliest angiosperms: evidence from mitochondrial, plastid and nuclear genomes

Angiosperms have dominated the Earths vegetation since the mid-Cretaceous (90 million years ago), providing much of our food, fibre, medicine and timber, yet their origin and early evolution have remained enigmatic for over a century. One part of the enigma lies in the difficulty of identifying the earliest angiosperms; the other involves the uncertainty regarding the sister group of angiosperms among extant and fossil gymnosperms. Here we report a phylogenetic analysis of DNA sequences of five mitochondrial, plastid and nuclear genes (total aligned length 8,733 base pairs), from all basal angiosperm and gymnosperm lineages (105 species, 103 genera and 63 families). Our study demonstrates that Amborella, Nymphaeales and Illiciales-Trimeniaceae-Austrobaileya represent the first stage of angiosperm evolution, with Amborella being sister to all other angiosperms. We also show that Gnetales are related to the conifers and are not sister to the angiosperms, thus refuting the Anthophyte Hypothesis. These results have far-reaching implications for our understanding of diversification, adaptation, genome evolution and development of the angiosperms.

Integration of morphological and ribosomal RNA data on the origin of angiosperms

Previous phylogenetic analyses of morphological and rRNA data indicated that Gnetales are the closest living relatives of angiosperms but gave different basal angiosperm relationships. A two-step morphological analysis of seed plants (including fossils) and angiosperms rooted the latter near Magnoliales, with tricolpate eudicots and paleoherbs (herbaceous magnoliids and monocots) forming a clade, whereas analyses of rRNA sequences rooted angiosperms among paleoherbs, with eudicots and woody magnoliids forming a clade. Experiments with a revised seed plant morphological data set raise further questions: when angiosperms are scored like different angiosperm subgroups, they associate with different outgroups, although Gnetales are their closest living relatives

Family-level relationships of Onagraceae based on chloroplast rbcL and ndhF data

Despite intensive morphological and molecular studies of Onagraceae, relationships within the family are not fully understood. One drawback of previous analyses is limited sampling within the large tribe Onagreae. In addition, the monophyly of two species-rich genera in Onagreae, Camissonia and Oenothera, has never been adequately tested. To understand relationships within Onagraceae, test the monophyly of these two genera, and ascertain the affinities of the newly discovered genus Megacorax, we conducted parsimony and maximum likelihood analyses with rbcL and ndhF sequence data for 24 taxa representing all 17 Onagraceae genera and two outgroup Lythraceae. Results strongly support a monophyletic Onagraceae, with Ludwigia as the basal lineage and a sister-taxon relationship between Megacorax and Lopezia. Gongylocarpus is supported as sister to Epilobieae plus the rest of Onagreae, although relationships within the latter clade have limited resolution. Thus, we advocate placement of Gongylocarpus in a monogeneric tribe, Gongylocarpeae. Most relationships within Onagreae are weakly resolved, suggesting a rapid diversification of this group in western North America. Neither Camissonia nor Oenothera appears to be monophyletic; however, increased taxon sampling is needed to clarify those relationships. Morphological characters generally agree with the molecular data, providing further support for relationships.

Phylogenetic analyses and perianth evolution in basal angiosperms

Using a compartmentalization approach, we conducted phylogenetic analyses of the basalmost extant angiosperms using sequences from six genes (over 12,000 bp per taxon) from all three genomes (chloroplast-atpB, rbcL; nuclear- 18S rDNA, 26S rDNA; mitochondrial-matR, atpA). Trees resulting from parsimony and maximum likelihood analyses of the compartmentalized data are identical. We find strong support (100% for each node) for the earliest-branching angiosperms: Amborellaceae, Nymphaeaceae, and an Austrobaileyales clade (Illiciaceae, Schisandraceae, Trimeniaceae, Austrobaileyaceae). Whereas most recent studies using multiple genes provided poor resolution and support for relationships among the remaining basal angiosperms (Ceratophyllaceae, Chloranthaceae, Canellales ( = Winterales), Piperales, monocots, Magnoliales, Laurales), with compartmentalization, we find high levels (> 90%) of bootstrap support for relationships among these clades. Canellales and Piperales form a strongly supported (100%) sister group that is, in turn, sister to a well-supported (100%) clade of Laurales and Magnoliales. Canellales + Piperales and Magnoliales + Laurales form a well-supported magnoliid clade. Ceratophyllaceae are strongly supported (100%) as sister to the monocots; the monocot/Ceratophyllaceae clade is well supported (86%) as sister to all remaining angiosperms (Chloranthaceae, the magnoliid clade, and eudicots). The addition of entire 26S rDNA sequences clearly contributed to this increased internal support. We examined the diversification of perianth phyllotaxis, merosity, and differentiation using our phylogenetic hypothesis for angiosperms. Ancestral perianth phyllotaxis and merosity are equivocal for each node of the Amborellaceae, Nymphaeaceae, Austrobaileyales grade; however, an undifferentiated perianth is reconstructed as the ancestral state for the angiosperms. Trimery and whorled perianth phyllotaxis have played a major role in basal angiosperm perianth evolution and represent the ancestral states for the large Glade comprising all angiosperms other than Amborella, Nymphaeaceae, and Austrobaileyales. A differentiated perianth has apparently evolved multiple times.

Unraveling the Evolutionary Radiation of the Families of the Zingiberales Using Morphological and Molecular Evidence

The Zingiberales are a tropical group of monocotyledons that includes bananas, gingers, and their relatives. The phylogenetic relationships among the eight families currently recognized are investigated here by using parsimony and maximum likelihood analyses of four character sets: morphological features (1), and sequence data of the (2) chloroplast rbcL gene, (3) chloroplast atpB gene, and (4) nuclear 18S rDNA gene. Outgroups for the analyses include the closely related Commelinaceae + Philydraceae + Haemodoraceae + Pontederiaceae + Hanguanaceae as well as seven more distantly related monocots and paleoherbs. Only slightly different estimates of evolutionary relationships result from the analysis of each character set. The morphological data yield a single fully resolved most-parsimonious tree. None of the molecular datasets alone completely resolves interfamilial relationships. The analyses of the combined molecular dataset provide more resolution than do those of individual genes, and the addition of the morphological data provides a well-supported estimate of phylogenetic relationships: (Musaceae ((Strelitziaceae, Lowiaceae) (Heliconiaceae ((Zingiberaceae, Costaceae) (Cannaceae, Marantaceae))))). Evidence from branch lengths in the parsimony analyses and from the fossil record suggests that the Zingiberales originated in the Early Cretaceous and underwent a rapid radiation in the mid-Cretaceous, by which time most extant family lineages had diverged.

A Preliminary Phylogeny of Alloplectus (Gesneriaceae): Implications for the Evolution of Flower Resupination

Abstract Monophyly of the neotropical plant genus Alloplectus (Gesneriaceae) was tested using maximum parsimony and maximum likelihood phylogenetic analyses of molecular sequence data from the nuclear ribosomal (nrDNA) internal transcribed spacer region (ITS). As currently circumscribed, Alloplectus is polyphyletic and includes taxa in three different clades. The clade that contains the type species is described as Alloplectus sensu stricto and is characterized by the presence of resupinate flowers. The Alloplectus s.s. clade is weakly supported as the sister-group to Columnea. A separate clade of non-resupinate “Alloplectus” species nests within a paraphyletic Drymonia. A third taxon, Alloplectus cristatus, endemic to the Lesser Antilles and northwestern South America, is also resupinate and unresolved in a basal polytomy, removed from the other species of Alloplectus. The fourth taxon, Alloplectus peruvianus, which was originally described as Columnea peruviana, is strongly supported as nesting within Columnea. Resupination of flowers is an important feature that has not been previously reported and should be recognized as a morphological synapomorphy for Alloplectus s.s. Within the tribe Episcieae, flower resupination is a convergent feature that is independently derived in the Alloplectus s.s. clade, Alloplectus cristatus, and a clade comprising some Nematanthus species.

On the Evolutionary Origins of the Cacti

Understanding evolutionary responses of plants to desert environments depends upon phylogenetic knowledge of desert plants. The diverse American desert family Cactaceae has been presumed, on the basis of distinctiveness, to be phylogenetically isolated and relatively ancient (> 65 million years old). Using maximum likelihood and parsimony analyses of the rapidly evolving internal transcribed spacer (ITS) sequences of nuclear ribosomal DNA (nrDNA), we show that the cacti are phylogenetically nested among other aridity-adapted lineages of the angiosperm family Portulacaceae. The ITS divergence between pereskioid cacti and the genus Talinum (Portulacaceae) is less than that between many Portulacaceae genera. Synthesis of the ITS data with morphological and chloroplast DNA evidence suggests an origin of cacti in mid-Tertiary, c. 30 million years ago, and a later Tertiary diversification coincident with development of the American desert. This, in turn, implies that the diversification rate in cacti was much higher than in their nearest relatives. The present results illustrate the central role of phylogenetic reconstruction in ecological and evolutionary theory.

Molecular evolution : producing the biochemical data

Isolation of DNA from plants with large amounts of secondary metabolites Nucleic Acid Isolation from Environmental Aqueous Samples Nucleic acid isolation from ecological samplesvertebrate gut flora Nucleic acid isolation from ecological samples fungal associations, lichens Nucleic acid isolation from ecological samplesfungal associations, mycorrhizae Nucleic acid isolation from ecological samplesanimal scat and other associated materials Isolation and analysis of DNA from archaeological, clinical and natural history specimens Isolation and characterization of proteins from archaeological and ancient specimens Animal Phylogenomics: Multiple Interspecific Genome Comparisons ISSR techniques for evolutionary biology Use of Amplified Fragment Length Polymorphism (AFLP) markers in surveys of vertebrate diversity Use of AFLP markers in surveys of arthropod diversity Use of AFLP markers in surveys of plant diversity Isolating microsatellite DNA loci Use of microsatellites for parentage and kinship analyses in animals Use of capillary array electrophoresis single strand conformational polymorphism analysis to estimate genetic diversity of candidate genes in germplasm collections Ribosomal RNA probes and microarrays: Their potential use in assessing microbial biodiversity The role of geographic analyses in locating, understanding and using plant genetic diversity In Situ Hybridization of Phytoplankton Using Fluorescently-Labelled rRNA Probes Sequencing and comparing whole mitochondrial genomes of animals Methods for obtaining and analyzing whole chloroplast genome sequences Construction of Bacterial Artificial Chromosome libraries for use in phylogenetic studies Comparative EST analyses in plant systems Isolation of genes from plant Y chromosomes Preparation of samples for comparative studies of plant chromosomes using in situ hybridization methods Preparation of samples for comparative studies of arthropod chromosomes: visualization, in situ hybridization, and genome size estimation Experimental methods for assaying natural transformation and inferring horizontal gene transfer Use of confocal microscopy in comparative studies of vertebrate morphology PrimerSelect: A transcriptome-wide oligonucleotide primer pair design program for kinetic RT-PCR-based transcript profiling Detecting differential expression of parental or progenitor alleles in genetic hybrids and allopolyploids genome-wide analysis of gene expression changes in polyploids Designing experiments using spotted microarrays to detect gene regulation differences within and among species Methods for studying the evolution of plant reproductive structures: Comparative gene expression techniques Developing antibodies to synthetic peptides based on comparative DNA sequencing of multigene families Application of ancestral protein reconstruction in understanding protein function: GFP-like proteins Advances in phylogeny reconstruction from gene order and content data Analytical methods for detecting paralogy in molecular datasets Analytical methods for studying the evolution of paralogs using duplicate gene data sets Supertree construction in the genomic age Maximum-likelihood methods for phylogeny estimation Context Dependence and Co-Evolution among Amino Acid Resideue in Proteins

Phylogenetic and biogeographic complexity of Magnoliaceae in the Northern Hemisphere inferred from three nuclear data sets.

This study employs three nuclear genes (PHYA, LFY, and GAI1) to reconstruct the phylogenetic and biogeographic history of Magnoliaceae. A total of 104 samples representing 86 taxa from all sections and most subsections were sequenced. Twelve major groups are well supported to be monophyletic within Magnoliaceae and these groups are largely consistent with the recent taxonomic revision at the sectional and subsectional levels. However, relationships at deeper nodes of the subfamily Magnolioideae remain not well resolved. A relaxed clock relying on uncorrelated rates suggests that the complicated divergent evolution of Magnolioideae began around the early Eocene (54.57mya), concordant with paleoclimatic and fossil evidence. Intercontinental disjunctions of Magnoliaceae in the Northern Hemisphere appear to have originated during at least two geologic periods. Some occurred after the middle Miocene, represented by two well-recognized temperate lineages disjunct between eastern Asia and eastern North America. The others may have occurred no later than the Oligocene, with ancient separations between or within tropical and temperate lineages.

Using nuclear gene data for plant phylogenetics: Progress and prospects

The paper reviews the current state of low and single copy nuclear markers that have been applied successfully in plant phylogenetics to date, and discusses case studies highlighting the potential of massively parallel high throughput or next-generation sequencing (NGS) approaches for molecular phylogenetic and evolutionary investigations. The current state, prospects and challenges of specific single- or low-copy plant nuclear markers as well as phylogenomic case studies are presented and evaluated.