Research in my lab encompasses a wide diversity of topics in molecular systematics and evolution, genomics, and bioinformatics. Below I have outlined five primary areas of research.
(1) Chloroplast Genome Organization and Evolution - The chloroplast genome of land plants is highly conserved with most groups having the same general organization and gene order. In some instances, however, changes have occurred including inversions, large deletions and insertions, gene losses and/or transfers, and intron losses. These changes not only provide interesting insights into the evolution of chloroplast genomes but they also provide powerful characters for phylogeny reconstruction because of the low levels of homoplasy. My lab has been sequencing chloroplast genomes in a wide diversity of seed plant lineages, with an emphasis on several angiosperm families that have experienced genomic rearrangements including Asteraceae, Campanulaceae, Fabaceae, Geraniaceae, Goodeniaceae and Oleaceae. These studies focus in three general areas: examination of mechanisms of genomic rearrangements, characterization and phylogenetic utility of genomic changes, and examination of rates and patterns of sequence evolution. Some of the more general results of recent comparative genomic studies are: the extent chloroplast genome reorganization is correlated with the presence of dispersed repeats that are prevalent at rearrangement endpoints; there is a correlation between the extent of genomic rearrangements and rates of base substitution; and in the Geraniaceae, rates of base substitution are significantly accelerated, especially for ribosomal protein, ATPase, and RNA polymerase genes.
(2) Computational Biology and Bioinformatics - As part of my interest in comparative chloroplast genomics my lab has been actively involved in developing computational tools and databases. This includes the development of an annotation program for organellar genomes (DOGMA, Dual Organellar GenoMe Annotator) that currently annotates both chloroplast and animal mitochondrial genomes. We have also collaborated with Claude dePamphilis' lab to develop and chloroplast genome database. We are currently working on a multiple sequence alignment tool that is specifically designed to handle many gene sequences from completely sequence genomes.
(3) Phylogenetic Relationships among the Major Clades of Angiosperms based on Complete Chloroplast Genome Sequences - We have been examining phylogenetic relationships among angiosperms by using gene sequences of protein-coding genes from the plastid genome. Our phylogenetic studies have included up to 81 genes for 65 completely sequenced plastid genomes. Phylogenetic analyses of these data have been performed using maximum parsimony, maximum likelihood, and Bayesian methods. The results have provided strong support for relationships among several major clades of angiosperms including: the position of Amborella as sister to the remaining angiosperms, the placement of Chloranthales sister to magnoliids, a sister relationship between monocots and eudicots, the placement of the Vitaceae as the earliest diverging lineage of rosids, and a sister relationships between the Caryophyllales and asterids.
(4) Systematics and Evolution of the Angiosperm families Asteraceae and Campanulaceae - Much of the systematic work in my lab focuses on two derived asterid families, Asteraceae and Campanulaceae. In both of these families, we are performing molecular phylogenetic investigations to address both taxonomic issues and for testing hypotheses regarding the biogeographic history and character evolution.
The Asteraceae is one of the largest and most successful families of flowering plants with approximately 1,500 genera and 23,000 species. Fossil evidence and biogeographical data suggest that the family originated as recently as 30 million years ago in the middle to upper Oligocene. The extensive morphological and biological diversification of the Asteraceae must have occurred rapidly. This explosive radiation of the family has made it very difficult to reconstruct the origin and systematic relationships in the Asteraceae. During the past 20 years I have been assessing phylogenetic relationships of the Asteraceae using three primary approaches to examining chloroplast DNA variation; genome organization, restriction site analysis, and DNA sequencing. The most significant finding to emerge from these studies was the identification of two cpDNA inversions in the Asteraceae, which marked an ancient evolutionary split in the family. These characters indicated that a small group of nine genera (now recognized as the subfamily Barnadesioideae) from South America is sister to the remaining members of the family. Another significant finding concerns the identification of the sister group to the family. Molecular phylogenies have provided strong evidence that the Calyceraceae is sister to the Asteraceae.
The Campanulaceae is a much smaller member of the Asterales with 35-50 genera and 900 species. Although the Campanulaceae has a nearly cosmopolitan distribution, most taxa occur in four centers of diversity: Asia, Europe (especially the Mediterranean), South Africa and western North America. Two features of the geographic distribution of the family are particularly interesting and amenable to biogeographic studies. The first concerns the relationships among the primary centers of taxonomic diversity. The second concerns the origin of taxa endemic to Macaronesia. There has also been considerable controversy about generic circumscription and intrafamilial classification of the Campanulaceae largely due to the lack of a comprehensive phylogenetic study of the family. Finally, chloroplast genomes in this family are among the most highly rearranged of any land plant group. My lab has been involved in generating estimates of phylogenetic relationships in the family based on DNA sequences from the chloroplast and nuclear genomes and cpDNA rearrangements. The resulting phylogenies are being used to address taxonomic and biogeograpic questions, and they serve as a framework for examining chloroplast genome evolution. Some noteworthy results of these studies are: gene order data generate phylogenies that are congruent with trees generated from DNA sequences and relationships in these trees are congruent; Campanulaceae is comprised of three strongly supported monophyletic groups, Platycodonoids, Wahlenbergioids, and Campanuloids; and the two largest genera Campanula and Wahlenbergia are polyphyletic.
(5) Origin and Evolution of Oceanic Island Plants - Oceanic islands are relatively simple systems where both patterns of dispersal and natural selection can be more easily examined than in most continental regions. Several characteristics of volcanic archipelagos make them particularly attractive for evolutionary studies. First, many have had a recent origin compared with continental areas. Moreover, volcanic archipelagos often form sequentially, generating a series of islands of different ages. Thus, the ages of these islands can often be estimated accurately, making it possible to set age limits for endemic taxa. Second, given sufficient elevation there is a high diversity of ecological zones in a very small geographic area, which produces a wide variety of habitats for new colonizers. Third, islands are isolated from the continental sources of the flora and fauna. This geographic isolation provides immediate spatial isolation and cuts reproductive ties between founder and progenitor populations. Most oceanic islands have an exceptionally diverse and highly endemic flora and fauna. Estimates of levels of endemism in some major oceanic archipelagos include 90% in Hawaii, 40% in the Galapagos, and 25% in the Canaries. The most alarming statistic about island biota is that they have the highest incidence of endangered species. One third of the endangered plants in the world occur on volcanic islands.
During the past 10 years my lab has been examining the origin, evolution, and conservation biology of endemic plants from the five archipelagos that comprise Macaronesia. These archipelagos have several distinctive features that make them interesting systems for understanding the origin and evolution of island floras and faunas. Macaronesia includes 32 islands in five major archipelagos (Azores, Canaries, Cape Verde, Madeira, and Selvagens) that range in age from 0.8 to 21 million years. Unlike most volcanic archipelagos, the region exhibits a wide range of distances from the mainland with the closest island, Fuerteventura, only 100 km from the coast of Africa and the most distant islands of the Azores 1000 km from the continent. The Macaronesian flora is also distinct because it has been suggested to contain relicts of an older Tertiary flora from southern Europe and northern Africa.
My lab has completed phylogenetic investigations of several endemic Macaronesian groups from six different flowering plant families. These studies have generated significant results in three areas: (A) Origin of the flora - Previous workers have suggested that, unlike other oceanic islands, the Macaronesian flora comprises relictual plants that found refuge on the islands following a series of major geologic and climatic events that began 22 million years ago. Phylogenies for most groups indicate that many of the Macaronesian endemics occur in a derived position, indicating that they have had a recent origin. Furthermore, in all but two cases there has been a single colonization of the islands. Most of the groups studied have their closest continental relatives in the Mediterranean and north Africa. (B) Correlation between ecology and phylogeny – One of the most significant results of the island studies is that inter-island colonization between similar ecological zones is in an important factor in the evolution of the flora. These results are in contrast with the pattern of ecological radiation in Hawaii, where major ecological shifts accompanied speciation in island-endemic lineages. (C) Hybridization - Hybridization has generally been considered to play a minor role in the evolution of insular plants, even though there is usually a lack of genic barriers to hybridization between congeneric endemic species. Our studies have identified several instances of both ancient and recent hybridization, suggesting that this process has been very important in the plant evolution on these islands.
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