The research on the Funariaceae was supported by three grants from the US National Science Foundation:
DEB-1753811 (2018–2020): Collaborative Proposal: Diversity of Physcomitrium pyriforme in North America and Europe: significance of autopolyploidy within a phylogenomic and experimental framework. Collaborators: Matthew Johnson (Texas Tech. University) and Rafael Medina (Augustana College, IL).
Whole genome duplication or autopolyploidy occurred repeatedly during the evolution of land plants and likely act as a major driver of evolutionary change. Such duplications first occurred within species, likely reproductively isolating autopolyploids. They may also trigger significant genomic restructuring, preventing meiotic pairing and hence interbreeding between two independent autodiploids. Genome duplications are thus effective mechanisms of microevolutionary change. They characterize many macroevolutionary lineages, and are expected to be frequent enough within species, for some to give rise to new evolutionary lineages. The proposed project seeks to test whether shifts in ploidy are phylogenetically structured within a complex of cryptic moss species, the Physcomitrium pyriforme complex It harbors seven karyotypes worldwide and exhibits much morphological variation, as reflected by its 29 synonyms. These annual, bisexual and selfing mosses are easily grown, and genome doubling is readily induced in vitro from sporophytic tissue, enabling tests of reproductive isolation among wild and artificial autopolyploids. This project addresses four objectives toward assessing the evolutionary significance of autopolyploidy: (1) reconstruct the phylogeny of the complex based on sub genome data, (2) infer frequencies of ploidal shifts within the complex; (3) identify morphological signatures of artificial genome duplication and through comparison with wild populations test whether these erode through time; and (4) test if wild and artificial polyploids are reproductively isolated.
Intellectual Merit: Whole genome duplications played a major role in the diversification of land plants and are a recurrent process at the species level yielding polyploid series within morphological species throughout the land plant tree of life. This project would be the first to explore the phylogenetic distribution and rates of such duplications within a plant species complex, to test microevolutionary hypotheses via experimental reproductive biology, and integrate these observations in revised taxonomic concepts. An existing bioinformatics pipeline for targeted sequence data, currently in use by many research groups, will be extended to efficiently analyze genetic data for species delimitation, within a morphological, karyological and experimental framework. Considering that many plant species harbor more than one karyotype, the expected outcomes may dramatically alter our plant diversity estimates. This project would promote future research on the consequences of whole genome duplication on chromosomal architecture or ecophysiological and phenotypic variation at a microevolutionary scale. Such studies would also provide (1) an opportunity to contrast consequences of genome duplication in autopolyploids and interspecific hybrid polyploids, and (2) an independent test for the universality of predicted consequences of autopolyploidy drawn from observations in angiosperms. Available genomic resources and tools developed for the evo-devo model taxon, Physcomitrella patens, a relative of the P. pyriforme-complex, would greatly facilitate these studies, thereby deepening our understanding of autopolyploidy as a speciation mechanism in plants.
Broader Impacts: Human resources: This collaborative project will offer opportunities 1) to train one graduate student and two postdoctoral researchers in integrative evolutionary biology, and 2) to annually engage six undergraduates at UCONN, Texas Tech and Augustana College, an undergraduate institution, in the development of independent hypothesis-based research, with opportunities to present their results at professional meetings. Support will be requested for students from Augustana College to visit UCONN, an R1 institution and interact with graduate students and postdocs. Outreach activities will consist in (1) A Citizen Science project articulated on iNaturalist aimed at inviting the public to help improve the knowledge on P. pyriforme (2) annual professional development opportunities for high-school biology teachers focusing on tree-thinking; (3) development of 2 educational videos on moss biology (with students in Communications Sciences) and bilingual dissemination via science blogs of the core concepts of this project; (4) develop through annual public talks and nature walks an awareness among local residents of bryophytes as integral components of their natural heritage and (5) instruct evolutionary biologists in targeted sequencing techniques through a bioinformatics workshop.
DEB-1146295 (2012-2015): Rapid radiation and sporophyte evolution in the Funariaceae: inferences from phylogenomics and cross generational cuticle development studies.
The unique ancestor to bryophytes (mosses) arose in the Devonian, and their evolutionary history over the next 400 million years resulted in approximately 13,000 extant species. Although often considered sphinxes of the past, recent evidence highlights episodes of rapid and sometimes recent diversification events, which at least in one case correlates with global climatic change. Furthermore, below the seemingly simple morphology, hides a broad genetic diversity, distinct ploidy levels and likely also subtle physiological adaptations in these typically desiccation tolerant organisms. Intensive populations sampling over the geographical and ecological spectrum of bryophytes often reveals a robust partitioning of the genetic diversity, indicative of cryptic speciation. Bryophytes have not only withstood extinction, they are dynamic evolutionary entities, which thrive in virtually all terrestrial ecosystems. The macroevolutionary history of mosses is characterized by increasing architectural complexity in the mode of dehiscence and mechanisms controlling spore dispersal. However, these innovations are lost in some lineages, resulting in ancestral character-states defining highly derived taxa, often obfuscating their phylogenetic affinities. Whether such reverse evolution is irreversible or results in a dead-end remains unexplored. Reduction in sporophytic architecture may be correlated to features of the calyptra, a hood of maternal tissue covering the developing sporophyte throughout its growth and providing essential protection against desiccation, until the emerging sporophyte has developed its own waxy cuticle that seals its body off against water loss. The architecture of the hood varies among species and we predict that the shortening of the hood is correlated with a shortening and simplification of the sporophyte or compensated by an acceleration of cuticle development on the sporophyte. We seek to test these two hypotheses using the Funariaceae as our model. This family comprises about 150 species representing a broad gradient in architectural complexity of their spore producing generation and their associated hood. The morphological spectrum is defined by Funaria with long stalks subtending the arched capsule, shedding a lid and bearing two rings of teeth and covered by a large hood, and Physcomitrella, with sessile capsules disintegrating at maturity, lacking mechanisms to control spore release and barely covered by a tiny hood. We will reconstruct the transformations of morphological characters based on a phylogenomic history of the family drawn from all three genomes for a total of 210,000 bps, and characterize cuticle development on the calyptrae and sporophyte of species with contrasting combinations of calyptra and sporophyte sizes.
Intellectual merit: This first phylogenomic reconstruction for any group of non-vascular plant will provide a robust evolutionary hypothesis for Physcomitrella patens – an essential model system in the study of the evolution of genes and genetic developmental networks in land plants – and the foundation for the study of homoplasy in bryophytes. The contribution of 100 new organellar genomes and sequences of the universal nrDNA repeat will promote studies in the molecular evolution of these regions within land plants and across the tree of life. The phylogenetic inference is complemented by an ontogenetic reconstruction of cuticle development on maternal and sporophytic tissue to test a novel hypothesis that sporophyte diversification is shaped by constraints to withstand drought during its differentiation.
Broader impact: The proposed project provides two innovative graduates in bryophyte biology opportunities to strengthen their training in evolutionary biology, acquire experience in undergraduate education and develop their own future research foci. Two undergraduates will be recruited annually to complement their academic training by leading question driven projects complementing the proposed study. During the funding period a traveling exhibit on the regional hidden biodiversity will be developed by undergraduates from UConn’s EcoHouse learning community to promote awareness of regional and global bryophytes diversity and evolution.
DEB 0919284 (2009-2012) (Co-PI : Dr. C. Jones; UCONN): Reduction & reversal in the Funariaceae: phylogenetic perspective on sporophyte complexity and role of the calyptra.
Macroevolutionary trends are widely associated with increases in morphological, anatomical or physiological complexity. Complex characters have also been lost multiple times across the tree of life, consequently erasing the evolutionary signature shared by descendants from a unique common ancestor. The result is that phenetically similar taxa are often artificially grouped together. Such has been the case in mosses, where reduction is hypothesized in many lineages and is particularly prevalent in the Funariaceae. Much of our knowledge of fundamental aspects of moss biology is based on studies of members of this family, a significance that continues today with the recent emergence of Physcomitrella patens as a model organism in plant biology. Nevertheless, P. patens is currently a classic example of a morphologically reduced taxon of uncertain phylogenetic placement. Character reduction in the Funariaceae takes several forms, ranging, for example, from virtual loss of the stalk (seta) that elevates the sporangium to reduction in complexity of the spore dispersing structure, the peristome. The structure of the peristome and mode of dehiscence of the sporangium have long been treated as essential systematic characters — the peristome is analogous to the flower in moss classification — yet at the same time frequent reversals render classifications based solely on morphological traits tenuous. To assess polarity of character transformations and the significance of character-states in the family’s evolutionary history, we propose to construct a phylogenetic hypothesis for the Funariaceae based on 15 loci and a minimum of 60 ingroup taxa. Taxon sampling will approach 90% of the generic diversity and represent a broad spectrum of sporophyte reduction. We will score at least 60 morphological characters and reconstruct ancestral character-states to identify synapomorphies and test whether the loss of complex traits is reversible in the Funariaceae. The sporophyte of all bryophytes remains attached to the maternal plant throughout its short life. Maternal care for the developing sporophyte is a unifying feature of all land plants. Mosses are further characterized by a unique maternal plant-sporophyte interaction, one that involves retention of a hat (i.e. the calyptra) of maternal tissue covering the apex of the developing sporophyte. The calyptra is essential for normal sporophyte ontogeny: precocious removal of the calyptra results in sporophyte abortion. The precise mechanism of this interaction is unknown. In this proposal we describe a novel observation: the outer epidermal cells of the calyptra have a relatively well-developed cuticle in Funaria hygrometrica . We suggest that one role of the calyptra is to provide an essential barrier to water loss from the meristematic regions of the sporophyte that lack a proper cuticle. This suggestion in turn leads to the hypothesis that the evolution of sporophyte complexity is linked to the presence of the calyptral cuticle. We will survey the phylogenetic pattern of cuticle deposition on calyptrae using transmission electron microscopy and test for correlations between calyptra cuticular traits and sporophyte complexity to provide phylogenetic evidence for a potential role of the calyptra in preventing dehydration of the sporophyte.
Intellectual merits of proposal. The proposed project is transformative in three regards. First, it will provide a robust phylogenetic hypothesis of the Funariaceae, a diverse lineage whose classification to date has been obfuscated by morphological reversals. In so doing, the project will establish a robust phylogenetic framework for the model organism, Physcomitrella patens. Second, this project represents the first attempt to characterize rates of character loss and re-emergence in an important moss lineage and will serve as baseline for evolutionary interpretations in other moss lineages characterized by character reduction. Third, this study will be the first analysis of functional traits in mosses from a phylogenetic perspective. Specifically, the project tests a novel hypothesis that the complexity of the sporophyte in the Funariaceae is evolutionarily linked to the expression of cuticle in the calyptra.
Broader impact. Despite the tremendous importance of bryophytes as components of systematic and ecological diversity and their emerging role in studies of development and evolution, bryophytes receive almost NO attention in K-12 education. As part of this project we will work with local pre-college biology teachers to develop workshops that will increase general literacy in botany and promote curricular integration of bryophytes. We will produce local and regional guides for moss identification. For both the educational and research components of the project, we will establish cultures of representatives of all genera of the Funariaceae that will be available to educators and researchers. The project will involve training of one female doctoral student in phylogenetics, systematics, and cell ultrastructure and one postdoctoral fellow in systematics and phylogenetic analysis. Undergraduates will be mentored in all aspects of the research.