Amanda L. Grusz

The evolution of chloroplast genes and genomes in ferns

Most of the publicly available data on chloroplast (plastid) genes and genomes come from seed plants, with relatively little information from their sister group, the ferns. Here we describe several broad evolutionary patterns and processes in fern plastid genomes (plastomes), and we include some new plastome sequence data. We review what we know about the evolutionary history of plastome structure across the fern phylogeny and we compare plastome organization and patterns of evolution in ferns to those in seed plants. A large clade of ferns is characterized by a plastome that has been reorganized with respect to the ancestral gene order (a similar order that is ancestral in seed plants). We review the sequence of inversions that gave rise to this organization. We also explore global nucleotide substitution patterns in ferns versus those found in seed plants across plastid genes, and we review the high levels of RNA editing observed in fern plastomes.

Deciphering the origins of apomictic polyploids in the Cheilanthes yavapensis complex (Pteridaceae)

Deciphering species relationships and hybrid origins in polyploid agamic species complexes is notoriously difficult. In this study of cheilanthoid ferns, we demonstrate increased resolving power for clarifying the origins of polyploid lineages by integrating evidence from a diverse selection of biosystematic methods. The prevalence of polyploidy, hybridization, and apomixis in ferns suggests that these processes play a significant role in their evolution and diversification. Using a combination of systematic approaches, we investigated the origins of apomictic polyploids belonging to the Cheilanthes yavapensis complex. Spore studies allowed us to assess ploidy levels; plastid and nuclear DNA sequencing revealed evolutionary relationships and confirmed the putative progenitors (both maternal and paternal) of taxa of hybrid origin; enzyme electrophoretic evidence provided information on genome dosage in allopolyploids. We find here that the widespread apomictic triploid, Cheilanthes lindheimeri, is an autopolyploid derived from a rare, previously undetected sexual diploid. The apomictic triploid Cheilanthes wootonii is shown to be an interspecific hybrid between C. fendleri and C. lindheimeri, whereas the apomictic tetraploid C. yavapensis is comprised of two cryptic and geographically distinct lineages. We show that earlier morphology-based hypotheses of species relationships, while not altogether incorrect, only partially explain the complicated evolutionary history of these ferns.

The Utility of Nuclear gapCp in Resolving Polyploid Fern Origins

Abstract Although polyploidy is rampant in ferns and plays a major role in shaping their diversity, the evolutionary history of many polyploid species remains poorly understood. Nuclear DNA sequences can provide valuable information for identifying polyploid origins; however, remarkably few nuclear markers have been developed specifically for ferns, and previously published primer sets do not work well in many fern lineages. In this study, we present new primer sequences for the amplification of a portion of the nuclear gapCp gene (encoding a glyceraldehyde-3-phosphate dehydrogenase). Through a broad survey across ferns, we demonstrate that these primers are nearly universal for this clade. With a case study in cheilanthoids, we show that this rapidly evolving marker is a powerful tool for discriminating between autopolyploids and allopolyploids. Our results indicate that gapCp holds considerable potential for addressing species-level questions across the fern tree of life.

DNA barcoding exposes a case of mistaken identity in the fern horticultural trade.

Using cheilanthoid ferns, we provide an example of how DNA barcoding approaches can be useful to the horticultural community for keeping plants in the trade accurately identified. We use plastid rbcL, atpA, and trnG‐R sequence data to demonstrate that a fern marketed as Cheilanthes wrightii (endemic to the southwestern USA and northern Mexico) in the horticultural trade is, in fact, Cheilanthes distans (endemic to Australia and adjacent islands). Public and private (accessible with permission) databases contain a wealth of DNA sequence data that are linked to vouchered plant material. These data have uses beyond those for which they were originally generated, and they provide an important resource for fostering collaborations between the academic and horticultural communities. We strongly advocate the barcoding approach as a valuable new technology available to the horticulture industry to help correct plant identification errors in the international trade.

Toward a monophyletic Cheilanthes: The resurrection and recircumscription of Myriopteris (Pteridaceae)

Abstract The fern genus Cheilanthes (Pteridaceae) has perplexed taxonomists for more than two centuries. Complex patterns of evolution involving rampant morphological convergence, polyploidy, hybridization, and apomixis have made the taxonomy of this group especially difficult. Fortunately, recent phylogenetic analyses have helped to clarify relationships among cheilanthoid taxa. Based on these findings, we here formalize an updated taxonomy for one monophyletic clade comprising 47 primarily North and Central American taxa usually included in Cheilanthes. Because the type species of Cheilanthes (Cheilanthes micropteris) is only distantly related to this clade, we resurrect the genus Myriopteris to accommodate these taxa, and present a revised circumscription for the group, including 36 new combinations.

Patterns of Diversification in the Xeric-adapted Fern Genus Myriopteris (Pteridaceae)

Abstract Strong selective pressures imposed by drought-prone habitats have contributed to extensive morphological convergence among the 400 + species of cheilanthoid ferns (Pteridaceae). As a result, generic circumscriptions based exclusively on macromorphology often prove to be non-monophyletic. Ongoing molecular phylogenetic analyses are providing the foundation for a revised classification of this challenging group and have begun to clarify its complex evolutionary history. As part of this effort, we generated and analyzed DNA sequence data for three plastid loci (rbcL, atpA, and the intergenic spacer trnG-trnR) for the myriopterid clade, one of the largest monophyletic groups of cheilanthoid ferns. This lineage encompasses 47 primarily North and Central American taxa previously included in Cheilanthes but now placed in the recircumscribed genus Myriopteris. Here, we infer a phylogeny for the group and examine key morphological characters across this phylogeny. We also include a brief discussion of the three well-supported Myriopteris subclades, along with a review of reproductive mode and known ploidy levels for members of this early diverging lineage of cheilanthoid ferns.

Studies of Costa Rican Gelidiales (Florideophyceae). II. Two pacific taxa including Gelidium microglossum, n. sp.

Abstract: Detailed morphological and rbcL sequence analyses are presented for two species of Gelidium collected along the Pacific coast of Costa Rica. Although relatively well known in the tropical eastern Pacific, Gelidium sclerophyllum W. R. Taylor had previously been collected only once in Costa Rica. Four current G. sclerophyllum collections were found to have identical rbcL sequences and differed from a partial sequence for an isotype specimen at only one base pair. Phylogenetic analyses revealed that G. sclerophyllum and G. floridanum W. R. Taylor are geminate sister species. Development of the female reproductive system and cystocarps were observed to follow the usual patterns described for Gelidium species. Spermatangial development in G. sclerophyllum was also observed for the first time and revealed the cutting off of spermatia by transverse divisions as is characteristic of Gelidiales. The new species, Gelidium microglossum Grusz & Freshwater, was also collected and described. This is a small species with a prostrate habit, generally compressed axes of variable width, and clavate to obphyriform ultimate branches. Distinctive characteristics include spatulate tetrasporangial branchlets, medullary cells often forming a meshlike network, variably oriented rhizines, and an unusual attachment haptera structure. Phylogenetic analyses resolve G. microglossum within Gelidium, but placement within the genus remains uncertain.

Myriopteris windhamii sp. nov., a New Name For Cheilanthes villosa (Pteridaceae)

Abstract Recent studies examining the evolutionary relationships of species assigned to Cheilanthes (Pteridaceae) reveal that the genus is highly polyphyletic. To achieve a monophyletic generic classification of the 400+ taxa of cheilanthoid ferns, it is necessary to transfer species that are only distantly related to the type species (Cheilanthes micropteris) to other genera. One of these species is Cheilanthes villosa Davenp. ex Maxon, which needs to be reassigned to the genus Myriopteris. Because the epithet villosa is preoccupied in Myriopteris and there are no synonyms for this distinctive taxon, a new name is required. The species is herein renamed Myriopteris windhamii.