Unfurling Fern Biology in the Genomics Age

Twenty-first century technology is addressing many of the questions posed by 20th-century biology. Although the new approaches, especially those involving genomic data and bioinformatic tools, were first applied to model organisms, they are now stretching across the tree of life. Here, we review some recent revelations in the ferns. We first examine how DNA sequence data have contributed to our understanding of fern phylogeny. We then address evolution of the fern plastid genome, including reports of high levels of RNA editing. Recent studies are also shedding light on the evolution of fern nuclear genomes. Initial analyses of genomic data suggest that despite their very high chromosome numbers homosporous ferns may have experienced relatively few rounds of genome duplication. Genomic data are enabling researchers to examine speciation rates and the mechanisms underlying the formation of new fern species. We also describe genetic tools that have been used to study gene function and development in ferns. Recent findings in fern biology are providing insights that are not only pertinent to this major component of the land flora but can also help to provide an improved evolutionary context for research on flowering plants

Extreme Makeover: Fern Edition

With a few exceptions, all plants have chloroplasts. Chloroplasts are the organelles responsible for photosynthesis in plants. Interestingly, chloroplasts have their own genome -- called a plastome -- which is separate from the nuclear genome. The genetic composition of ferns, gymnosperm, and angiosperm plastomes are remarkably similar, revealing very little change over evolutionary time. There are however a few notable exceptions to the apparent stability of the plastome. A few lineages of both angiosperm and gymnosperm show dramatically higher rates of mutation and genetic rearrangement than those of their relatives, suggesting major genome destabilization. Vittariods are a group of ferns that live on the trunks and in the branches of trees in forests. Vittariods are so unique among ferns in structure and life cycle that they have long been thought to be their own family, but recent genetic research has shown they reside within the genus Adiantum. Vittariods bear little resemblance to their closest relatives and appear to have quite rapidly diverged from them

Teaching Species

A clear understanding of the term species is fundamental to the subject of evolution. However, introductory textbooks often fail to address this topic until one of the later chapters, after having used the term species in all preceding chapters. Furthermore, definitions of terms critical to a clear understanding of this subject are often vague or absent in chapters on species concepts. We feel the popular notion of a species problem has been unnecessarily inflated by this less-than-effective educational approach. Clearly addressing this essential subject at the beginning of a course on evolution will prepare students to learn the details and complexities of evolution. Here we provide the background for an alternative approach to this foundational topic, followed by an outlined lesson plan. We emphasize early introduction of this subject in texts and courses using unambiguous terminology and including the historical development of species concepts

Atomic vapor-based high efficiency optical detectors with photon number resolution

We propose a novel approach to the important fundamental problem of detecting weak optical fields at the few photon level. The ability to detect with high efficiency (>99%), and to distinguish the number of photons in a given time interval is a very challenging technical problem with enormous potential pay-offs in quantum communications and information processing. Our proposal diverges from standard solid-state photo-detector technology by employing an atomic vapor as the active medium, prepared in a specific quantum state using laser radiation. The absorption of a photon will be aided by a dressing laser, and the presence or absence of an excited atom will be detected using the ``cycling transition'' approach perfected for ion traps. By first incorporating an appropriate upconversion scheme, our method can be applied to a wide variety of optical wavelengths.Comment: 4 pages, 2 figure

Do Genetic Differences Explain the Ability of an Alkaline Shrub to Grow in Both Uplands and Wetlands?

The hydrophyte Allenrolfea occidentalis (S. Watson) Kuntze (iodinebush) is a halophytic shrub of the arid southwest that is listed as a facultative wetland species on the National Wetland Plant List. This rating means that the species is usually a hydrophyte but occasionally is found in uplands. We tested for genetic (ecotypic) differences between plants sampled from wetlands versus uplands. We used the technique of genotyping by sequencing to generate data from 132 plants from 30 locations representing both wetland and upland occurrences for over 1300 loci. Analyses indicated that the strongest genetic signal is from differences in geographic distribution: samples that are in close geographic proximity tend to be more similar genetically regardless of whether they occur in wetland or upland locations. We detected no effect of habitat on overall genetic structure, and we found only 2 (of the 1381) loci with a positive association between genotype and habitat; in both cases the association was very weak. We infer that A. occidentalis occurrences near or in wetlands are not influenced by significant differences in genetics, and we find no evidence for wetland and upland ecotypes of this species

Genomic Variation of Introduced \u3ci\u3eSalvinia minima\u3c/i\u3e in Southeastern United States

Common salvinia, Salvinia minima Baker (Salviniaceae), is a small, floating aquatic fern native to Central and South America that has invaded fresh water bodies in southeastern United States since the 1930s. We examined genetic variation across much of the introduced range of this species in the United States using codominant RAD-seq markers. Data from over 600 variable loci showed a reduction in heterozygosity from east to west in addition to a corresponding trend in assignment of samples to one of two genetic groups. Our data are consistent with previous published work and with the hypothesis that common salvinia had a single introduction on the east end of its current range in the United States. From there it migrated westward, losing genetic diversity during this spread. The data are also consistent with sexual reproduction, although we are unable to estimate the extent of this relative to asexual spreading. Future genetic work should include sampling from the native range to help determine the original sources of North American common salvinia

How Many Tree Species of Birch Are in Alaska? Implications for Wetland Designations

Wetland areas are critical habitats, especially in northern regions of North America. Wetland classifications are based on several factors, including the presence of certain plant species and assemblages of species, of which trees play a significant role. Here we examined wetland species of birch (Betula) in North America, with a focus on Alaska, and the use of birche tree species in wetland delineation. We sampled over 200 trees from sites, including Alaska, Alberta, Minnesota, and New Hampshire. We used genetic data from over 3000 loci detected by restriction site associated DNA analysis. We used an indirect estimate of ploidy based on allelic ratios and we also examined population genetic structure. We find that inferred ploidy is strongly associated with genetic groupings. We find two main distinct groups; one found throughout most of Alaska, extending into Alberta. This group is probably attributable to Betula kenaica, Betula neoalaskana, or both. This group has a diploid genetic pattern although this could easily be a function of allopolyploidy. The second major genetic group appears to extend from Eastern North America into parts of southeastern Alaska. This group represents Betula papyrifera, and is not diploid based on allelic ratios. Published chromosome counts indicate pentaploidy. Because B. papyrifera is the only one of the above species that is distinctly associated with wetland habitats, our findings indicate that tree species of birch found in most parts of Alaska are not reliable indicators of wetland habitats. These results help to support stronger wetland ratings assigned to the tree species of birch for delineation purposes

Investigating Human Impact in the Environment With Faded Scaffolded Inquiry Supported by Technologies

Teaching science as inquiry is advocated in all national science education documents and by leading science and science teaching organizations. In addition to teaching science as inquiry, we recognize that learning experiences need to connect to students’ lives. This article details how we use a sequence of faded scaffolded inquiry supported by technologies to engage students meaningfully in science connected to their lives and schoolyards. In this approach, more teacher guidance is provided earlier in the inquiry experiences before this is faded later in the sequence, as students are better prepared to complete successful inquiries. The sequence of inquiry experiences shared in this article offers one possible mechanism for science teaching supported by technologies as an exemplar for translating teaching “science as inquiry” into practice

Complete Nucleotide Sequence of the Chloroplast Genome from a Leptosporangiate Fer, Adiantum capillus-veneris L.

We determined the complete nucleotide sequence of the chloroplast genome of the leptosporangiate fern, Adiantum capillus-veneris L. (Pteridaceae). The circular genome is 150,568 bp, with a large single-copy region (LSC) of 82,282 bp, a small-single copy region (SSC) of 21,392 bp and inverted repeats (IR) of 23,447 bp each. We compared the sequence to other published chloroplast genomes to infer the location of putative genes. When the IR is considered only once, we assigned 118 genes, of which 85 encode proteins, 29 encode tRNAs and 4 encode rRNAs. Four protein-coding genes, all four rRNA genes and six tRNA genes occur in the IR. Most (57) putative protein-coding genes appear to start with an ATG codon, but we also detected five other possible start codons, some of which suggest tRNA editing. We also found 26 apparent stop codons in 18 putative genes, also suggestive of RNA editing. We found all but one of the tRNA genes necessary to encode the complete repertoire required for translation. The missing trnK gene appears to have been disrupted by a large inversion, relative to other published chloroplast genomes. We detected several structural rearrangements that may provide useful information for phylogenetic studies