Ecophysiological differentiation between life stages in filmy ferns (Hymenophyllaceae)

Nitta, Joel H.; Watkins, James E.; Holbrook, Noel Michelle; Wang, Tristan W.; Davis, Charles C.

doi:10.1007/s10265-021-01318-z

Cited by 14 publications

(8 citation statements)

References 74 publications

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“…There are other potential uses for TD‐PCR that can greatly encourage ecologists and pteridologists to study fern gametophytes within their topics of interest. First, because a very limited amount (1 mm 2 or less after dilution) of tissue is required for a single TD‐PCR reaction (Table 1 ), it is not necessary to destroy the entire gametophyte individual, which can therefore be reserved for other experiments, such as tests of desiccation tolerance (Watkins et al, 2007 ; Nitta et al, 2021 ). Second, compared with a DNA extraction approach, the equipment required for TD‐PCR is low tech, less expensive, smaller, and more portable, allowing for easy set‐up outside the lab, including in the field.…”

Section: Discussionmentioning

confidence: 99%

Integrating tissue‐direct PCR into genetic identification: An upgraded molecular ecology approach to survey fern gametophytes in the field

Chan

et al. 2022

Appl Plant Sci

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Premise The gametophytes of different fern species collected in the field can be difficult to distinguish because of their morphological similarities. Nonetheless, emerging molecular ecology techniques are starting to be used to tackle such limitations. Here, using case studies and a detailed protocol, we demonstrate a convenient methodology, tissue‐direct PCR (TD‐PCR), that foregoes a traditional DNA extraction and facilitates the identification of fern gametophytes, as well as enabling the elucidation of their natural distribution. Methods Based on updated plastome information, we designed a universal primer set targeting the trnL‐L‐F region, which is effective across extant ferns. We used this primer set to perform TD‐PCR on the case‐studied populations of Taiwanese Lomariopsis gametophytes, using the generated sequences for their identification. In the case study concerning the microhabitat preference of Vaginularia junghuhnii , we designed and used a taxon‐specific primer set. Results Compared with approaches requiring DNA extraction, the use of TD‐PCR with either universal or taxon‐specific primers could save significant time, money, labor, and research materials in the genetic identification of fern gametophytes. Discussion The use of modern genetic tools can aid in the identification of fern gametophytes. An updated TD‐PCR strategy not only facilitates the DNA‐based identification of gametophytes, but also promotes new avenues of research for investigating these plants in the field.

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Section: Discussionmentioning

confidence: 99%

Integrating tissue‐direct PCR into genetic identification: An upgraded molecular ecology approach to survey fern gametophytes in the field

Chan

et al. 2022

Appl Plant Sci

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“…To resolve species names, we used the taxastand R package (Nitta et al, 2021), which can account for differences in formatting of taxonomic authors ( e.g. , parenthetical basionym author present or absent) and perform fuzzy matching, which is needed to account for spelling errors or variations in author names.…”

Section: Methodsmentioning

confidence: 99%

An Open and Continuously Updated Fern Tree of Life

Nitta

Schuettpelz

Ramírez‐Barahona

et al. 2022

Preprint

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Ferns, with about 12,000 species, are the second most diverse clade of vascular plants after angiosperms. They have been the subject of numerous molecular phylogenetic studies, resulting in the publication of trees for every major clade and DNA sequences from nearly half of all species. Global fern phylogenies have been published periodically, but as molecular systematics research continues at a rapid pace, these become quickly outdated. Here, we develop a mostly automated, reproducible, open pipeline to generate a continuously updated fern tree of life (FTOL) from DNA sequence data available in GenBank. Our tailored sampling strategy combines whole plastomes (few taxa, many loci) with commonly sequenced plastid regions (many taxa, few loci) to obtain a global, species-level fern phylogeny with high resolution along the backbone and maximal sampling across the tips. We use an curated reference taxonomy to resolve synonyms in general compliance with the community-driven Pteridophyte Phylogeny Group I classification. The current FTOL includes 5,563 species, an increase of ca. 40% relative to the most recently published global fern phylogeny. Using an updated and expanded list of 65 fern fossil constraints, we find estimated ages for most families and deeper clades to be considerably older than earlier studies. FTOL and its accompanying datasets, including the fossil list and taxonomic database, will be updated on a regular basis and are available via a web portal (https://fernphy.github.io) and R packages, enabling immediate access to the most up-to-date, comprehensively sampled fern phylogeny. FTOL will be useful for anybody studying this important group of plants over a wide range of taxonomic scales, from smaller clades to the entire tree. We anticipate FTOL will be particularly relevant for macroecological studies at regional to global scales and will inform future taxonomic systems with the most recent hypothesis of fern phylogeny.

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“…Other studies have also built upon previous DNA barcoding results to better understand fern ecology. Nitta et al ( 2020b ) and Nitta et al ( 2021 ) both leveraged the DNA barcoding results of fern gametophytes on the islands of Mo'orea and Tahiti by Nitta et al ( 2017 ). Nitta et al ( 2020b ) scored morphological traits including morphotype and presence of hairs, glands, and gemmae in the gametophytes surveyed by Nitta et al ( 2017 ), then included these trait data in a comparison of the functional community structure of terrestrial vs. epiphytic fern communities.…”

Section: Other Ecological Studiesmentioning

confidence: 99%

“…Nitta et al ( 2021 ) took a unique approach that, to our knowledge, has not been used in any other study. To compare adaptations to water stress between terrestrial and epiphytic filmy ferns, they conducted desiccation tolerance assays on gametophytes of unknown species at the field station where they conducted their field survey, then later identified the individuals to species using DNA barcoding in the lab.…”

Section: Other Ecological Studiesmentioning

confidence: 99%

“…One of the most surprising results of this study was that the gametophytes of C. apiifolia , which had by far the broadest distribution compared to other species, were incapable of tolerating even slight amounts of desiccation. Nitta et al ( 2021 ) hypothesized that C. apiifolia gametophytes exploit small, well‐protected microhabitats at the bases of rocks and trees to avoid desiccation and thus attain a broader geographic range than conspecific sporophytes. This highlights the importance of microhabitat for understanding the distribution of fern gametophytes, which has also been supported by the finding of wide intraspecific variation in desiccation tolerance in vittarioid gametophytes mirroring variation in their environmental conditions (Stevens and Emery, 2015 ; Chambers and Emery, 2016 ; Chambers et al, 2017 ).…”

Section: Other Ecological Studiesmentioning

confidence: 99%

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Identifying cryptic fern gametophytes using DNA barcoding: A review

Nitta

Chambers

2022

Appl Plant Sci

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Ferns and lycophytes are unique among land plants in having sporophyte (diploid) and gametophyte (haploid) generations that can grow independently of each other. While most studies of fern ecology focus on the more visible sporophytic stage, the gametophyte is critically important, as it is the sexual phase of the life cycle. Yet, fern gametophytes have long been neglected in field studies due to their small size and cryptic morphology. DNA barcoding is a powerful method that can be used to identify field‐collected gametophytes to species and allow for detailed study of their ecology. Here, we review the state of DNA barcoding as applied to fern gametophytes. First, we trace the history of DNA barcoding and how it has come to be applied to fern gametophytes. Next, we summarize case studies that show how DNA barcoding has been used to better understand fern species distributions, gametophyte ecology, and community ecology. Finally, we propose avenues for future research using this powerful tool, including next‐generation DNA sequencing for in‐field identification of cryptic gametophytes.

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Ecophysiological differentiation between life stages in filmy ferns (Hymenophyllaceae)

Cited by 14 publications

References 74 publications

Integrating tissue‐direct PCR into genetic identification: An upgraded molecular ecology approach to survey fern gametophytes in the field

Integrating tissue‐direct PCR into genetic identification: An upgraded molecular ecology approach to survey fern gametophytes in the field

An Open and Continuously Updated Fern Tree of Life

Identifying cryptic fern gametophytes using DNA barcoding: A review

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