A taxonomic and molecular survey of the pteridophytes of the Nectandra Cloud Forest Reserve, Costa Rica

Abstract

Floristic surveys are crucial to the conservation of biodiversity, but the vast majority of such surveys are limited to listing species names, and few take into account the evolutionary history of species. Here, we combine classical taxonomic and molecular phylogenetic (DNA barcoding) approaches to catalog the biodiversity of pteridophytes (ferns and lycophytes) of the Nectandra Cloud Forest Reserve, Costa Rica. Surveys were carried out over three field seasons (2008, 2011, and 2013), resulting in 176 species representing 69 genera and 22 families of pteridophytes. Our literature survey of protected areas in Costa Rica shows that Nectandra has an exceptionally diverse pteridophyte flora for its size. Plastid rbcL was selected as a DNA barcode marker and obtained for >95% of pteridophyte taxa at this site. Combined molecular and morphological analyses revealed two previously undescribed taxa that appear to be of hybrid origin. The utility of rbcL for species identification was assessed by calculating minimum interspecific distances and found to have a failure rate of 18%. Finally we compared the distribution of minimum interspecific rbcL distances with two other areas that have been the focus of pteridophyte molecular surveys: Japan and Tahiti. The comparison shows that Nectandra is more similar to Japan than Tahiti, which may reflect the biogeographic history of these floras.

Life barcoded by DNA barcodes

“…So far, the nuclear-encoded ribosomal internal transcribed spacer (ITS) region and the chloroplast intergenic spacer trnH-psbA have emerged as candidates for barcoding plants, followed by others including coding sequences from plastid Since a standard plant barcode has been complicated by the trade-off that arises between the high variability of sequences and high conservation of primers, it is then recommended to simultaneously utilize more than one marker as a compromise that best matches the barcoding criteria (Lahaye et al 2008). As a consequence, combinations of multiple barcode markers were shown to improve the ability to classify plants maximally by 60% when compared to a single barcode, which has persuaded researchers out of botany to take the same measures when barcoding other organisms (Group 2009;Li et al 2021;Nitta et al 2020;Zhang et al 2013).…”

The Expanding Role of DNA Barcodes: Indispensable Tools for Ecology, Evolution, and Conservation

“…Forest monitoring plots, such as the Smithsonian's Forest Global Earth Observatories (ForestGEO) and the National Science Foundation's Long Term Ecological Research (LTER) sites, are rich resources because they have well-verified identifications, vouchered collections, and individually tagged trees that can be revisited by botanists if necessary [43][44][45][46]. Even if no specific monitoring plots have been established, many studies have generated DNA barcode libraries for specific habitats [47], plant communities [48], or regional taxa [49][50][51] and are thereby expanding the global plant genetic library. Individual taxonomists are also generating DNA barcodes for specific groups of plants as either standard markers (e.g., [52][53][54][55]) or as an offshoot of their basic molecular phylogenetic investigations aimed at understanding evolutionary relationships.…”

Identifying cryptic fern gametophytes using DNA barcoding: A review

“…The trnL‐F spacer performed well in terms of both amplification success and power to discriminate species in the ferns of Europe (de Groot et al, 2011 ) and vittarioid ferns in East Asia (Chen et al, 2013 ). Recently, Nitta et al ( 2020a ) compared rates of interspecific variation in rbcL in three fern floras (French Polynesia, Costa Rica, and Japan) and found that this marker had a higher identification failure rate in continental areas (Costa Rica and Japan) compared with the isolated islands of French Polynesia, which they attributed to the possibility of higher rates of in situ speciation in continental regions vs. long‐distance dispersal in remote oceanic islands. This highlights the need to consider biogeography in DNA barcoding of fern gametophytes, at least when the provenance of specimens is known.…”