Monday, January 16, 2017

Monday reads

Another week, another suite of interesting papers to read.

I wrote about this one in a separate blog post:

Their relatively slow rates of molecular evolution, as well as frequent exposure to hybridization and introgression, often make it difficult to discriminate species of vascular plants with the standard barcode markers (rbcL, matK, ITS2). Previous studies have examined these constraints in narrow geographic or taxonomic contexts, but the present investigation expands analysis to consider the performance of these gene regions in discriminating the species in local floras at sites across Canada. To test identification success, we employed a DNA barcode reference library with sequence records for 96% of the 5108 vascular plant species known from Canada, but coverage varied from 94% for rbcL to 60% for ITS2 and 39% for matK. Using plant lists from 27 national parks and one scientific reserve, we tested the efficacy of DNA barcodes in identifying the plants in simulated species assemblages from six biogeographic regions of Canada using BLAST and mothur. Mean pairwise distance (MPD) and mean nearest taxon distance (MNTD) were strong predictors of barcode performance for different plant families and genera, and both metrics supported ITS2 as possessing the highest genetic diversity. All three genes performed strongly in assigning the taxa present in local floras to the correct genus with values ranging from 91% for rbcL to 97% for ITS2 and 98% for matK. However, matK delivered the highest species discrimination (~81%) followed by ITS2 (~72%) and rbcL (~44%). Despite the low number of plant taxa in the Canadian Arctic, DNA barcodes had the least success in discriminating species from this biogeographic region with resolution ranging from 36% with rbcL to 69% with matK. Species resolution was higher in the other settings, peaking in the Woodland region at 52% for rbcL and 87% for matK. Our results indicate that DNA barcoding is very effective in identifying Canadian plants to a genus, and that it performs well in discriminating species in regions where floristic diversity is highest.

Ornamental horticulture has been identified as an important threat to plant biodiversity and the major pathway for plant invasions worldwide. In this context, the family Cactaceae is particularly interesting and challenging for three main reasons-it is considered the fifth most threatened major taxonomic group in the world; several cactus species are amongst the most widespread and damaging invasive species; and Cactaceae is one of the most popular horticultural plant groups. Based on CITES trade data and the eleven main auction sites selling cacti on the internet we document a substantial global trade from and to almost all continents. While less than 20 % of this trade involves threatened species, and less than 3% involves known invasive species, many species are sold without a valid scientific name. Importantly, however, hardly any of the globally traded cacti are collected from wild populations. In order to provide an in-depth look at the dynamics of the industry, we surveyed the businesses involved in the cactus trade in South Africa (one of the main hotspots of cactus trade and invasions). Despite a large commercial network, all South African imports (of which only 15 % and 1.5 % were of species listed as threatened and invasive, respectively) came from the same source. We purchased seeds of every available species and, based on DNA-barcoding techniques, could only identify 24 % of the species to genus level. If trade restrictions are placed on the small proportion of cacti that are invasive and there is no major increase in harvesting of native populations, the commercial cactus horticultural trade will pose a negligible environmental threat. However, there are currently no effective methods for easily identifying which cacti are traded, and both the illicit harvesting of cacti from the wild and the informal trade in invasive taxa pose on-going conservation challenges.

This one made some news headlines:
Seafood mislabeling is common in both domestic and international markets. Previous studies on seafood fraud often report high rates of mislabeling (e.g. >70%), but these studies have been limited to a single sampling year, making it difficult to assess the impact of stricter governmental truth-in-labeling regulations. This study uses DNA barcoding to assess seafood mislabeling in Los Angeles over a four-year period. Sushi restaurants had a consistently high percentage of mislabeling (47%) from 2012 to 2015, yet mislabeling was not homogenous across species. Menu-listed halibut, red snapper, yellowfin tuna, and yellowtail had consistently high occurrences of mislabeling, whereas mislabeling of salmon and mackerel were typically low. All sampled sushi restaurants had at least one case of mislabeling. Mislabeling of sushi-grade fish from high-end grocers was also identified in red snapper, yellowfin tuna, and yellowtail, but at a slightly lower frequency (42%) than sushi restaurants. Results show that despite increased regulatory measures and media attention, seafood mislabeling continues to be prevalent. 

Fungal pathogens severely impact global food and fibre crop security. Fungal species that cause plant diseases have mostly been recognized based on their morphology. In general, morphological descriptions remain disconnected from crucially important knowledge such as mating types, host specificity, life cycle stages and population structures. The majority of current fungal species descriptions lack even the most basic genetic data that could address at least some of these issues. Such information is essential for accurate fungal identifications, to link critical metadata and to understand the real and potential impact of fungal pathogens on production and natural ecosystems. Because international trade in plant products and introduction of pathogens to new areas is likely to continue, the manner in which fungal pathogens are identified should urgently be reconsidered. The technologies that would provide appropriate information for biosecurity and quarantine already exist, yet the scientific community and the regulatory authorities are slow to embrace them. International agreements are urgently needed to enforce new guidelines for describing plant pathogenic fungi (including key DNA information), to ensure availability of relevant data and to modernize the phytosanitary systems that must deal with the risks relating to trade-associated plant pathogens.This article is part of the themed issue 'Tackling emerging fungal threats to animal health, food security and ecosystem resilience'.

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