Tuesday, January 17, 2017

From the Inbox: BioSyst.EU conference Barcoding Symposium

Dear colleagues, I would like to draw your attention to the upcoming BioSyst.EU conference in August 2017 in Sweden, Gothenburg, where we will organize a half-day symposium on “DNA-barcoding and the future of biodiversity monitoring”, with a special focus on metabarcoding approaches for biodiversity monitoring. We are aiming at bringing together the experts on this topic and would like to cover as many aspects as possible in a balanced fashion - given the time limitation for approx. 1 plenary talk and 8 regular talks. There is of course room for poster contributions as well. Registration for presentations closes at February 1st. It would be great if you let us know if you are interested in bringing the audience up to date with the latest findings from your field of research. 

Application for presenters is done by sending an e-mail . The e-mail should contain the following information: -Which symposium you would prefer to be assigned to -The title of your presentation -If it is an Oral presentation or Poster -An abstract in either doc/pdf/txt -format. Please find further details on the conference here.

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'.

Wednesday, January 11, 2017

Reference Library for Canadian vascular plants

Just finished reading a paper by some of my colleagues here at the institute. They summarize the results of a large study which employed a DNA barcode library for the vascular plants of Canada to determine the method with the best species resolution and the barcode marker (rbcL, matK, ITS2) with the highest performance. 

The colleagues build a barcode reference library for 4923 of the 5108 species of non-hybrid origin (~96%) with coverage for all 1153 genera and 171 families in the Database of Vascular Plants of Canada. Of course coverage for the three markers differs. The rbcL dataset is most complete with almost 94% coverage. The ITS2 library includes almost 60% of the species and the matK dataset 39%. Overall, 78% of the species possess records for some combination of two markers, but only 1074 species (22%) have data for all three. Despite such gaps the results are more than promising and certainly very impressive. For almost all vascular plants in Canada the library contains barcode sequences for at least one marker and given their individual effectiveness it is possible to make species and genus assignments at a considerable level:

Analyses based on this library indicate that any one of the three barcode regions is very effective (>90%) in delivering a generic assignment while species resolution is often possible with ITS2 (72%) and matK (80%). BLAST demonstrated higher performance than mothur in assigning specimens to a species in all datasets, including those at a community level and for 1074 species with data for all three barcode regions. The higher performance of BLAST reflects its consideration of indel variation and absolute length of the marker, leading matK to deliver the highest resolution. Although ITS2 showed slightly lower performance, it has two important advantages; its short length makes it suitable for HTS-based applications, and it is readily recovered from diverse taxa, including vascular plants and fungi.

Tuesday, January 10, 2017

Saving two birds with one stone

Across the planet, poachers have reached into the last remote habitats to harvest wildlife populations used for clothing, eaten, or kept as pets in faraway cities. In some cases, the traded organisms have escaped and are now thriving in their introduced habitats.

The exhaustive international trade of wildlife has pushed many species to the brink of extinction. Coincidentally, many of the same species have been introduced to urban centres or wilderness areas outside their natural ranges. Ironically, a recent study shows that these introduced populations may provide hope for these threatened species

A research team from Hong Kong and Australia identified 49 globally threatened species (listed by the International Union for the Conservation of Nature as Vulnerable, Endangered, or Critically Endangered) which have established introduced populations outside their native distribution. These include amphibians, reptiles, mammals, and birds, as well as insects and plants, with introduced populations found on all continents except Antarctica.

One example is the Yellow-crested Cockatoo (Cacatua sulphurea), a species in peril due to extensive pet trade. Many of these pet birds were accidentally or deliberately released in their new environments and as a result about 200 of them, an estimated 10% of the bird's global population, are now found on Hong Kong Island although the native range of them lies in Indonesia and East Timor.

Reintroduction of this species to its native range in Indonesia and East Timor could help to buffer populations there, which are rapidly declining due to poaching.

In addition to the reintroduction of birds to their native range harvesting of introduced cockatoos in Hong Kong could offset pressure on their native counterparts. Both approaches could also eliminate threats the introduced population might pose to native species in its introduced environment, such as monopolising nesting sites and triggering population declines of local birds.

Combined, augmenting declining populations in their native ranges and eliminating the threats to native ecosystems could save two birds with one stone. This creative tactic could be essential to save species imperiled by wildlife trade as well as eliminate threats the same species pose in their adopted territories.

Monday, January 9, 2017

Monday reads

A very happy New Year to all readers out there. I am back to posting after a brief holiday hibernation. Lots of interesting papers have been published in the last few weeks:

DNA barcoding is a global initiative for species identification through sequencing of short DNA sequence markers. Sequences of two loci, ITS and LSU, were generated as barcode data for all (ca. 9k) yeast strains included in the CBS collection, originally assigned to ca. 2 000 species. Taxonomic sequence validation turned out to be the most severe bottleneck due to the large volume of generated trace files and lack of reference sequences. We have analysed and validated CBS strains and barcode sequences automatically. Our analysis shows that there were 6 and 9.5 % of CBS yeast species that could not be distinguished by ITS and LSU, respectively. Among them, ∼3 % were indistinguishable by both loci. Except for those species, both loci were successfully resolving yeast species as the grouping of yeast DNA barcodes with the predicted taxonomic thresholds was more than 90 % similar to the grouping with respect to the expected taxon names. The taxonomic thresholds predicted to discriminate yeast species were 98.41 % for ITS and 99.51 % for LSU. To discriminate current yeast genera, thresholds were 96.31 % for ITS and 97.11 % for LSU. Using ITS and LSU barcodes, we were also able to show that the recent reclassifications of basidiomycetous yeasts in 2015 have made a significant improvement for the generic taxonomy of those organisms. The barcodes of 4 730 (51 %) CBS yeast strains of 1 351 (80 %) accepted yeast species that were manually validated have been released to GenBank and the CBS-KNAW website as reference sequences for yeast identification.

Inflow of matter and organisms may strongly affect the local density and diversity of organisms. This effect is particularly evident on shores where organisms with aquatic larval stages enter the terrestrial food web. The identities of such trophic links are not easily estimated as spiders, a dominant group of shoreline predator, have external digestion. We compared trophic links and the prey diversity of spiders on different shore types along the Baltic Sea: on open shores and on shores with a reed belt bordering the water. A priori, we hypothesized that the physical structure of the shoreline reduces the flow between ecosystem and the subsidies across the sea-land interface. To circumvent the lack of morphologically detectable remains of spider prey, we used a combination of stable isotope and molecular gut content analyses. The two tools used for diet analysis revealed complementary information on spider diets. The stable isotope analysis indicated that spiders on open shores had a marine signal of carbon isotopes, while spiders on reedy shores had a terrestrial signal. The molecular analysis revealed a diverse array of dipteran and lepidopteran prey, where spiders on open and reedy shores shared a similar diet with a comparable proportion of chironomids, the larvae of which live in the marine system. Comparing the methods suggests that differences in isotope composition of the two spider groups occurred because of differences in the chironomid diets: as larvae, chironomids of reedy shores likely fed on terrestrial detritus and acquired a terrestrial isotope signature, while chironomids of open shores utilized an algal diet and acquired a marine isotope signature. Our results illustrate how different methods of diet reconstruction may shed light on complementary aspects of nutrient transfer. Overall, they reveal that reed belts can reduce connectivity between habitats, but also function as a source of food for predators.

Amphibians are one of the most threatened vertebrate classes, yet at the same time new species are being described every year, demonstrating that the number of existing species is grossly underestimated. In groups such as amphibians, with high extinction rates and poorly known species boundaries, DNA barcoding is a tool that can rapidly assess genetic diversity and estimate species richness for prioritizing conservation decisions. However, reliable recovery of the 5' region of the cytochrome c oxidase subunit 1 (COI) gene is critical for the ongoing effort to gather DNA barcodes for all amphibian species. Here we provide new PCR conditions and tested new primers that increase the efficiency of barcode recovery in amphibians. We found that a low extension temperature for PCR cycles significantly improves the efficiency of amplification for all combinations of primers. Combining low PCR extension temperature and primers AnF1 + AnR1 we were able to recover COI sequences for 100% of the species analyzed (N=161), encompassing ~15% of the species known from Brazil (representing 77 genera and 23 families), which is an important improvement over previous studies. The preliminary assessment of species diversity suggested that number of species might be underestimated by about 25%. We conclude that DNA barcoding is an efficient, simple, and standardized protocol for identifying cryptic diversity in amphibians and advocate for its use in biodiversity inventories and across widespread populations within known species.

The Antarctic marine environment is a diverse ecosystem currently experiencing some of the fastest rates of climatic change. The documentation and management of these changes requires accurate estimates of species diversity. Recently, there has been an increased recognition of the abundance and importance of cryptic species, i.e. those that are morphologically identical but genetically distinct. This article presents the largest genetic investigation into the prevalence of cryptic polychaete species within the deep Antarctic benthos to date. We uncover cryptic diversity in 50% of the 15 morphospecies targeted through the comparison of mitochondrial DNA sequences, as well as 10 previously overlooked morphospecies, increasing the total species richness in the sample by 233%. Our ability to describe universal rules for the detection of cryptic species within polychaetes, or normalization to expected number of species based on genetic data is prevented by taxon-specific differences in phylogenetic outputs and genetic variation between and within potential cryptic species. These data provide the foundation for biogeographic and functional analysis that will provide insight into the drivers of species diversity and its role in ecosystem function.

DNA barcoding has been used extensively to solve taxonomic questions and identify new species. Neotropical fishes are found in a wide variety of shapes and sizes, with a large number of species yet to be described, many of which are very difficult to identify. Characidae is the most species-rich family of the Characiformes, and many of its genera are affected by taxonomic uncertainties, including the widely-distributed, species-rich genus Astyanax. In this study, we present an extensive analysis of Astyanax covering almost its entire area of occurrence, based on DNA barcoding. The use of different approaches (ABGD, GMYC and BIN) to the clustering of the sequences revealed ample consistency in the results obtained by the initial cutoff value of 2% divergence for putative species in the Neighbor-Joining analysis using the Kimura-2-parameter model. The results indicate the existence of five Astyanax lineages. Some groups, such as that composed by the trans-Andean forms, are mostly composed of well-defined species, and in others a number of nominal species are clustered together, hampering the delimitation of species, which in many cases proved impossible. The results confirm the extreme complexity of the systematics of the genus Astyanax and show that DNA barcoding can be an useful tool to address these complexes questions.

The sacoglossan sea slug species complex Plakobranchus ocellatus is a common algivore throughout the tropical Pacific, including the Hawaiian Islands. Plakobranchus ocellatus is kleptoplastic - it sequesters and retains algal chloroplasts - a characteristic that can be exploited to molecularly characterize diminutive bryopsidalean algae that are typically difficult to locate, collect, and identify. Previous DNA barcode analyses of both P. ocellatus and its kleptoplasts have been conducted primarily in the western Pacific and have only minimally sampled the most eastern populations in the Hawaiian Islands. Using two chloroplast markers rbcL and tufA, kleptoplast samples from an O'ahu population of P. ocellatus were amplified and cloned to identify their algal sources. Plakobranchus ocellatus sequester chloroplasts from up to 11 bryopsidalean algal species, all but one being diminutive in thallus size. Notably, eight of the detected algal species were new records to the Hawaiian Islands. A sequestration preference study demonstrated that the O'ahu population of P. ocellatus preferentially sequesters chloroplasts from diminutive, epilithic taxa. Using coxI barcoding of P. ocellatus we showed the O'ahu population to be part of a clade that includes sequences from the neighboring island Maui, Australia, and the Philippines. The use of P. ocellatus as a novel sampling tool allows the exploration of the green algal community diversity and composition at a fine scale. 

Friday, December 16, 2016

Thursday, December 15, 2016

New discoveries at Dragon's breath

I am always excited to see reports about new discoveries from the deep sea. Today I saw a news release on a study published in Scientific Reports:

The Southwest Indian Ridge is the longest section of very slow to ultraslow-spreading seafloor in the global mid-ocean ridge system, but the biogeography and ecology of its hydrothermal vent fauna are previously unknown. We collected 21 macro- and megafaunal taxa during the first Remotely Operated Vehicle dives to the Longqi vent field at 37° 47′S 49° 39′E, depth 2800 m

Longqi also known as 'Dragon's Breath' lies 2000 km southeast of Madagascar and the research team explored an area the size of a football stadium on the ocean floor, pinpointing the locations of more than a dozen mineral spires known as 'vent chimneys'. These spires, many of which rise more than two storeys above the seabed, are rich in copper and gold that is now attracting interest for future seafloor mining. However, the spires are also populated with deep-sea animals, nourished by hot fluids gushing out of the vent chimneys.

The expedition, which took place in November 2011, provides a record of what lives on the ocean floor in the area, which is licensed for mineral exploration by the International Seabed Authority of the United Nations, before any mining surveys are carried out. 

The deep-sea animals that are so far only known from Longqi include: a species of hairy-chested 'Hoff' crab, closely related to 'Hoff' crabs at Antarctic vents; two species of snail and a species of limpet; a species of scaleworm; and another species of deep-sea worm. Apart from one species of snail, which has been given the scientific name Gigantopelta aegis, most have not yet been formally described. By the way, the colleagues used DNA barcoding (without using the term) to help with these discoveries.

We can be certain that the new species we've found also live elsewhere in the southwest Indian Ocean, as they will have migrated here from other sites, but at the moment no-one really knows where, or how well-connected their populations are with those at Longqi. Our results highlight the need to explore other hydrothermal vents in the southwest Indian Ocean and investigate the connectivity of their populations, before any impacts from mineral exploration activities and future deep-sea mining can be assessed.

The researchers also found species at Longqi that are known at other vents far away in other oceans. Another new species of scaleworm lives at vents on the East Scotia Ridge in the Antarctic, 6,000 km away, while a species of ragworm lives at vents in the eastern Pacific, more than 10,000 km away.

Finding these two species at Longqi shows that some vent animals may be more widely distributed across the oceans than we realised.