Thursday, February 23, 2017

From the inbox

Two symposia are held back-to-back in Uppsala 11-15 Sept, 2017: the 3rd Symposium on Ecological Networks and the 3rd Symposium on Molecular Analysis of Trophic Interactions.

Please note that registration is now open. To aim for a program where all attendants can participate with a talk or poster, we have opted for a two-stage process of registration. In the first stage open now, we ask you to submit a notice of interest and the abstract of a talk or poster. All themes from within the broad remits of the respective symposia are warmly welcome. In submitting the abstract, you are asked are to choose from whether you want to submit an oral presentation or a poster -- and whether (should your oral presentation not fit into the oral program) you will still be happy to present it as a poster. Once the final acceptance of abstracts is completed (31 May), you will be invited to update this notice of interest to a final conference registration, at which stage we will also ask you to deposit the conference fee.

Friday, February 17, 2017

Invasions continue

For all groups of organisms on all continents, the number of alien species has increased continuously during the last 200 years. For most groups, even the rate of introduction is highest recently. Barring mammals and fishes, there are no signs of a slow-down and we have to expect more new invasions in the near future.

Quite a sobering statement. However, it summarizes the results of a new study in which a large international group of researchers analysed alien species accumulation during the last centuries. They used more than 45,000 first occurrence records for more than 16,000 alien species.

The colleagues found that 37% of all recorded alien species have been introduced between 1970-2014 and thus recently. At its peak 585 new species were recorded within one year. This corresponds to more than 1.5 new alien species per day globally. This is likely an underestimate as the date of first record is not available for most alien species.

The trends of increase vary among taxonomic groups, which can be attributed to human activities. We observe a distinct increase in first record rates of vascular plants in the 19th century, probably as a result of the intensification of horticulture. The rates of new introductions of other organisms such as algae, molluscs or insects increased steeply after 1950. This is most likely a consequence of the ongoing globalisation of trade.

Although it was known that the number of alien species increased during the last decades, it remained unclear whether or not the accumulation of alien species has already reached a point of slow-down. Well, it clearly hasn't.

Tuesday, February 14, 2017

Climate change is not a future threat anymore

The rate of warming over the past 50 years (0.13 °C ± 0.03 °C per decade) is nearly twice that for the previous 50 years, and the global temperature by 2100 is likely to be 5–12 standard deviations above the Holocene mean. The effects of climate change on some species are already being witnessed, with changes documented in spatial distribution, abundance, demography, phenology and morphology. However, to date, no quantification of the number of species for which at least one population has been currently impacted by climate change, and the extent of these impacts, has been conducted, even for the better-studied taxa such as birds and mammals. 

In an international study published yesterday a team of international researchers present evidence of observed responses to recent climate changes in some 700 bird and mammal species. The researchers reviewed the observed impacts of climate change on birds and mammals using a total of 130 studies, making it the most comprehensive assessment to date on how climate change has affected our most well studied species.

Only 7% of mammals and 4% of birds for which the colleagues found evidence of a negative response are actually coded on the IUCN Red List of Threatened Species as threatened by ‘climate change and severe weather'. This severe under-reporting is also very likely in less studied species groups which represent the vast majority of life. The authors strongly argue for big improvements of assessments of the impacts of climate change on all species right now:

We need to communicate the impacts of climate change to the wider public and we need to ensure key decision makers know significant change needs to happen now to stop species going extinct. Climate change is not a future threat anymore.

Monday, February 13, 2017

Monday reads

Another week that begins with some interesting reads. I find it fascinating that every week I am able to find a good number of academic publications which use DNA-based identifications and/or DNA barcoding in particular. The field is now large enough and gained sufficient momentum that new discoveries and findings appear on a more or less daily basis. As a result every week I am in the fortunate situation to pick a few of many publications to highlight in the Monday reads:

Until now, the potential of NGS for the construction of barcode libraries or integrative taxonomy has been seldom realised. Here, we amplified (two-step PCR) and simultaneously sequenced (MiSeq) multiple markers from hundreds of fig wasp specimens. We also developed a workflow for quality control of the data. Illumina and Sanger sequences accumulated in the past years were compared. Interestingly, primers and PCR conditions used for the Sanger approach did not require optimisation to construct the MiSeq library. After quality controls, 87% of the species (76% of the specimens) had a valid MiSeq sequence for each marker. Importantly, major clusters did not always correspond to the targeted loci. Nine specimens exhibited two divergent sequences (up to 10%). In 95% of the species, MiSeq and Sanger sequences obtained from the same sampling were similar. For the remaining 5%, species were paraphyletic or the sequences clustered into divergent groups on the Sanger + MiSeq trees (>7%). These problematic cases may represent coding NUMTS or heteroplasms. Our results illustrate that Illumina approaches are not artefact-free and confirm that Sanger databases can contain non-target genes. This highlights the importance of quality controls, working with taxonomists and using multiple markers for DNA-taxonomy or species diversity assessment.

We compare the diversity of Chilean bees as understood from traditional taxonomy-based catalogues with that currently known from DNA barcodes using the BIN system informed by ongoing morphology-based taxonomy. While DNA barcode surveys of the Chilean bee fauna remain incomplete; it is clear that new species can readily be distinguished using this method and that morphological differentiation of distinct barcode clusters is sometimes very easy. We assess the situation in two genera in detail. In Lonchopria Vachal one "species" is readily separable into two BINs that are easily differentiated based upon male mandibular and genitalic morphology (characters generally used in this group) as well female hair patterns. Consequently, we describe Lonchopria (Lonchopria) heberti Packer and Ruz, new species. For Liphanthus Reed, a large number of new species has been detected using DNA barcoding and considerable additional traditional morphological work will be required to describe them. When we add the number of BINs (whether identified to named species or not) to the number of Chilean bee species that we know have not been barcoded (both described and new species under study in our laboratories) we conclude that the bee fauna of Chile is substantially greater than the 436 species currently known.

The escalating growth in illegal wildlife trade and anthropogenic habitat changes threaten the survival of pangolin species worldwide. All eight extant species have experienced drastic population size reductions globally with a high extinction risk in Asia. Consequently, forensic services have become critical for law enforcement, with a need for standardised and validated genetic methods for reliable identifications. The seizure of three tonnes of pangolin scales, believed to have originated from Africa, by Hong Kong Customs Authorities provided an opportunity for the application of DNA barcoding in identifying scales. Three mitochondrial DNA gene regions (COI, Cyt b, and D-loop) were amplified for a subsample of the confiscated material and compared with taxonomically verified references. All four African species were recovered as monophyletic with high interspecific uncorrected p-distance estimates (0.048-0.188) among genes. However, only three of four African species (Phataginus tricuspis, Phataginus tetradactyla, and Smutsia gigantea, originating from West and Central Africa) and one of four Asian species (Manis javanica from Southeast Asia) were identified among scales. Although the assignment of unknown scales to specific species was reliable, additional genetic tools and representative reference material are required to determine geographic origins of confiscated pangolin specimens.

Kampo is the general designation for traditional Japanese herbal medicines, which are recognized as official medicines and listed in the Japanese pharmacopoeia (JP). In most cases, it is difficult to identify the crude drug materials to species level using only traditional identification methods. We report the first online DNA barcode identification system, which includes standard barcode sequences from approximately 95% of the species recorded in the JP (16th edition). This tool provides users with basic information on each crude drug recorded in the JP, DNA barcoding identification of herbal material, and the standard operating procedure (SOP) from sampling to data analysis. ITS2 sequences (psbA-trnH was an alternative when ITS2 could not be amplified) were generated from a total of 576 samples to establish the database. An additional 100 samples (from different medicinal parts, from both single origin and multiple origins and from both retailers and the planting base) were identified using the system. A total of 78% of the test samples were identified as the species listed on their label. This system establishes a model platform for other pharmacopeias from countries like China, Korea, the US and the European Union, for the safe and effective utilization of traditional herbal medicines.

Friday, February 10, 2017

Potato psyllid detection with DNA barcoding

zebra chip disease
The potato psyllid (Bactericera cockerelli) is a hemipteran native to southern North America. It can significantly impact crop production, attacking a range of plants in the Solanaceae family including potato, tomato, eggplant, capsicum and chilli. The psyllid can also carry the bacterium Candidatus Liberibacter solanacearum, causing the ‘zebra chip’ disease in potato. The latter is a recently diagnosed disease of potatoes that causes discolouration of tubers which often becomes more clear during frying of potato chips. This disease causes very significant losses to potato farmers specializing on growth of tubers for chips or fries.

Bactericera cockerelli has been reported from Central America and New Zealand and has caused significant loss in potato yields during periods of major population increase. Maximum potato yield loss appears to be related to infestations occurring early in the growing season, or on crops with a significant leaf canopy by summer. The psyllids are not heat tolerant and it is thought they survive summer temperatures in crops with sufficient leaf canopy through summer to offer shade.

The Department of Agriculture and Food, Western Australia is currently undertaking surveillance in commercial crops and backyard gardens in the Perth area, following the suspect detection of potato psyllid in a commercial property north of the city and a couple of backyards. As this would be a first for Australia, authorities have been very vigilant in their reaction. The impacted properties have been quarantined and the movement of host material from these properties has been restricted. They also started DNA barcoding analysis to determine the exact species of the pest. The results are expected this week. Great to see that barcoding becomes state-of-the-art for such regulatory actions.

Monday, February 6, 2017

Monday reads

Welcome to another week -  a couple of interesting reads to get you started:

This study tested the effectiveness of COI barcodes for the discrimination of anuran species from the Amazon basin and other Neotropical regions. Barcodes were determined for a total of 59 species, with a further 58 species being included from GenBank. In most cases, distinguishing species using the barcodes was straightforward. Each species had a distinct COI barcode or codes, with intraspecific distances ranging from 0% to 9.9%. However, relatively high intraspecific divergence (11.4-19.4%) was observed in some species, such as Ranitomeya ventrimaculata, Craugastor fitzingeri, Hypsiboas leptolineatus, Scinax fuscomarginatus and Leptodactylus knudseni, which may reflect errors of identification or the presence of a species complex. Intraspecific distances recorded in species for which samples were obtained from GenBank (Engystomops pustulosus, Atelopus varius, Craugastor podiciferus, and Dendropsophus labialis) were greater than those between many pairs of species. Interspecific distances ranged between 11-39%. Overall, the clear differences observed between most intra- and inter-specific distances indicate that the COI barcode is an effective tool for the identification of Neotropical species in most of the cases analyzed in the present study.

In marine and estuarine benthic communities, the inventory and estimation of species richness are often hampered by the need for broad taxonomic expertise across several phyla. The use of DNA metabarcoding has emerged as a powerful tool for the fast assessment of species composition in a diversity of ecological communities. Here, we tested the amplification success of five primer sets targeting different COI-5P regions by 454 pyrosequencing to maximize the recovery of two simulated macrobenthic communities containing 21 species (SimCom1 and SimCom 2). Species identification was first performed against a compiled reference library of macrobenthic species. Reads with similarity results to reference sequences between 70% and 97% were then submitted to GenBank and BOLD to attempt the identification of concealed species in the bulk sample. The combination of at least three primer sets was able to recover more species than any primer set alone, achieving 85% of represented species in SimCom1 and 76% in SimCom2. Our approach was successful to detect low-frequency specimens, as well as concealed species, in the bulk sample, indicating the potential for the application of this approach on marine bioassessment and inventory, including the detection of "hidden" biodiversity that would hardly be possible based on morphology only.

Integrative taxonomy, a multi-disciplinary approach adding modern techniques to traditional morphology-based methods (e.g. molecular and morphological criteria), can play an important role in bioinvasion research to identify introduced taxa, discover pathways of introduction and inform authorities to control and prevent future introductions. The present study is the first on introduced populations of Callosciurus, Asiatic tree squirrels, known as potentially invasive species in Europe (Italy, Belgium and France). We combined molecular (mitochondrial DNA markers: CoxI, D-loop) and morphometric analysis on skulls, comparing them to the widest morphological and molecular datasets ever assembled for Callosciurus. Squirrels collected in Italy and Belgium share the same haplotypes and skull characteristics, but are conspicuously different from the French population in Antibes. Genetic data revealed close similarity between French squirrels and Pallas's squirrels, Callosciurus erythraeus, from Taiwan, China. Italian and Belgian squirrels formed an independent taxonomic lineage in genetic analyses, whose taxonomic rank needs further investigation. The morphological and morphometric characteristics of these 2 populations are, however, similar to known specimens assigned to Callosciurus erythraeus. These results may indicate a common origin for the populations found in Belgium and Italy. In contrast, French specimens suggest an independent introduction event of squirrels originating from Asia.

The E. dispunctella and E. triseriatella complexes sensu Traugott-Olsen are merged. The newly delineated E. dispunctella complex is re-defined and diagnosed. Until now, a total of 64 species has been assigned to this species complex. The taxonomy of the constituent species has been obscure owing to their identities based on unvalidated traits, in particular subtle differences on branching points of forewing veins. The taxonomy of the E. dispunctella complex is revised on the basis of new material, new and reevaluated information obtained from morphology and biology, as well as from the standard barcode region of COI, with at least partial barcode data derived from 194 recently collected specimens and 33 holotypes. As a result, the number of species considered valid is markedly reduced, with only 19 species now recognized. The following 43 new synonymies are established: Elachista dispunctella (Duponchel, 1843) = E. cahorsensis Traugott-Olsen, 1992, syn. nov., E. imbi Traugott-Olsen, 1992, syn. nov., E. karsholti Traugott-Olsen, 1992, syn. nov., E. mannella Traugott-Olsen, 1992, syn. nov., E. multipunctella Traugott-Olsen, 1992, syn. nov., E. pocopunctella Traugott-Olsen, 1992, syn. nov., E. povolnyi Traugott-Olsen, 1992, syn. nov., E. punctella Traugott-Olsen, 1992, syn. nov., E. hallini Traugott-Olsen, 1992, syn. nov., E. intrigella Traugott-Olsen, 1992, syn. nov., E. skulei Traugott-Olsen, 1992 and E. nielspederi Traugott-Olsen, 1992, syn. nov.; E. tribertiella Traugott-Olsen, 1985 = E. toveella Traugott-Olsen, 1985, syn. nov., E. baldizzonella Traugott-Olsen, 1985, syn. nov., E. veletaella Traugott-Olsen, 1992, syn. nov., E. bazaella Traugott-Olsen, 1992, syn. nov. and E. louiseae Traugott-Olsen, 1992, syn. nov.; E. parvula Parenti, 1978 = E. minusculella Traugott-Olsen, 1992, syn. nov. and E. blancella Traugott-Olsen, 1992, syn. nov.; E. maboulella Chr├ętien, 1915 = E. catalunella Traugott-Olsen, 1992, syn. nov., E. gerdmaritella Traugott-Olsen, 1992, syn. nov. and E. gielisi Traugott-Olsen, 1992, syn. nov.; E. glaseri Traugott-Olsen, 1992 = E. rikkeae Traugott-Olsen, 1992, syn. nov., E. totanaensis Traugott-Olsen, 1992, syn. nov., E. olemartini Traugott-Olsen, 1992, syn. nov., E. bengtssoni Traugott-Olsen, 1992, syn. nov., E. senecai Traugott-Olsen, 1992, syn. nov., E. wadielhiraensis Traugott-Olsen, 1992, syn. nov., E. rissaniensis Traugott-Olsen, 1992, syn. nov. and E. michelseni Traugott-Olsen, 1992, syn. nov.; E. hispanica Traugott-Olsen, 1992 = E. vivesi Traugott-Olsen, 1992, syn. nov., E. cuencaensis Traugott-Olsen, 1992, syn. nov., E. vanderwolfi Traugott-Olsen, 1992, syn. nov., E. amparoae Traugott-Olsen, 1992, syn. nov., E. varensis Traugott-Olsen, 1992, syn. nov., E. luqueti Traugott-Olsen, 1992, syn. nov., E. occidentella Traugott-Olsen, 1992, syn. nov. and E. clintoni Traugott-Olsen, 1992, syn. nov.; E. berndtiella Traugott-Olsen, 1985 = E. casascoensis Traugott-Olsen, 1992, syn. nov.; E. triseriatella Stainton, 1854 = E. contisella Chr├ętien, 1922, syn. nov., E. gregori Traugott-Olsen, 1988, syn. nov., and E. lerauti Traugott-Olsen, 1992, syn. nov.; E. elsaella Traugott-Olsen, 1988 = E. svenssoni Traugott-Olsen, 1988, syn. nov.; E. galactitella (Eversmann, 1844) = E. madridensis Traugott-Olsen, 1992, syn. nov. E. deresyensis Traugott-Olsen, 1988 is resurrected as a valid species, stat. rev. Evidence from DNA barcodes suggests that there may exist further species, but in the absence of distinct morphological differences, they are not formally described as new.

Friday, February 3, 2017

From the inbox: Metabarcoding Spring School 2017

We are pleased to announce that this year the seventh DNA Metabarcoding Spring School will held in Porto (Portugal) and will be organized in collaboration with Simon Jarman and the CBIO Research Center in Biodiversity and Genetic resources. The DNA metabarcoding spring school will be held from May 1st to 5th, 2017.

The school will be divided in two parts:
Two days of lectures, May 1st and 2nd.
Three days of practicals

All the lectures and the practicals will be taught in English
The number of participants in the lecture portion is not limited, but registration is mandatory.

The number of participants in the practical portion is limited to 24.

Candidates can apply for the school by sending an email. The email must contain a brief curriculum vitae and a short letter of motivation. For applicants wishing to participate in the practical sessions, we request a more complete letter indicating how your research will benefit from DNA metabarcoding and what you are hoping to learn from this school. As part of the course, each participant in the practical portion will give a flash talk (5 minutes) about your research and how it is related to DNA metabarcoding.

More information you'll find here.