Friday, July 29, 2016

7th International Barcode of Life Conference website

The website for the 7th International Barcode of Life Conference is up and running. Have a look, most keynote speakers are already up and a draft program as well. Impressive!  Registration starts in December.

Wednesday, July 27, 2016

Environmental tests on livestock drugs

Dung pat with a specific concentration of ivermectin. Credit: UZH
The authorization of veterinary medicinal products requires assessments for nontarget effects in the environment. Numerous field studies have assessed these effects on dung organisms. However, few studies have examined effects on soil-dwelling organisms, which might be exposed to veterinary medicinal product residues released during dung degradation.

Drugs for livestock can harm beneficial organisms that break down dung. Therefore newly developed medical substances need to be tested on single species in the lab. The problem is that sensitivity to toxic substances can vary significantly even among closely related species. This begs the question as to how representative tests on individual animal species are. Such tests on key species bear the risk that more sensitive species will continue to be harmed by a substance, thereby jeopardizing key ecosystem functions. 

An international research group now proposes to extend the current standard testing scheme and designed a panel consisting of a representative selection of all organisms that break down dung. The researchers tested the implementation of a more comprehensive higher-tier ecotoxicological field test based on the anti-parasitic drug ivermectin at four climatically different locations. Study sites were located in different ecoregions in Switzerland (Continental), The Netherlands (Atlantic), France (Mediterranean), and Canada (Northern Mixed Grassland) also representing different climates.

For the most part organisms were identified using classical morphology-based methods which worked reasonably well in well-studied environments but the authors had to resort to DNA barcoding in less known areas and they also pointed out that traditional methods won't cover the entire fauna that might be affected. Overall they were very pleased with the results:

Our field approach was therefore a success and in principle can be recommended. The regulation authorities responsible, such as the European Medicines Agency EMA, now have to decide whether this more conclusive yet more complex test should be required in the future. Classifying species via so-called DNA barcoding, based on each organism's unique genetic fingerprint, is possible in principle and will probably be more cost-effective in the future. However, this approach requires the establishment of a complete database for coprophilous organisms, which does not yet exist. 

We should be able to help with that.

Tuesday, July 26, 2016

We're getting there!

An ideal targeted sequencing approach would allow the selection of any subset of DNA from a pool of molecules with minimal specialized library preparation. Current methods are sophisticated but not perfect, and can result in unnecessary sequencing of regions that are not of interest. Similarly, it is difficult to balance multiple sources of input DNA for a single sequencing library, such as are found in amplicon-based sequencing, and ratios cannot subsequently be modified after library preparation is complete. These problems cannot be detected until the sequencing run is complete and data are available for analysis.

Nanopore sequencing, auch as Oxford Nanopore's MinION, is based on the readout of electrical signals occurring when DNA nucleotides passing by protein nanopores. Change in the electric current is dependent on the shape, size and length of the DNA sequences. The DNA is moved through the pore by a motor protein. The small current changes, termed 'squiggles' are converted to DNA nucleotide information using base caller software, often located in the cloud. A team from the University of Nottingham now used signal processing techniques to map these squiggles to reference sequences, by passing this step.

The colleagues show that this squiggle matching technique can be performed at a rate that enables decisions to be made about the fragment of DNA that is being sequenced before it has completely passed through the nanopore. Depending on the sequence, individual nanopores within the MinION can then be instructed to continue sequencing or to eject the current DNA fragment and start sequencing another. They show that this real-time selective sequencing, or as some have called it DNA tasting, can reduce the time needed to sequence DNA fragments or enable the targeted analysis of fragments in mixed samples.

The anticipated speed increases in nanopore sequencing ('fast mode' is currently 300 b/s and may outpace this in the future) and scaling of the MinION to 3,000 channels and PromethION to 144,000 channels will challenge the implementation of Read Until and require algorithmic enhancements and computational power. However, we expect that selective sequencing will enable new approaches such as exon sequencing without target capture, controlled depth of coverage over entire genomes, counting applications for RNA-seq and many applications that have yet to be imagined.

I have one - DNA barcoding. Imagine a world in which you can identify any species on the spot, in an instant, anywhere on the planet. Sounds familiar? This was a slogan that stand at the beginning of iBOL only six years ago. We're getting close!

Thursday, July 21, 2016

Online course on Metabarcoding


If I remember correctly I had mentioned this here and there - in collaboration the the University of Guelph Open Ed department we are developing a distance education course on metabarcoding. I am happy to report that the development is in its final stages and the first course will be held from October 3 to 28, 2016 - registration is open

This 4-week, web-based course will provide an overview of the state of current technology and the various platforms used. The course consists of a series of online lectures and research exercises introducing different aspects of metabarcoding and environmental DNA research. We will also touch on the suite of bioinformatics tools available for sequence analysis and data interpretation.

We tried to cover as much as possible given the online format and the limited time participants usually have available to do such training. The course is designed for four weekly instructional hours. The current plan is to run the course once a year.

And now on to the next - there will be another such announcement coming soon for yet another course (Regulatory and Forensic Applications of DNA Barcoding).  

Wednesday, July 20, 2016

All the lonely sequences. Where do they all come from?

Comparative phylogeography across a large number of species allows investigating community-level processes at regional and continental scales. An effective approach to such studies would involve automatic retrieval of georeferenced sequence data from nucleotide databases (a first step towards an ‘automated phylogeography’).

A team of researchers from Austria, Germany and Italy evaluated the geographical information available in GenBank accessions of tetrapods. They were particularly interesting in exploring temporal and geographical patterns, and wanted to quantify data available for automated phylogeography. 

The study began with about 1.1M accessions representing over 20,000 species but these impressive numbers shrank quite rapidly. Not unexpectedly, only 6.2% (some 70,000) of the retrieved GenBank submissions actually reported geographical coordinates and, even more concerning, the colleagues didn't noted any increase in recent years. The team also made an attempt to increase this number by developing scripts that assign geographical coordinates from textual context (e.g. keywords in publication, country information and so on). This geocoding raised the number of georeferenced accessions to 15.1%.

What I find most remarkable is that BOLD accessions, which represent only 3.4% of the analysed data, contributed a large portion of the total georeferenced (including accessions with geocoding) sequences (20.2%), and about half (47.3%) of the originally georeferenced accessions. This is not surprising as the DNA barcoding community naturally sees the value in sharing this information and BOLD supports as part of its metadata package. Actually, it is at least partially enforced as it is not possible to generate records on BOLD without basic information on the country of origin. The same requirement is part of the to-dos in order to obtain the BARCODE keyword for a GenBank record. Furthermore, researchers are always encouraged to provide lat/lon information to BOLD. Interestingly, tetrapod barcoding data are likely rather small in comparison with other datasets, e.g. fish or arthropods. A similar analysis of the latter should provide even higher proportions because the amount of fully geo-references records of insects on BOLD should reach 4 Million. 

The authors try to answer the question why so many date are submitted without detailed georeferencing and they come up with three of them:

(1) genuine lack of precise geographical information;
(2) unwillingness to reveal sensitive data (e.g. for samples from threatened species or populations); (3) lack of interest and awareness about the potential importance of direct georeferencing of data deposited in nucleotide databases for large-scale reanalysis of sequence data

I am afraid that (3) accounts for most cases. The vast majority of modern field collections use GPS data and the percentage of sensitive data is very small. Often, GPS data are still used but the precise location is masked by manually decreasing the GPS precision (cutting off some decimals or seconds/minutes does the trick). It is far too easy to just submit sequences with the minimum requirement for metadata to the INDSC databases. Only community efforts with agreed upon standards (such as barcoding campaigns and projects, e.g. iBOL) can lead to an improvement unless GenBank and Co want to change their rules.

Although geocoding offers a partial solution to the scarcity of direct georeferencing, the amount of data potentially useful for automated phylogeography is still limited. Strong underrepresentation of hard-to-access areas suggests that sampling logistics represent a main hindrance to global data availability. We propose that, besides enhancing georeferencing of genetic data, future research agendas should focus on collaborative efforts to sample genetic diversity in biodiversity-rich tropical areas.

Tuesday, July 19, 2016

Postdoctoral Research Fellow - DNA Metabarcoring of Herbivore Diet


Postdoctoral Research Fellow in DNA Metabarcoring of Herbivore Diet


A three year position as postdoctoral research fellow available available at Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo.

Within the framework of the position duties may be assigned. The position is available from September 2016. No one can be appointed for more than one fixed-term period at the same institution.

Project description

We generate DNA based diet data and study species and human interactions of the reindeer - one of the last remnants of the Beringian megafauna in the Arctic, keystone species, with high cultural and economic value for indigenous residents. Using DNA metabarcoding we analyze geographic, climatic and seasonal patterns of reindeer diet variation in different socio-economic settings. We will study diet overlap and infer trophic interactions with other herbivore species in the Arctic, such as geese, ptarmigan (Svalbard) and rodents (Finnmark). Our study will test whether reindeer diet changes correlate with warmer/longer summers or variation in population density. We integrate this ecosystem-based information with socio-economic data and local knowledge of reindeer herders to apply adaptive governance for developing co-management actions and implementation of alternative reindeer husbandry practices and mitigation measures for climate and/or land use change. The project is closely linked to the PhyloAlps (LECA, CNRS, Grenoble), ECOGEN (TromsΓΈ University Museum) and REINCLIM (NTNU, Trondheim) projects. Project partners: CEU (Budapest, Hungary) and James Hutton Institute (Aberdeen, Scotland) provide necessary expertise on socio-economic and adaptive governance approaches.

Qualifications:

The Faculty of Mathematics and Natural Sciences has a strategic ambition of being a leading research faculty. Candidates for these fellowships will be selected in accordance with this, and expected to be in the upper segment of their class with respect to academic credentials.

Applicants must hold a PhD-degree in Biology (or other corresponding education equivalent to a Norwegian doctoral degree). Additionally some years of post-doctoral research experience or research experience at this level are considered an advantage. In particular, research experience in DNA metabarcoding including data processing from high-throughput sequencing and bioinformatic analyses, herbivore diet analyses, as well as experience/knowledge of herbivore and arctic community ecology, arctic biodiversity, molecular biology and biostatistics are very relevant. Experience in field work in arctic/boreal regions and student supervision are a strong asset.

The candidate will be hosted by the Centre for Ecological and Evolutionary Synthesis (CEES) at the Dept. of Biosciences and work on the NCR funded research grant to Galina Gusarova, project nr257642 entitled REININ - Reindeer interactions from plants and birds to humans: balancing the odds of climate change. The work will be done in close collaboration with research teams from the linked projects. The candidate will be engaged in field collecting, laboratory and data analyses stages of the project with the focus on DNA metabarcoding/metagenomics and ecological data analyses and interpretations.

We seek a highly motivated, enthusiastic person with the ambition to push research and methodology frontier and publish papers in leading international journals, and in possession of good interpersonal skills and willingness to work in close collaboration with others.

The main purpose of post-doctoral research fellowships is to qualify researchers for work in top academic positions within their disciplines.

Please also refer to the regulations pertaining to the conditions of employment for post-doctoral fellowship positions.

A good command of English is required.

Salary:
Position code 1352, NOK 486,100 – 567,100 per year, (Pay Grade: 57 – 65) depending on qualifications and seniority.  

The application (Reference number: 2016/8420) must include:

  • Application letter including a statement of interest, describing how your background and previous experience relate to the project in general, and how your skills fit into the framework outlined for the postdoc
  • CV (summarizing education, positions, pedagogical experience, administrative experience and other relevant activities)
  • Copies of educational certificates, transcript of records, letters of recommendationA complete list of publications and unpublished work, and up to 5 academic papers that the applicant wishes to be considered by the evaluation committee
  • Names and contact details of 2-3 references (name, relation to candidate, e-mail and telephone number)

Please remember that all documents should be in English or a Scandinavian language.

Application deadline: 15 August, 2016

In accordance with the University of Oslo’s equal opportunities policy, we invite applications from all interested individuals regardless of gender or ethnicity.

UiO has an agreement for all employees, aiming to e.g. secure rights to research results.


Contacts:
Dr. Galina Gusarova
Questions regarding Easycruit, contact HR Officer Torunn Standal Guttormsen
Telephone: +47 22 85 42 72

Monday, July 18, 2016

World's greatest concentration of endemic mammals

Tree-mouse, Credit: Larry Heaney
Luzon is the largest island in the Philippines; at about 103,000 square kilometers, it's the 15th largest island in the world. The island has never been connected to any continental land which means that a lot of its biodiversity has been isolated, like the animals that live in Hawaii. But Luzon is much larger and at least five times older than the oldest island in Hawaii, and so has had time for the few species that arrived from the Asian mainland to evolve and diversify greatly.

On islands, we sometimes see an acceleration of evolution. Animals are closed off from the rest of the world in places where there are few or no predators or competitors. This enables them to branch out into special adaptations, eventually forming new species. And not only is the island of Luzon isolated, but it's covered in mountains. Mountaintops form "sky islands", little pockets of distinctive habitat that the animals further adapt to.

A team of American and Filipino authors have studied the mammalian fauna of Luzon Island over 15-years and summarized their findings in a new paper. They showed that out of 56 species of non-flying mammal species that are now known to live on the island, 52 are endemic. Of those 56 species, 28 were discovered during the course of the project. 

We started our study on Luzon in 2000 because we knew at the time that most of the native mammal species on the island were unique to the island, and we wanted to understand why that is the case. We did not expect that we would double the number already known.

Among the 28 new species discovered by the team are four species of tiny tree-mice with whiskers so long they reach nearly to their ankles, and five species of mice that look like shrews and feed primarily on earthworms. Most of the new species live in tropical cloud forest high in the mountains, where frequent typhoons can drop four or five meters of rain per year.

All 28 of the species we discovered during the project are members of two branches on the tree of life that are confined to the Philippines. There are individual mountains on Luzon that have five species of mammals that live nowhere else. That's more unique species on one mountain than live in any country in continental Europe. The concentration of unique biodiversity in the Philippines is really staggering.

We reject the general assumption that mammals on tropical oceanic islands are sufficiently well known that analysis and modeling of the dynamics of species richness may be conducted with precision. In the development of conceptual biogeographic models and implementation of effective conservation strategies, existing estimates of species richness, levels of endemism, and the number of subcenters of endemism should be actively reassessed and verified through robust field, museum, and laboratory studies.



Friday, July 15, 2016

Amazonian tree diversity - 300 more years of work

...we need far better data on the geographic ranges and abundances of tropical tree species to finally put the “how many species?” question to rest. It seems to me that our priorities are misplaced. We spend many billions of dollars to look for extra-terrestrial life but far less to understand life and its distribution on our own planet. (SP Hubbell)

There are more different tree species in the Amazon rainforest than anywhere else on earth, but the exact number has long been a mystery. In 2013, scientists estimated that the number of species was around 16,000. However, no one had ever counted them all up nor been able to describe them all.

In a new study, the same scientists delved into museum collections from around the world to confirm just how many tree species have been recorded for the Amazon region so far and how many have yet to be discovered. The study relied upon the digitization of museum collections data, photographs and digital records of the specimens housed in museum collections that are shared worldwide through aggregator sites like IDigBio.

We report 530,025 unique collections of trees in Amazonia, dating between 1707 and 2015, for a total of 11,676 species in 1225 genera and 140 families.


The researchers interpret this to mean that their earlier estimate of 16,000 species is valid, and that about 4,000 Amazonian trees remain to be discovered and described. There is a bit of a problem though. The colleagues also state that since 1900, between fifty and two hundred new trees have been discovered in the Amazon every year. Based on the new results this would mean that it will take us more than 300 years to discover the rest. It is likely that some of them will be gone by the time we would be able to find them. According to the authors if deforestation were to increase to levels of the early 2000s, most of the rare - and possibly unknown - species in eastern and southern Amazonia would face threat of extinction.


The colleagues have some suggestion to speed up the process a bit:
  • Digitize all Amazonian herbarium specimens as there might be up to 50% of the undiscovered species hiding in some collections.
  • Support and develop taxonomic and floristic expertise
  • Accelerate and facilitate information exchange on Amazonian trees
  • More focus on Amazonian research
  • Target geographic areas where collection effort is low and expected diversity is high
  • Embrace new technologies (they explicitly include DNA barcoding in this)





Thursday, July 14, 2016

Underwater microscopy

Benthic Underwater Microscope
Many important biological processes in the ocean take place at microscopic scales, but when researchers remove organisms from their native habitats to study them under laboratory conditions, much of the information and its context are lost.

Colleagues from the Scripps Institution of Oceanography in San Diego have developed a new type of underwater microscope to image marine microorganisms in their natural settings without disturbing them. The Benthic Underwater Microscope, or BUM, is a two-part system.  An underwater computer with a diver interface tethered to a microscopic imaging unit allows researchers to study marine subjects at nearly micron resolution. The instrument has a high magnification lens, a ring of focused LED lights for fast exposures, fluorescence imaging capabilities, and a flexible tunable lens, similar to the human eye, to change focus for viewing structures in 3-D.

To test the new technology's ability to capture small-scale processes the imaging system was used to view millimeter-sized coral polyps off the coast of Israel in the Red Sea, and off Maui, Hawaii. During the experiments in the Red Sea, the researchers set up the BUM to capture the interactions of two corals species placed close to each other. The images revealed processes in which corals emit string-like filaments that secrete enzymes from their stomach cavity to wage a chemical turf battle to destroy the tissue of other species in a competition for seafloor space. 

The team also looked at temporal processes such as the algal colonization and overgrowth of bleaching corals. Off Maui they followed one of the largest coral-bleaching events on record, which occurs when single-celled algae that live inside the coral polyp eject themselves during high ocean temperature events. Recently bleached corals are still alive, but in their weakened state can be rapidly invaded and overgrown by filamentous turf algae. Using the microscope, the research team observed a previously unreported honeycomb pattern of initial algal colonization and growth in areas between the individual coral polyps during coral bleaching.

This underwater microscope is the first instrument to image the seafloor at such small scales. The system is capable of seeing features as small as single cells underwater. This instrument is a part of a new trend in ocean research to bring the lab to the ocean, instead of bringing the ocean to the lab.


Wednesday, July 13, 2016

Biodiversity and evolution

Pseudomonas fluorescens, bacterial species used
There is a growing awareness that biodiversity not only drives ecosystem services but also affects evolutionary dynamics. However, different theories predict contrasting outcomes on when do evolutionary processes occur within a context of competition. We tested whether functional diversity can explain diversification patterns.

Past studies on ecosystem changes showed both increase and decrease of the net number of new species evolving. In other words evolution can slow down as the result of increased competition for existing niches or the same competition can actually cause adaptive radiation. 

In a new study colleagues from France and Germany explored the evolutionary dynamics of a bacterial species growing in communities with varying levels of biodiversity especially looking at the effects of higher biodiversity. The controlled environment and experimental conditions allowed them to probe into the potential reasons for the contrasting results of prior research.

They found that higher biodiversity stimulates the evolution of species especially under resource constraints:

High functional diversity reduced the fitness of the focal species and, at the same time, fostered its diversification. This pattern was linked to resource competition: High diversity increased competition on a portion of the resources while leaving most underexploited. The evolved phenotypes of the focal species showed a better use of underexploited resources, albeit at a cost of lower overall growth rates. 

The study shows that extinctions not only have an effect to current ecosystem functions but also slow down evolutionary diversification. The authors also believe that as a consequence of the nested structure and compartmentalization of many food webs, higher functional diversity fosters the evolution of new species even at high species richness.



Tuesday, July 12, 2016

Citizen science for taxonomy

The “rings” belonging to the genus Ypthima are amongst the most common butterflies in Peninsular Malaysia. However, the species can be difficult to tell apart, with keys relying on minor and often non-discrete ring characters found on the hindwing. Seven species have been reported from Peninsular Malaysia, but this is thought to be an underestimate of diversity.

This sounds like a typical intro to a DNA-barcoding-can-help story, almost too trivial to write about after so many similar posts. However, what makes this standing out to me is the way samples were collected for a new study that appeared in Genome. Results were in part obtained by the Peninsular Malaysia Butterfly Count which is a citizen science project involving school children.

165 DNA barcodes later, bolstered with data on wing and genital morphology, the colleagues are ready to reappraise the local species diversity of this genus. The study raised the species count of Ypthima for Malaysia from seven species to eight but:

We also found evidence for two previously unrecorded species of undetermined correspondence to any Linnaean species names based on samples provided by citizen scientists.

These two BINs of the genus Ypthima were collected by the citizen science project and indeed they did not correspond to any species previously reported for Peninsular Malaysia.

The example here of Ypthima is just another case demonstrating the role of DNA barcodes, and particularly databases like BOLD, allowing “online quantum contributions” for advancing taxonomic progress and efficient biodiversity communication.

Monday, July 11, 2016

Some fish like it cold


It's Monday morning and there aren't a lot of stories I find particular blog-worthy. That is not to say that there isn't anything interesting happening in the world of DNA barcoding and biodiversity sciences. I just can't find anything compelling enough to get the creative juices flowing.


Therefore, I use the 'free space' for some shameless self-advertising and to introduce a publication I co-authored. The Pacific Arctic Marine Fishes Atlas provides detailed documentation of all local species with maps depicting geographic distribution supported by citation of voucher specimens, catch records, and literature. It was already published in May through the Arctic Council, just in time for the field season as it is our hope that this new publication will help with trawls and expeditions heading out into the Pacific Arctic. 

What makes this volume special is the fact that we went through the lengths of barcoding almost all (98 of 101) species presented. The remaining 3 have been recalcitrant so far but I haven't given up on squeezing a barcode out of them. All of these are part of a larger dataset with over 200 species so far spanning the entire Arctic Ocean. We are currently working on a full atlas - stay tuned. 

Friday, July 8, 2016

Foraminifera taxonomy with DNA barcoding and morphology

The first formal classification system of the foraminifera was proposed in 1826 by d’Orbigny, and since then their identification and delineation as distinct species has been the subject of continued and active enquiry. Despite, or perhaps because of, numerous taxonomic studies spanning nearly 200 years, the current status of benthic foraminiferal taxonomy might be perceived as one of extreme confusion.

Foraminifera are well-established biomarkers of pollution in marine environments. They possess attributes of a reliable bioindicator, namely ubiquity, short life and reproductive cycles, and sensitivity to local abiotic conditions, making them highly responsive to environmental perturbations such as organic matter enrichment and physical disturbance. However, most studies have been restricted to the morphological identification and counting of hard-shelled foraminiferal species in dried sediment samples. It might come to no surprise that about 10–25% of modern benthic foraminiferal names have been suggested to be synonyms. Consequently, there are only very few established quantitative morphological frameworks enabling researchers to consistently identify and assign a specimen to a species.

In a new publication colleagues from France and Scotland attempted to combine and reconcile molecular systematics and traditional morphology-based taxonomy to come up with a new taxonomic framework that encompasses both components. They chose the suggested barcode region for foraminifera, a fragment of the small subunit ribosomal RNA (SSU rRNA) gene, in conjunction with 16 quantitative morphometric variables. As a proof of principle the researchers tested live contemporary topotypic specimens, original fossil type specimens and specimens of genetic outliers to characterize the benthic foraminiferal species Elphidium williamsoni and it obviously worked quite well:

This case study of Elphidium williamsoni highlights the importance of an integrated taxonomic approach to resolving the taxonomic complexity faced by the benthic foraminiferal community today. Since Williamson’s first description in 1858 of E. williamsoni, which he incorrectly assigned to P. umbilcatula (itself first named by Walker and Jacob in 1798 [55]), this study now presents the first clear link between morphologically characterised type material (to which the formal name E. williamsoni is directly attributable) and the unique genetic type of E. williamsoni. The taxonomic framework proposed here provides a bridge between molecular and morphological evidence, and its implementation could provide increased rigour for species identification and discovery. It also has the potential to be robust enough for new character definitions, new species and new lines of taxonomic evidence to be added in the future. If other key taxa are systematically redefined, this would provide a foundation for a transformational change to benthic foraminiferal taxonomy.


Wednesday, July 6, 2016

Beardtongue pollination

Beardtongues of  the genus Penstemon are largely pollinated by hymenoptera such as bees and wasps, but there have been repeated independent transitions to pollination by hummingbirds. With these shifts come alterations in floral color, morphology, nectar traits, and pollen dispensing. A typical "bee" Penstemon is blue or sometimes yellow/white with wide corollas and concentrated nectar. A typical "hummingbird" Penstemon is red with narrow corollas and dilute plentiful nectar.

The floral diversity and repeated shifts in pollination have inspired a number of studies looking at adaptive evolution in the genus. But many of the species relationships have been unresolved and hampered by the very thing that makes studying the genus so appealing. The rapid speciation and evolutionary radiation that makes studying adaptation in these groups so interesting have also meant the species relationships have been difficult to resolve.

A new study now demonstrates the utility of multiplexed shotgun genotyping (MSG), a variation of restriction site-associated DNA sequencing (RADseq), to infer phylogenetic relationships within a subset of species in this genus. 

We sampled genomic DNA, primarily from herbarium material, and subjected it to MSG library preparation and Illumina sequencing. The resultant sequencing reads were clustered into homologous loci, aligned, and concatenated into data matrices that differed according to clustering similarity and amount of missing data.

The MSG approach resolved species relationships and confirmed both the ancestral state of hymenoptera pollination and several independent transitions to hummingbird pollination. The study also confirmed that relationships within Penstemon are difficult to resolve due to gene tree discordance which is likely the result of incomplete lineage sorting.

This study demonstrates that phylogenomic approaches yielding thousands of variable sites can greatly improve species-level resolution of recent and rapid radiations. Similar to other studies, we found that less conservative similarity and missing data thresholds resulted in more highly supported
topologies. 

Tuesday, July 5, 2016

From the inbox: PostDoc Cornell University

POSTDOCTORAL POSITION IN AQUATIC CONSERVATION BIOLOGY
David Lodge Lab, Cornell University

A postdoctoral research position is available to pursue collaborative research that would inform the management and policy of freshwater and/or marine ecosystems, with a focus on invasive species and their interactions with other drivers of global change. Experience with environmental DNA (eDNA) or related genetic methods and/or coastal marine ecosystems would be especially valuable. The postdoctoral fellow would join an interdisciplinary team of researchers, and lead one or more efforts within an NSF Coastal SEES project that includes a global network of collaborators working in coastal environments. Subprojects might focus on one or more of the following: metagenetic characterization of freshwater and marine communities with eDNA; quantitative analysis to forecast species dispersal and range changes caused by shipping and other vectors, and interactions with climate change; quantification of the ecological and economic impacts of invasions; and management and policy of invasive species at local, national or global scales. Intellectual leadership would be expected, with the choice of topic(s) depending on experience and interests. Opportunities for collaborations exist with other biologists, big data scientists, economists, and policy experts. The postdoc would assist with the organization and administration of projects, including organizing eDNA sampling with collaborators around the world, and contribute to on-going publication preparation. 

Funding is available for at least two years. Applicant screening is rolling; the desired start date is as soon as possible (summer/fall 2016) but not later than spring 2017. Salary and benefits will be competitive. 

The postdoc would be supervised by David Lodge, who has recently moved to Cornell from Notre Dame (Lodge Lab website in transition). Collaborations with other researchers at Cornell, Notre Dame, and other universities will be encouraged. 

Applicants should email (in one pdf document) a letter describing prior research experience and current interests, a curriculum vitae, and the names and contact information of three references to David Lodge. The subject line of the email should read “Coastal SEES Postdoctoral Application 2016.” Additional postdoctoral opportunities at Cornell’s Atkinson Center for a Sustainable Future may also interest prospective applicants.

Monday, July 4, 2016

Biocontrol of Comstock mealybug

The polyphagus Comstock mealybug (Pseudococcus comstocki), native to Eastern Asia, is an invasive pest in other regions of the world. It is a serious pest in apple, pear and citrus orchards. It is also damaging to several ornamental and shade trees. The bug injures the plant by extracting large quantities of sap and producing honeydew that serves as a substrate for the development of sooty mould, which prevents photosynthesis. Fruit can be damaged by spotting and producing a change in the skin texture. Feeding activity can also stimulate the growth of gall-like formations on the bark and near the leaf veins.

In Asia and North America successful biocontrol programs using e.g. the beetle Cryptolaemus montrouzieri, also known “Crypt” or “Mealybug Destroyer” or some hymenopteran parasitoids were established in the 1960s and 1970s. The species arrived in Europe in the early 2000s and e.g. France initiated biocontrol investigations in 2008. Researchers of the French National Institute of Agronomy (INRA) began with a study of the French populations of Pseudococcus comstocki and surveyed their the natural enemies in France. Subsequently, they investigated populations and their natural enemies elsewhere (Italy, Syria, China, Japan, Turkey). For each step molecular methods were used and 28S, ITS2 and the barcode region were studied.

Three mealybug species (P. comstocki, P. viburni and P. cryptus) were identified during the survey, together with at least 16 different parasitoid taxa. We selected candidate biological control agent populations for use against P. comstocki in France, from the species Allotropa burrelli (Hymenoptera: Platygastridae) and Acerophagus malinus (Hymenoptera: Encyrtidae).

The authors list several advantages of the use of molecular data:

  • Facilitation of the choice of relevant material for examination and the sharing of complementary information (sequence haplotypes versus morphological characters), leading to particularly fruitful collaborations.
  • Identifications were consistent despite the heterogeneity of the material to be identified, in terms of both sample conservation state and development stage.
  • Identification was repeatable throughout the program, providing reliable and consistent identifications on which the team could base decisions.
  • The availability of DNA barcodes made it possible to comply with the requirements of the French government regarding import and use of exotic biological material. In particular, the existence of multilocus DNA data for Allotropa burrelli facilitated the authorization for import by French government services.