Friday, July 28, 2017

Weekend reads

Another busy week with no further posts. That should change next week as I have build quite a list of things to write about. Nevertheless, I wanted to ensure that I provide my weekly dose of interesting new reads. Here we go.

Culicoides (Diptera: Ceratopogonidae) are vectors of pathogens that affect wildlife, livestock and, occasionally, humans. Culicoides imicola (Kieffer, 1913) is considered to be the main vector of the pathogens that cause bluetongue disease (BT) and African horse sickness (AHS) in southern Europe. The study of blood-feeding patterns in Culicoides is an essential step towards understanding the epidemiology of these pathogens. Molecular tools that increase the accuracy and sensitivity of traditional methods have been developed to identify the hosts of potential insect vectors. However, to the present group's knowledge, molecular studies that identify the hosts of C. imicola in Europe are lacking. The present study genetically characterizes the barcoding region of C. imicola trapped on farms in southern Spain and identifies its vertebrate hosts in the area. The report also reviews available information on the blood-feeding patterns of C. imicola worldwide. Culicoides imicola from Spain feed on blood of six mammals that include species known to be hosts of the BT and AHS viruses. This study provides evidence of the importance of livestock as sources of bloodmeals for C. imicola and the relevance of this species in the transmission of BT and AHS viruses in Europe.

Analysis of physical evidence is typically a deciding factor in forensic casework by establishing what transpired at a scene or who was involved. Forensic geoscience is an emerging multi-disciplinary science that can offer significant benefits to forensic investigations. Soil is a powerful, nearly 'ideal' contact trace evidence, as it is highly individualistic, easy to characterise, has a high transfer and retention probability, and is often overlooked in attempts to conceal evidence. However, many real-life cases encounter close proximity soil samples or soils with low inorganic content, which cannot be easily discriminated based on current physical and chemical analysis techniques. The capability to improve forensic soil discrimination, and identify key indicator taxa from soil using the organic fraction is currently lacking. The development of new DNA sequencing technologies offers the ability to generate detailed genetic profiles from soils and enhance current forensic soil analyses. Here, we discuss the use of DNA metabarcoding combined with high-throughput sequencing (HTS) technology to distinguish between soils from different locations in a forensic context. Specifically, we provide recommendations for best practice, outline the potential limitations encountered in a forensic context and describe the future directions required to integrate soil DNA analysis into casework.

OBJECTIVE:
Analysis of environmental DNA (eDNA) is a method that has been used for the detection of various species within water bodies. The great crested newt (Triturus cristatus) has a short eDNA survey season (mid-April to June). Here we investigate whether this season could be extended into other months using the current methodology as stipulated by Natural England.
RESULTS:
Here we present data to show that in monthly water samples taken from two ponds (March 2014-February 2015) we were able to detect great crested newt DNA in all months in at least one of the ponds. Similar levels of great crested newt eDNA (i.e. highly positive identification) were detected through the months of March-August, suggesting it may be possible to extend the current survey window. In order to determine how applicable these observations are for ponds throughout the rest of the UK, further work in multiple other ponds over multiple seasons is suggested. Nevertheless, the current work clearly demonstrates, in two ponds, the efficacy and reproducibility of eDNA detection for determining the presence of great crested newts.

Gelatinous zooplankton are a large component of the animal biomass in all marine environments, but are considered to be uncommon in the diet of most marine top predators. However, the diets of key predator groups like seabirds have conventionally been assessed from stomach content analyses, which cannot detect most gelatinous prey. As marine top predators are used to identify changes in the overall species composition of marine ecosystems, such biases in dietary assessment may impact our detection of important ecosystem regime shifts. We investigated albatross diet using DNA metabarcoding of scats to assess the prevalence of gelatinous zooplankton consumption by two albatross species, one of which is used as an indicator species for ecosystem monitoring. Black-browed and Campbell albatross scats were collected from eight breeding colonies covering the circumpolar range of these birds over two consecutive breeding seasons. Fish was the main dietary item at most sites, however cnidarian DNA, primarily from scyphozoan jellyfish was present in 42% of samples overall and up to 80% of samples at some sites. Jellyfish was detected during all breeding stages and consumed by adults and chicks. Trawl fishery catches of jellyfish near the Falkland Islands indicate a similar frequency of jellyfish occurrence in albatross diets in years of high and low jellyfish availability, suggesting jellyfish consumption may be selective rather than opportunistic. Warmer oceans and overfishing of finfish are predicted to favour jellyfish population increases and we demonstrate here that dietary DNA metabarcoding enables measurements of the contribution of gelatinous zooplankton to the diet of marine predators.

An increasing number of studies are showing that Antarctic mega- and macrofauna are highly diverse, however, little is known about meiofaunal biodiversity in sediment communities, which are a vital part of a healthy and functional ecosystem. This is the first study to analyse community DNA (targeting meiofauna) using metabarcoding to investigate biodiversity levels in sediment communities of the Antarctic Peninsula. The results show that almost all of the meiofaunal biodiversity in the benthic habitat has yet to be characterised, levels of biodiversity were higher than expected and similar to temperate regions, albeit with the existence of potentially new and locally adapted species never described before at the molecular level. The Rothera meiofaunal sample sites showed four dominant eukaryotic groups, the nematodes, arthropods, platyhelminthes, and the annelids; some of which could comprise species complexes. Comparisons with deep-sea data from the same region suggest little exchange of Operational Taxonomic Units (OTUs) between depths with the nematodes prevalent at all depths, but sharing the shallow water benthos with the copepods. This study provides a preliminary analysis of benthic Antarctic Peninsula meiofauna using high throughput sequencing which substantiates how little is known on the biodiversity of one of the most diverse, yet underexplored communities of the Antarctic: the benthos.

Friday, July 21, 2017

Weekend reads

It is Friday again - time for another batch of papers to read over the weekend. Thanks to a very active community there is never a shortage of studies to chose from.

Advances in detection of genetic material from species in aquatic ecosystems, including environmental DNA (eDNA), have improved species monitoring and management. eDNA from target species can readily move in streams and rivers and the goal is to measure it, and with that infer where and how abundant species are, adding great value to delimiting species invasions, monitoring and protecting rare species, and estimating biodiversity. To date, we lack an integrated framework that identifies environmental factors that control eDNA movement in realistic, complex, and heterogeneous flowing waters. To this end, using an empirical approach and a simple conceptual model, we propose a framework of how eDNA is transported, retained, and resuspended in stream systems. Such an understanding of eDNA dispersal in streams will be essential for designing optimized sampling protocols and subsequently estimating biomass or organismal abundance. We also discuss guiding principles for more effective use of eDNA methods, highlighting the necessity of understanding these parameters for use in future predictive modeling of eDNA transport.

DNA sequencing brings another dimension to exploration of biodiversity, and large-scale mitochondrial DNA cytochrome oxidase I barcoding has exposed many potential new cryptic species. Here, we add complete nuclear genome sequencing to DNA barcoding, ecological distribution, natural history, and subtleties of adult color pattern and size to show that a widespread neotropical skipper butterfly known as Udranomia kikkawai (Weeks) comprises three different species in Costa Rica. Full-length barcodes obtained from all three century-old Venezuelan syntypes of U. kikkawai show that it is a rainforest species occurring from Costa Rica to Brazil. The two new species are Udranomia sallydaleyae Burns, a dry forest denizen occurring from Costa Rica to Mexico, and Udranomia tomdaleyi Burns, which occupies the junction between the rainforest and dry forest and currently is known only from Costa Rica. Whereas the three species are cryptic, differing but slightly in appearance, their complete nuclear genomes totaling 15 million aligned positions reveal significant differences consistent with their 0.00065-Mbp (million base pair) mitochondrial barcodes and their ecological diversification. DNA barcoding of tropical insects reared by a massive inventory suggests that the presence of cryptic species is a widespread phenomenon and that further studies will substantially increase current estimates of insect species richness.

Over the past decade, DNA barcoding has become a staple of low-cost molecular systematic investigations. The availability of universal primers and subsidized sequencing projects (PolarBOL, SharkBOL, SpongeBOL) have driven this popularity, often without appropriate investigation into the utility of barcoding data for the taxonomic group of interest. Here, our primary aim is to determine the phylogenetic value of DNA barcoding (mitochondrial locus COI) within the gecko genus Cyrtodactylus. With >40 new species described since last systematic investigation, Cyrtodactylus represents one of the most diverse extant squamate genera, and their contemporary distribution spans the Indian subcontinent, eastward through Indochina, and into AustraloPapua. The complex biogeographic history of this group, and morphology-only designation of many species have complicated our phylogenetic understanding of Cyrtodactylus. To highlight the need for continued inclusive molecular assessment, we use Vietnamese Cyrtodactylus as a case study showing the geopolitically paraphyletic nature of their history. We compare COI to the legacy marker ND2, and discuss the value of COI as an interspecific marker, as well as its shortcomings at deeper evolutionary scales. We draw attention back to the Cold Code as a subsidized method for incorporating molecular methods into species descriptions in the effort to maintain accurate phylogenies.

One of the fundamental patterns in macroecology is the increase in the number of observed taxa with size of sampled area. For microbes, the shape of this relationship remains less clear. The current study assessed the diversity of aquatic fungi, by the traditional approach based on conidial morphology (captures reproducing aquatic hyphomycetes) and next generation sequencing (NGS; captures other fungi as well), on graded sizes of alder leaves (0.6 to 13.6 cm2). Leaves were submerged in two streams in geographically distant locations: the Oliveira Stream in Portugal and the Boss Brook in Canada. Decay rates of alder leaves and fungal sporulation rates did not differ between streams. Fungal biomass was higher in Boss Brook than in Oliveira Stream, and in both streams almost 100% of the reads belonged to active fungal taxa. In general, larger leaf areas tended to harbour more fungi, but these findings were not consistent between techniques. Morphospecies-based diversity increased with leaf area in Boss Brook, but not in Oliveira Stream; metabarcoding data showed an opposite trend. The higher resolution of metabarcoding resulted in steeper taxa-accumulation curves than morphospecies-based assessments (fungal conidia morphology). Fungal communities assessed by metabarcoding were spatially structured by leaf area in both streams. Metabarcoding promises greater resolution to assess biodiversity patterns in aquatic fungi and may be more accurate for assessing taxa-area relationships and local to global diversity ratios.

BACKGROUND:
Bats are a highly successful, globally dispersed order of mammals that occupy a wide array of ecological niches. They are also intensely parasitized and implicated in multiple viral, bacterial and parasitic zoonosis. Trypanosomes are thought to be especially abundant and diverse in bats. In this study, we used 18S ribosomal RNA metabarcoding to probe bat trypanosome diversity in unprecedented detail.
METHODOLOGY/PRINCIPAL FINDINGS:
Total DNA was extracted from the blood of 90 bat individuals (17 species) captured along Atlantic Forest fragments of Espírito Santo state, southeast Brazil. The 18S ribosomal RNA was amplified by standard and/or nested PCR, then deep sequenced to recover and identify Operational Taxonomic Units (OTUs) for phylogenetic analysis. Blood samples from 34 bat individuals (13 species) tested positive for infection by 18S rRNA amplification. Amplicon sequences clustered to 14 OTUs, of which five identified as Trypanosoma cruzi I, T. cruzi III/V, Trypanosoma cruzi marinkellei, Trypanosoma rangeli, and Trypanosoma dionisii, and seven identified as novel genotypes monophyletic to basal T. cruzi clade types of the New World. Another OTU was identified as a trypanosome like those found in reptiles. Surprisingly, the remaining OTU was identified as Bodo saltans-closest non-parasitic relative of the trypanosomatid order. While three blood samples featured just one OTU (T. dionisii), all others resolved as mixed infections of up to eight OTUs.
CONCLUSIONS/SIGNIFICANCE:
This study demonstrates the utility of next-generation barcoding methods to screen parasite diversity in mammalian reservoir hosts. We exposed high rates of local bat parasitism by multiple trypanosome species, some known to cause fatal human disease, others non-pathogenic, novel or yet little understood. Our results highlight bats as a long-standing nexus among host-parasite interactions of multiple niches, sustained in part by opportunistic and incidental infections of consequence to evolutionary theory as much as to public health.


Thursday, July 20, 2017

A look into a rumen

Roe Deer (Capreolus capreolus)
Dietary choices are central to our understanding of ecology and evolution. Still, many aspects of food choice have been hampered by time consuming procedures and methodological problems. Faster and cheaper methods, such as DNA metabarcoding, have therefore been widely adopted.

Traditional visual techniques based on morphology for diet analysis are often limited in their ability to identify all items found in a stomach. Unrecognizable content has to be ignored which can shift relative proportions within analysis. This happens mostly when digestion is well advanced, leaving researchers without any characters that would enable visual identification. It is well known that this can lead to biased results in studies of processes such as food web interactions and energy flow through an ecosystem. DNA barcoding has been suggested as a tool to overcome these issues and over the last 6-7 years a number of studies has been published all of which showed the increase of resolution by utilizing molecular techniques. 

A new study by Swedish researchers looked at the use of metabarcoding to assess ungulate diet through rumen content. They were interested in the diet of Fallow Deer (Dama dama) and Roe Deer (Capreolus capreolus).  In addition they set out to empirically compare metabarcoding to visual identifications. Not surprisingly, metabarcoding provided higher yield and precision of results although  they found that the methods were comparable, but they did not completely overlap. Sometimes the DNA method failed to identify food items that were found macroscopically...

When the colleagues applied both sets of data they found some very encouraging things.  In niche overlap analyses, presence/absence data showed that both methods came to very similar conclusions. When using the sequence count data and macroscopic weight, niche overlap was lower than when using presence-absence data yet tended to increase when using DNA compared to macroscopy. Nevertheless, the significant positive correlation between macroscopic quantity and number of DNA sequences counted from the same plant group give support for the use of metabarcoding to quantify plants in the rumen. 

Again, very promising evidence for the power of DNA barcoding in the context of dietary analysis. It would be very interesting to see how the results of this study correlate with an analysis of fecal samples. As a non-invasive method would increase sample size and effort quite extensively. The other suggestion I have is to use more than just one marker (here trnL). Include ITS or rbcL as well which might boost the metabarcoding success even more.

Wednesday, July 19, 2017

Biodiversity and climate warming

Meadow plots at Long-Term Ecological Research Station in Cedar Creek
Climate warming is predicted to alter species interactions, which could potentially lead to extinction events. However, there is an ongoing debate whether the effects of warming on biodiversity may be moderated by biodiversity itself.

A team of ecologists from the German Centre for Integrative Biodiversity Research (iDiv) and the University of Minnesota conducted long-running field experiments in 30 different meadow plots, some with only one plant species , and others with up to 16 different plant species. They warmed the meadows with heating lamps to approximately 3°C above ambient temperature. Subsequently, they recorded how this affected soil nematodes which were chosen for their important role for several ecosystem functions.

The colleagues found that warming can both increase and decrease biodiversity, and that the direction of the effect depends on how much biodiversity there is in the first place. After warming the monoculture plots the diversity of nematodes in those substantially declined. However, when the researchers warmed the plots with a high number of different plant species, the number of nematode species increased. However, those nematode species were also more closely related to each other. The reason was that these species had all been selected for a common characteristic, namely tolerance to a warmer environment. This increase in similarity can have implications for how well biological communities can respond to future environmental changes, potentially limiting the "insurance" effect inherent in a higher numbers of species.

The monoculture meadow created for the experiment resembled meadows found in intensively managed agricultural land. These new research findings therefore support conservationists who are advocating for more species-rich ecosystems and farmland to sustain biodiversity, in a warmer world. 

Friday, July 14, 2017

Weekend reads

Another week comes to an end and I have a few things I recommend reading. Enjoy!

The biodiversity of Mediterranean freshwater bodies is among the most threatened worldwide; therefore, its accurate estimation is an urgent issue. However, traditional methods are likely to underestimate freshwater zooplankton biodiversity due to its high species seasonality and cryptic diversity. We test the value of applying DNA barcoding to diapausing egg banks, in combination with the creation of a reference collection of DNA barcodes using adult individual samples, to characterize rotifer communities. We use monogonont rotifers from two lakes in Doñana National Park and one from Ruidera Natural Park in Spain as models to create a reference collection of DNA barcodes for taxonomically diagnosed adult individuals sampled from the water column, to compare with the sequences obtained from individual eggs from the diapausing egg banks. We apply two different approaches to carry out DNA taxonomy analyses, the generalized mixed Yule coalescent method (GMYC) and the Automatic Barcode Gap Discovery (ABGD), to the obtained sequences and to publicly available rotifer sequences. We obtained a total of 210 new rotifer COI sequences from all three locations (151 diapausing eggs and 59 adults). Both GMYC and ABGD generated the same 35 operational taxonomic units (OTUs), revealing four potential cryptic species. Most sequences obtained from diapausing eggs (85%) clustered with sequences obtained from morphologically diagnosed adults. Our approach, based on a single sediment sample, retrieved estimates of rotifer biodiversity higher than or similar to those of previous studies based on a number of seasonal samples. This study shows that DNA barcoding of diapausing egg banks is an effective aid to characterize rotifer diversity in Mediterranean freshwater bodies.

In this study, species-specific identification of five toxic mushrooms, Chlorophyllum molybdites, Gymnopilus junonius, Hypholoma fasciculare, Pleurocybella porrigens, and Tricholoma ustale, which have been involved in food-poisoning incidents in Japan, was investigated. Specific primer pairs targeting internal transcribed spacer (ITS) regions were designed for PCR detection. The specific amplicons were obtained from fresh, cooked, and simulated gastric fluid (SGF)-treated samples. No amplicons were detected from other mushrooms with similar morphology. Our method using one-step extraction of mushrooms allows rapid detection within 2.5 hr. It could be utilized for rapid identification or screening of toxic mushrooms.

As rabies in carnivores is increasingly controlled throughout much of the Americas, bats are emerging as a significant source of rabies virus infection of humans and domestic animals. Knowledge of the bat species that maintain rabies is a crucial first step in reducing this public health problem. In North America, several bat species are known to be rabies virus reservoirs but the role of bats of the Myotis genus has been unclear due to the scarcity of laboratory confirmed cases and the challenges encountered in species identification of poorly preserved diagnostic submissions by morphological traits alone. This study has employed a collection of rabid bat specimens collected across Canada over a 25 year period to clearly define the role of particular Myotis species as rabies virus reservoirs. The virus was characterised by partial genome sequencing and host genetic barcoding, used to confirm species assignment of specimens, proved crucial to the identification of certain bat species as disease reservoirs. Several variants were associated with Myotis species limited in their Canadian range to the westernmost province of British Columbia while others were harboured by Myotis species that circulate across much of eastern and central Canada. All of these Myotis-associated viral variants, except for one, clustered as a monophyletic MYCAN clade, which has emerged from a lineage more broadly distributed across North America; in contrast one distinct variant, associated with the long-legged bat in Canada, represents a relatively recent host jump from a big brown bat reservoir. Together with evidence from South America, these findings demonstrate that rabies virus has emerged in the Myotis genus independently on multiple occasions and highlights the potential for emergence of new viral-host associations within this genus.

PREMISE OF THE STUDY:
To study pollination networks in a changing environment, we need accurate, high-throughput methods. Previous studies have shown that more highly resolved networks can be constructed by studying pollen loads taken from bees, relative to field observations. DNA metabarcoding potentially allows for faster and finer-scale taxonomic resolution of pollen compared to traditional approaches (e.g., light microscopy), but has not been applied to pollination networks.
METHODS:
We sampled pollen from 38 bee species collected in Florida from sites differing in forest management. We isolated DNA from pollen mixtures and sequenced rbcL and ITS2 gene regions from all mixtures in a single run on the Illumina MiSeq platform. We identified species from sequence data using comprehensive rbcL and ITS2 databases.
RESULTS:
We successfully built a proof-of-concept quantitative pollination network using pollen metabarcoding.
DISCUSSION:
Our work underscores that pollen metabarcoding is not quantitative but that quantitative networks can be constructed based on the number of interacting individuals. Due to the frequency of contamination and false positive reads, isolation and PCR negative controls should be used in every reaction. DNA metabarcoding has advantages in efficiency and resolution over microscopic identification of pollen, and we expect that it will have broad utility for future studies of plant-pollinator interactions.

Microbial eukaryotes can play prominent roles in the Arctic marine ecosystem, but their diversity and variability is not well known in the ice-covered ecosystems. We determined the community composition of microbial eukaryotes in an Arctic under-ice spring bloom north of Svalbard using metabarcoding of DNA and RNA from the hypervariable V4 region of 18S nrDNA. At the two stations studied, the photosynthetic biomass was dominated by protists >3 μm and was concentrated in the upper 70-80 m, above the thermocline and halocline. Hierarchical cluster analyses as well as ordination analyses showed a distinct clustering of the microbial eukaryote communities according to a combination of water mass and local environmental characteristics. While samples collected in the surface mixed layer differed distinctly between the two sites, the deeper communities collected in Atlantic Water were fairly similar despite being geographically distant. The differentiation of the microbial eukaryote communities of the upper mixed water was probably driven by local development and advection, while the lack of such differentiation in the communities of Atlantic Water reflects the homogenizing effect of water currents on microbial communities.

Thursday, July 13, 2017

Biological annihilation

Catarina pupfish
No bells tolled when the last Catarina pupfish on Earth died. Newspapers didn't carry the story when the Christmas Island pipistrelle vanished forever.

Two vertebrate species go extinct every year on average, but few people notice, perhaps because the rate seems relatively slow - not a clear and present threat to the natural systems we depend on. This view overlooks trends of extreme decline in animal populations, which tell a more dire story with cascading consequences.

In a new publication researchers from Stanford University and UNAM in Mexico City draw a bleak picture of the future by talking about biological annihilation in an ongoing sixth mass extinction. The new study looks beyond species extinctions to provide a picture of dwindling populations and ranges. The colleagues mapped the ranges of 27,600 species of birds, amphibians, mammals and reptiles (nearly half of known terrestrial vertebrate species) and analyzed population losses in a sample of 177 well-studied mammal species between 1990 and 2015.

It turns out that more than 30% of vertebrate species are declining in population size and range. Of the subset mammals for which the researchers had detailed data, all have lost 30% or more of their geographic ranges and more than 40% of them have actually lost more than 80% of their ranges, most of which in southeast Asia. In general tropical regions have had the greatest number of decreasing species while temperate regions have seen similar or higher proportions of decreasing species. The study's mapping exercise suggests that as much as 50% of the number of animal individuals that once shared Earth have disappeared, as have billions of animal populations.

This is the case of a biological annihilation occurring globally, even if the species these populations belong to are still present somewhere on Earth... The massive loss of populations and species reflects our lack of empathy to all the wild species that have been our companions since our origins. It is a prelude to the disappearance of many more species and the decline of natural systems that make civilization possible.

What concerns me even more is the fact that this paper and many other studies exclusively look at vertrebrate species which are among the least diverse groups of animals. What about invertebrate diversity? Unfortunately, there is only anecdotal data and evidence. Humans haven't amassed much data to have a closer look but it is likely very similar if not worse. Few reliable data exist on the fate of important insect species. Scientists have tracked alarming declines in domesticated honey bees, monarch butterflies, and lightning bugs. But few have paid attention to the moths, hover flies, beetles, and countless other insects that buzz and flitter through the warm months. A recent article in Science gives a glimpse of what is going on in the invertebrate world. If we want to use such strong language as biological annihilation or erosion of biodiversity we might want to look a bit closer at the bugs around us even if the insights we gain might be even more disturbing that what we already learned from vertebrate studies.

Wednesday, July 12, 2017

Citizen science for butterfly conservation

Simplified butterfly assessment scheme used in Viel-Falter
Ordinary citizens have become increasingly important to scientific research over the past decade. Today, mobile phone technologies, relatively cheap cameras and almost ubiquitous internet connectivity have opened up new opportunities for conservation organisations to engage with ordinary citizens and encourage citizen science. A citizen scientist is a volunteer who collects and/or processes data as part of a scientific inquiry. This could mean noting the plants found on a day trip or more systematically recording wildlife in a special area.

Colleagues in Austria developed a specific assessment scheme suitable for citizen scientists and tested it at 35 sampling sites in Tyrol. They wanted to find out if trained and supervised school kids are able to systematically collect occurrence data on diurnal butterflies, and how the data could contribute to a permanent butterfly monitoring system. In 2013 they launched the citizen science project Viel-Falter.

By comparing with independent assessments conducted by professional butterfly experts, we investigated if the achieved data quality is sufficient to support a permanent butterfly monitoring system. Additionally, we investigated how the pupil’s motivation to engage in butterfly observation activities develops during the course of the project and what project factors might be crucial to support a continuous engagement.

Not surprisingly this comparison revealed that the degree of accordance varied substantially between different species or species groups. However, the data collected was successfully applied to predict the general habitat quality for butterflies using a linear regression model. This is indeed very good news as it shows that well-designed and executed citizen science projects can provide biodiversity data comparable to data gathered by professionals. Our experience during the School Malaise Project was very similar. 

There is an increased need and demand for large scale biodiversity assessments and continuous monitoring schemes but professional resources for collecting such data are rather limited. Citizen science projects like Viel-Falter might become a very important factor for future collecting and processing of biodiversity data. Such projects also come with immense added value as they generate authentic opportunities for environmental education.

Friday, July 7, 2017

Weekend reads

This short week passed by quickly. Nevertheless, I was able to find some interesting weekend reads for you.

Fungi play a key role in soil-plant interactions, nutrient cycling, and carbon flow and are essential for the functioning of arctic terrestrial ecosystems. Some studies have shown that the composition of fungal communities is highly sensitive to variations in environmental conditions, but little is known about how the conditions control the role of fungal communities (i.e. their ecosystem function). We used DNA metabarcoding to compare taxonomic and functional composition of fungal communities along a gradient of environmental severity in Northeast Greenland. We analysed soil samples from fell fields, heaths, and snowbeds, three habitats with very contrasting abiotic conditions. We also assessed within-habitat differences by comparing three widespread microhabitats (patches with high cover of Dryas, Salix, or bare soil). The data suggest that, along the sampled mesotopographic gradient, the greatest differences in both fungal richness and community composition are observed among habitats, while the effect of microhabitat is weaker, although still significant. Furthermore, we found that richness and community composition of fungi are shaped primarily by abiotic factors and to a lesser, though still significant extent, by floristic composition. Along this mesotopographic gradient, environmental severity is strongly correlated with richness in all fungal functional groups: positively in saprotrophic, pathogenic, and lichenised fungi, and negatively in ectomycorrhizal and root-endophytic fungi. Our results suggest complex interactions amongst functional groups, possibly due to nutrient limitation or competitive exclusion, with potential implications on soil carbon stocks. These findings are important in light of the environmental changes predicted for the Arctic.

Monitoring biodiversity is essential to assess the impacts of increasing anthropogenic activities in marine environments. Traditionally, marine biomonitoring involves the sorting and morphological identification of benthic macro-invertebrates, which is time-consuming and taxonomic-expertise demanding. High-throughput amplicon sequencing of environmental DNA (eDNA metabarcoding) represents a promising alternative for benthic monitoring. However, an important fraction of eDNA sequences remains unassigned or belong to taxa of unknown ecology, which prevent their use for assessing the ecological quality status. Here, we show that supervised machine learning (SML) can be used to build robust predictive models for benthic monitoring, regardless of the taxonomic assignment of eDNA sequences. We tested three SML approaches to assess the environmental impact of marine aquaculture using benthic foraminifera eDNA, a group of unicellular eukaryotes known to be good bioindicators, as features to infer macro-invertebrates based biotic indices. We found similar ecological status as obtained from macro-invertebrates inventories. We argue that SML approaches could overcome and even bypass the cost and time-demanding morpho-taxonomic approaches in future biomonitoring.

Agricultural productivity relies on a wide range of ecosystem services provided by the soil biota. Plowing is a fundamental component of conventional farming, but long-term detrimental effects such as soil erosion and loss of soil organic matter have been recognized. Moving towards more sustainable management practices such as reduced tillage or crop residue retention can reduce these detrimental effects, but will also influence structure and function of the soil microbiota with direct consequences for the associated ecosystem services. Although there is increasing evidence that different tillage regimes alter the soil microbiome, we have a limited understanding of the temporal dynamics of these effects. Here, we used high-throughput sequencing of bacterial and fungal ribosomal markers to explore changes in soil microbial community structure under two contrasting tillage regimes (conventional and reduced tillage) either with or without crop residue retention. Soil samples were collected over the growing season of two crops (Vicia faba and Triticum aestivum) below the seedbed (15-20 cm). Tillage, crop and growing stage were significant determinants of microbial community structure, but the impact of tillage showed only moderate temporal dependency. Whereas the tillage effect on soil bacteria showed some temporal dependency and became less strong at later growing stages, the tillage effect on soil fungi was more consistent over time. Crop residue retention had only a minor influence on the community. Six years after the conversion from conventional to reduced tillage, soil moisture contents and nutrient levels were significantly lower under reduced than under conventional tillage. These changes in edaphic properties were related to specific shifts in microbial community structure. Notably, bacterial groups featuring copiotrophic lifestyles or potentially carrying the ability to degrade more recalcitrant compounds were favored under conventional tillage, whereas taxa featuring more oligotrophic lifestyles were more abundant under reduced tillage. Our study found that, under the specific edaphic and climatic context of central Belgium, different tillage regimes created different ecological niches that select for different microbial lifestyles with potential consequences for the ecosystem services provided to the plants and their environment.

Population-scale molecular studies of endangered and cryptic species are often limited by access to high-quality samples. The use of non-invasively collected samples or museum-preserved specimens reduces the pressure on modern populations by removing the need to capture and handle live animals. However, endogenous DNA content in such samples is low, making shotgun sequencing a financially prohibitive approach. Here, we apply a target enrichment method to retrieve mitochondrial genomes from 65 museum specimens and 56 non-invasively collected fecal samples of two endangered great ape species, Grauer's gorilla and the eastern chimpanzee. We show that the applied method is suitable for a wide range of sample types that differ in endogenous DNA content, increasing the proportion of target reads to over 300-fold. By systematically evaluating biases introduced during target enrichment of pooled museum samples we show that capture is less efficient for fragments shorter or longer than the baits, that the proportion of human contaminating reads increases post-capture although capture efficiency is lower for human compared to gorilla fragments with a gorilla-generated bait, and that the rate of jumping PCR is considerable, but can be controlled for with a double-barcoding approach. We succeed in capturing complete mitochondrial genomes from fecal samples, but observe reduced capture efficiency as sequence divergence increases between the bait and target species. As previously shown for museum specimens, we demonstrate here that mitochondrial genome capture from field-collected fecal samples is a robust, and reliable approach for population-wide studies of non-model organisms.

Wednesday, July 5, 2017

So many trees

Why is tree biodiversity so large around the equator, moderate at mid-latitudes and monotonous at higher ones? As this is a global phenomenon most possible explanations involve long-term or large-scale mechanisms, such as climate stability (no glaciers in the tropics), rates of speciation (higher in the tropics) or rates of extinction (lower in the tropics according to the fossil record).

In order to explain the high tree species biodiversity in tropical rainforests Daniel Janzen and Joseph Connell independently suggested a very different mechanism that operates at a much smaller scale (conspecific negative density dependence - CNDD). They proposed that host-specific natural enemies which kill seeds and seedlings clumped near parent trees might keep locally common species from dominating a forest and give locally rare species space to flourish. This Janzen-Connell hypothesis is now nearly 50 years old, but it has been hard to evaluate, especially at the global scale. 

Utilizing the Smithsonian Center for Tropical Forest Science-Forest Global Earth Observatory (CTFS-ForestGEO) researchers now analyzed the data from 24 forest plots. Together these plots are home to more than 3,000 tree species and roughly 2.4 million trees. The analysis provided the first evidence that the Janzen-Connell effect contributes to the biodiversity gradient across tropical and temperate latitudes.

The results of the new study show that global patterns in tree species diversity reflect not only stronger CNDD at tropical versus temperate latitudes but also a latitudinal shift in the relationship between CNDD and species abundance. CNDD was stronger for rare species at tropical versus temperate latitudes, potentially causing the persistence of greater numbers of rare species in the tropics.

The key observation on which the Janzen-Connell hypothesis is based is that seedfall is heaviest under a parent tree but the young tend to do better away from their parent. In the tropics, this is stronger for rare species than for common ones. In the temperate zone rare and common species are equally affected, or in some cases it flips and becomes stronger for the common species than the rare ones. The colleagues find this result exciting because it may explain a puzzling characteristic of tropical forests - their diversity is due not to large numbers of species in general but rather to large numbers of rare species.


How can you pack more than a thousand species in a 50-hectare plot in the tropics if the rare species are being negatively impacted by these specialized enemies? You'd think that if these species are rare they'd be more likely to go extinct, so what maintains them in the system? ...Paradoxically, enemies can be beneficial, they kill, but by killing they prevent population booms and busts. If you have no enemies, you're going to have exponential population growth followed by a crash. If you add an enemy that tracks abundance, over time the population stabilizes. It's never going to become large, but the flip side is it's never going to crash. And so these enemies are a stabilizing force.

Friday, June 30, 2017

Weekend reads

A long weekend for Canadians lies ahead. Lots of parties around the country to celebrate Canada's 150th birthday. But the rest of the world has a regular weekend and all of you might want some good reads. Here we go:

Symbiotic microalgae (Symbiodinium spp.) strongly influence the performance and stress-tolerance of their coral hosts, making the analysis of Symbiodinium communities in corals (and metacommunities on reefs) advantageous for many aspects of coral reef research. High-throughput sequencing of ITS2 nrDNA offers unprecedented scale in describing these communities, yet high intragenomic variability at this locus complicates the resolution of biologically meaningful diversity. Here, we demonstrate that generating operational taxonomic units by clustering ITS2 sequences at 97% similarity within, but not across, samples collapses sequence diversity that is more likely to be intragenomic, while preserving diversity that is more likely interspecific. We utilize this 'within-sample clustering' to analyze Symbiodinium from ten host taxa on shallow reefs on the north and south shores of St. John, US Virgin Islands. While Symbiodinium communities did not differ between shores, metacommunity network analysis of host-symbiont associations revealed Symbiodinium lineages occupying 'dominant' and 'background' niches, and coral hosts that are more 'flexible' or 'specific' in their associations with Symbiodinium. These methods shed new light on important questions in coral symbiosis ecology, and demonstrate how application-specific bioinformatic pipelines can improve the analysis of metabarcoding data in microbial metacommunity studies.


Assessing diet variability between species, populations and individuals is of main importance to better understand the biology of bats and design conservation strategies. Although the advent of metabarcoding has facilitated such analyses, this approach does not come without challenges. Biases may occur throughout the whole experiment, from fieldwork to biostatistics, resulting in the detection of false negatives, false positives or low taxonomic resolution. We detail a rigorous metabarcoding approach based on a two-step PCR protocol enabling the "all at once" taxonomic identification of bats and their arthropod preys for several hundreds of samples. Our study includes faecal pellets collected in France from 357 bats representing 16 species, as well as insect mock communities that mimic bat meals of known composition, negative and positive controls. All samples were analysed in triplicate. We compare the efficiency of DNA extraction methods and we evaluate the effectiveness of our protocol using the rate of bat identification success, taxonomic resolution, sensitivity, and amplification biases. Our strategy involves twice fewer steps than usually required in the other metabarcoding studies and reduces the probability to misassign preys to wrong samples. Controls and replicates enable to filter the data and limit the risk of false positives, hence guaranteeing high confidence results for both prey occurrence and bat species identification. Our results illustrate the power of this approach to assess diet richness and variability within and between colonies. We therefore provide a rapid, resolutive and cost-effective screening tool for addressing evolutionary ecological issues or developing "chirosurveillance" and conservation strategies.



Species diversity of metazoan bulk samples can be rapidly assessed using Cytochrome c oxidase I (COI) metabarcoding. However, in cases where only degraded DNA is available, e.g. from poorly conserved museum specimens, eDNA filtered from water or gut content analyses, universal primer sets that amplify only a short COI fragment are advantageous. Using PrimerMiner, we optimised two universal primer sets targeting freshwater macroinvertebrates based on NCBI and BOLD reference sequences. The fwh1 and fwh2 primer sets targeting a 178 and 205 bp region were tested in vivo by sequencing previously used freshwater macroinvertebrate mock communities of known composition and three monitoring samples from Romanian streams. They were further evaluated in silico for their suitability to amplify other insect groups. The fwh1 primer sets showed the most consistent amplification in silico and in vivo , detecting 92% of the taxa present in the mock communities, and allowing clear differentiation between the three macroinvertebrate communities from the Romanian streams. In silico analysis indicates that the short primers are likely to perform well even for non-freshwater insects. Comparing the performance of the new fwh1 primer sets to a highly degenerate primer set targeting a longer fragment (BF2/BR2) revealed that efficiency is slightly lower for the new primer set. Nevertheless, the shorter new primer pairs might be useful for studies that have to rely on degraded or poorly conserved DNA and thus be of importance for biomonitoring, conservation biological or molecular ecological studies. Furthermore, our study highlights the need for in silico evaluation of primer sets in order to detect design errors in primers (fwhR2) and find optimal universal primer sets for the target taxa of interest.

This data release provides COI barcodes for 366 species of parasitic flies (Diptera: Tachinidae), enabling the DNA based identification of the majority of northern European species and a large proportion of Palearctic genera, regardless of the developmental stage. The data will provide a tool for taxonomists and ecologists studying this ecologically important but challenging parasitoid family. A comparison of minimum distances between the nearest neighbors revealed the mean divergence of 5.52% that is approximately the same as observed earlier with comparable sampling in Lepidoptera, but clearly less than in Coleoptera. Full barcode-sharing was observed between 13 species pairs or triplets, equaling to 7.36% of all species. Delimitation based on Barcode Index Number (BIN) system was compared with traditional classification of species and interesting cases of possible species oversplits and cryptic diversity are discussed. Overall, DNA barcodes are effective in separating tachinid species and provide novel insight into the taxonomy of several genera.

Wednesday, June 28, 2017

Shelf Life Webseries

Today a post on an interesting video series which is produced by the American Museum of Natural History. I have to admit I wasn't aware of it at all until a few days ago when the newest episode on cryptic species was shared with me:



The web series Shelf Life highlights different aspects of the museums work and is certainly not the only one out there which is produced my the museum itself. The Smithsonian e.g. has its own channel with countless short videos on many many topics. What I like about the AMNH series is the right mixture of length (never over 10 min), topic and production quality. it all started about three years ago with this one:







h/t Paul Hebert




Monday, June 26, 2017

Image Data Resource

Much of the published research in the life sciences is based on image data sets that sample 3D space, time and the spectral characteristics of detected signal to provide quantitative measures of cell, tissue and organismal processes and structures. The sheer size of biological image data sets makes data submission, handling and publication challenging. An image-based genome-wide 'high-content' screen (HCS) may contain more than 1 million images, and new 'virtual slide' and 'light sheet' tissue imaging technologies generate individual images that contain gigapixels of data showing tissues or whole organisms at subcellular resolutions. At the same time, published versions of image data are often mere illustrations: they are presented in processed, compressed formats that cannot convey the measurements and multiple dimensions contained in the original image data and cannot easily be reanalyzed. Furthermore, conventional publications do not include the metadata that define imaging protocols, biological systems and perturbations or the processing and analytic outputs that convert the image data into quantitative measurements.

There are many resources worldwide in which people publish imaging data, but none of these repositories is both generic and linked to other relevant bio-molecular data. This means that for all the effort that goes into them, it is difficult to reuse these datasets in new studies. There are many reasons why sharing imaging data has been so difficult until now, most notably the heterogeneity and complexity of the image data, but also the lack of a critical mass of storage, compute and curation expertise.

To address this challenge, scientists at the University of Dundee, the European Bioinformatics Institute (EMBL-EBI), the University of Bristol and the University of Cambridge have launched a prototype repository for imaging data: the Image Data Resource (IDR). The new resource integrates imaging data with molecular and phenotype data. IDR includes information on experimental protocols: parameters, analyses and the effects scientists have observed in cells and features, for example.

To demonstrate the power of the new repository the researchers used data deposited in the IDR to identify genes from different studies that, when mutated or removed, caused cells to elongate and stretch out. Information from several different studies was used to built a gene network, which provides insights into how these genes affect cell shape which is an important property to consider in metastatic cancer. 

The prototype public image repository contains a broad range of data, including:


  • High-content screening
  • Super-resolution microscopy
  • Time-lapse imaging
  • Digital pathology imaging
  • Experimental protocol metadata
  • Observed effects in cells and features
  • Cross references with molecular archives


The next step is to secure the support and investment needed to transform the prototype into a production-ready imaging infrastructure. IDR's software and technology is open source, so it can be accessed and built into other image data publication systems. At this point this new project focuses on microscopic imaging but why not expanding into images of entire organisms or specific traits?

Friday, June 23, 2017

Weekend reads

New reading material for the weekend or for those of you that are blessed with some better weather perhaps for Monday morning back at work. 


Bird remains that are difficult to identify taxonomically using morphological methods, are common in the palaeontological record. Other types of challenging avian material include artefacts and food items from endangered taxa, as well as remains from aircraft strikes. We here present a DNA-based method that enables taxonomic identification of bird remains, even from material where the DNA is heavily degraded. The method is based on the amplification and sequencing of two short variable parts of the 16S region in the mitochondrial genome. To demonstrate the applicability of this approach, we evaluated the method on a set of Holocene and Late Pleistocene postcranial bird bones from several palaeontological and archaeological sites in Europe with good success.

Community-level data, the type generated by an increasing number of metabarcoding studies, is often graphed as stacked bar charts or pie graphs that use color to represent taxa. These graph types do not convey the hierarchical structure of taxonomic classifications and are limited by the use of color for categories. As an alternative, we developed metacoder, an R package for easily parsing, manipulating, and graphing publication-ready plots of hierarchical data. Metacoder includes a dynamic and flexible function that can parse most text-based formats that contain taxonomic classifications, taxon names, taxon identifiers, or sequence identifiers. Metacoder can then subset, sample, and order this parsed data using a set of intuitive functions that take into account the hierarchical nature of the data. Finally, an extremely flexible plotting function enables quantitative representation of up to 4 arbitrary statistics simultaneously in a tree format by mapping statistics to the color and size of tree nodes and edges. Metacoder also allows exploration of barcode primer bias by integrating functions to run digital PCR. Although it has been designed for data from metabarcoding research, metacoder can easily be applied to any data that has a hierarchical component such as gene ontology or geographic location data. Our package complements currently available tools for community analysis and is provided open source with an extensive online user manual.

Studying taxonomic and ecological diversity of phytoplankton assemblages is often difficult because morphological analysis cannot provide a complete description of their composition. Therefore, more robust and feasible approaches have to be chosen to elucidate the interactions between environmental and human pressures and phytoplankton assemblages. The Ocean Sampling Day (OSD) allowed collecting seawater samples from a wide range of oceanic regions including the Mediterranean Sea. In this study, a total of 754,167 V4-18S ribosomal DNA (rDNA) metabarcodes derived from 20 plankton samples collected at 19 sampling sites across the coastal areas of the Mediterranean Sea were analyzed to explore the relationships between phytoplankton assemblages' composition, sub-regional environmental features and human pressures. We reduced the whole set of autotroph plankton (1398 OTUs) to a smaller number of ecologically relevant entities (205 taxa) and used the latter for analysing the structure of phytoplankton assemblages. Chaetoceros was the only genus occurring in all the samples, while the number of taxa was maximum in the W Mediterranean. Based on the assigned OTUs, the structure of E Mediterranean phytoplankton was the most homogeneous. Further, phytoplankton assemblages from the three Mediterranean sub-regions (Western, Adriatic and Eastern) were significantly different (R=0.25, p=0.0136) based on Jaccard similarity. We also observed that phytoplankton diversity and human impact on marine ecosystems were not significantly related to each other based on Mantel's test.

Human impact on marine benthic communities has traditionally been assessed using visible morphological traits and has focused on the macrobenthos, whereas the ecologically important organisms of the meio- and microbenthos have received less attention. DNA metabarcoding offers an alternative to this approach and enables a larger fraction of the biodiversity in marine sediments to be monitored in a cost-efficient manner. Although this methodology remains poorly standardised and challenged by biases inherent to rRNA copy number variation, DNA extraction, PCR, and limitations related to taxonomic identification, it has been shown to be semi-quantitative and useful for comparing taxon abundances between samples. Here, we evaluate the effect of replicating genomic DNA extraction in order to counteract small scale spatial heterogeneity and improve diversity and community structure estimates in metabarcoding-based monitoring. For this purpose, we used ten technical replicates from three different marine sediment samples. The effect of sequence depth was also assessed, and in silico pooling of DNA extraction replicates carried out in order to maintain the number of reads constant. Our analyses demonstrated that both sequencing depth and DNA extraction replicates could improve diversity estimates as well as the ability to separate samples with different characteristics. We could not identify a "sufficient" replicate number or sequence depth, where further improvements had a less significant effect. Based on these results, we consider replication an attractive alternative to directly increasing the amount of sample used for DNA extraction and strongly recommend it for future metabarcoding studies and routine assessments of sediment biodiversity.

Terrestrial animals must have frequent contact with water to survive, implying that environmental DNA (eDNA) originating from those animals should be detectable from places containing water in terrestrial ecosystems. Aiming to detect the presence of terrestrial mammals using forest water samples, we applied a set of universal PCR primers (MiMammal, a modified version of fish universal primers) for metabarcoding mammalian eDNA. The versatility of MiMammal primers was tested in silico and by amplifying DNAs extracted from tissues. The results suggested that MiMammal primers are capable of amplifying and distinguishing a diverse group of mammalian species. In addition, analyses of water samples from zoo cages of mammals with known species composition suggested that MiMammal primers could successfully detect mammalian species from water samples in the field. Then, we performed an experiment to detect mammals from natural ecosystems by collecting five 500-ml water samples from ponds in two cool-temperate forests in Hokkaido, northern Japan. MiMammal amplicon libraries were constructed using eDNA extracted from water samples, and sequences generated by Illumina MiSeq were subjected to data processing and taxonomic assignment. We thereby detected multiple species of mammals common to the sampling areas, including deer (Cervus nippon), mouse (Mus musculus), vole (Myodes rufocanus), raccoon (Procyon lotor), rat (Rattus norvegicus) and shrew (Sorex unguiculatus). Many previous applications of the eDNA metabarcoding approach have been limited to aquatic/semiaquatic systems, but the results presented here show that the approach is also promising even for forest mammal biodiversity surveys.

Benthic communities are key components of aquatic ecosystems' biomonitoring. However, morphology-based species identifications remain a low-throughput, and sometimes ambiguous, approach. Despite metabarcoding methodologies have been applied for above-species taxa inventories in marine meiofaunal communities, a comprehensive approach providing species-level identifications for estuarine macrobenthic communities is still lacking. Here we report a combination of experimental and field studies that demonstrate the aptitude of cytochrome oxidase I (COI) metabarcoding to provide robust species-level identifications within a framework of high-throughput monitoring of estuarine macrobenthic communities. To investigate the ability to recover DNA barcodes from all species present in a bulk community DNA extract, we assembled experimentally 3 phylogenetically diverse communities, and used in each 4 different primer pairs to generate an equal number of different PCR products of the COI barcode region. Between 78 and 83% of the species in the tested communities were recovered through multi-primer high throughput sequencing (HTS). Two primer pairs were sufficient to attain these recovery rates. Subsequently, we compared morphology and metabarcoding-based approaches to determine the species composition of macrobenthos from four distinct sites of the Sado estuary, Portugal. Our results indicate that the species richness would be considerably underestimated if only morphological methods were used. Although further refinement is required for improving the efficiency and output of this approach, here we show the great aptitude of COI-multi-primer metabarcoding to provide high quality and auditable species identifications in macrobenthos monitoring.

Wednesday, June 21, 2017

2017 GBIF Ebbe Nielsen Challenge






For the third year GBIF is running its Ebbe Nielsen Challenge. Developers and data scientists have three months to create and submit tools capable of liberating species records from open data repositories for scientific discovery and reuse. Here some more details:

Background
This year's Challenge will seek to leverage the growth of open data policies among scientific journals and research funders, which require researchers to make the data underlying their findings publicly available. Adoption of these policies represents an important first step toward increasing openness, transparency and reproducibility across all scientific domains, including biodiversity-related research.

To abide by these requirements, researchers often deposit datasets in public open-access repositories. Potential users are then able to find and access the data through repositories as well as data aggregators like OpenAIRE and DataONE. Many of these datasets are already structured in tables that contain the basic elements of biodiversity information needed to build species occurrence records: scientific names, dates, and geographic locations, among others.

However, the practices adopted by most repositories, funders and journals do not yet encourage the use of standardized formats. This approach significantly limits the interoperability and reuse of these datasets. As a result, the wider reuse of data implied if not stated by many open data policies falls short, even in cases where open licensing designations (like those provided through Creative Commons) seem to encourage it.

The challenge
The 2017 GBIF Ebbe Nielsen Challenge seeks submissions that repurpose these datasets and adapting them into the Darwin Core Archive format (DwC-A), the interoperable and reusable standard that powers the publication of almost 800 million species occurrence records from the nearly 1,000 worldwide institutions now active in the GBIF network.

The 2017 Ebbe Nielsen Challenge will task developers and data scientists to create web applications, scripts or other tools that automate the discovery and extraction of relevant biodiversity data from open data repositories. Such tools might generate datasets ready for publication on GBIF.org by:

  • Automating searches of open data available in public repositories
  • Effectively mining the information needed to generate checklists, species occurrence and sampling-event datasets (e.g. scientific names, date and location of occurrence et al.) from datasets in these repositories
  • Mapping datasets’ column headings and/or contents with standardized Darwin Core terms
  • Routinely converting the reformatted data into Darwin Core archive formats ready for publication through GBIF.org

Friday, June 16, 2017

Weekend reads

Hot of the press - more reading material from the DNA barcoding community. Not as many as last week in which I had a lot of catch up to do. Nevertheless, very interesting reads.

Thirty-four species of Culicidae are present in the UK, of which 15 have been implicated as potential vectors of arthropod-borne viruses such as West Nile virus. Identification of mosquito feeding preferences is paramount to the understanding of vector-host-pathogen interactions which, in turn, would assist in the control of disease outbreaks. Results are presented on the application of DNA barcoding for vertebrate species identification in blood-fed female mosquitoes in rural locations. Blood-fed females (n = 134) were collected in southern England from rural sites and identified based on morphological criteria. Blood meals from 59 specimens (44%) were identified as feeding on eight hosts: European rabbit, cow, human, barn swallow, dog, great tit, magpie and blackbird. Analysis of the cytochrome c oxidase subunit I mtDNA barcoding region and the internal transcribed spacer 2 rDNA region of the specimens morphologically identified as Anopheles maculipennis s.l. revealed the presence of An. atroparvus and An. messeae. A similar analysis of specimens morphologically identified as Culex pipiens/Cx. torrentium showed all specimens to be Cx. pipiens (typical form). This study demonstrates the importance of using molecular techniques to support species-level identification in blood-fed mosquitoes to maximize the information obtained in studies investigating host feeding patterns.

We used a 227-bp fragment of the mitochondrial gene cytochrome oxidase I (DNA "barcode") in conjunction with morphological data to study specimens of the Neotropical genus Orthocomotis Dognin, 1906, acquired from natural history collections. We examined over 20 species of Orthocomotis from 17 localities in Colombia, Ecuador, and Peru. The analysis identified 32 haplotypes among the 62 specimens and found no haplotypes shared among species. The molecular study revealed not only the usefulness of short COI sequences in discriminating among Orthocomotis species but also showed distinctness of four clusters which correspond to those based on morphological (genitalia) characters. Moreover, the molecular results suggest the occurrence of rapid speciation in Orthocomotis. We hypothesize that this may be linked to the great biodiversity of potential host plants in Neotropical ecosystems.

Taxonomic identification of pollen has historically been accomplished via light microscopy but requires specialized knowledge and reference collections, particularly when identification to lower taxonomic levels is necessary. Recently, next-generation sequencing technology has been used as a cost-effective alternative for identifying bee-collected pollen; however, this novel approach has not been tested on a spatially or temporally robust number of pollen samples. Here, we compare pollen identification results derived from light microscopy and DNA sequencing techniques with samples collected from honey bee colonies embedded within a gradient of intensive agricultural landscapes in the Northern Great Plains throughout the 2010-2011 growing seasons. We demonstrate that at all taxonomic levels, DNA sequencing was able to discern a greater number of taxa, and was particularly useful for the identification of infrequently detected species. Importantly, substantial phenological overlap did occur for commonly detected taxa using either technique, suggesting that DNA sequencing is an appropriate, and enhancing, substitutive technique for accurately capturing the breadth of bee-collected species of pollen present across agricultural landscapes. We also show that honey bees located in high and low intensity agricultural settings forage on dissimilar plants, though with overlap of the most abundantly collected pollen taxa. We highlight practical applications of utilizing sequencing technology, including addressing ecological issues surrounding land use, climate change, importance of taxa relative to abundance, and evaluating the impact of conservation program habitat enhancement efforts.

BACKGROUND:
Claims abound that the Transvaal red milkwood, Mimusops zeyheri, indigenous to areas with tropical and subtropical commercial fruit trees and fruiting vegetables in South Africa, is relatively pest free owing to its copious concentrations of latex in the above-ground organs. On account of observed fruit fly damage symptoms, a study was conducted to determine whether M. zeyheri was a host to the notorious quarantined Mediterranean fruit fly (Ceratitis capitata).
RESULTS:
Fruit samples were kept for 16-21 days in plastic pots containing moist steam-pasteurised growing medium with tops covered with a mesh sheath capable of retaining emerging flies. Microscopic diagnosis of the trapped flies suggested that the morphological characteristics were congruent with those of C. capitata, which was confirmed through cytochrome c oxidase I (COI) gene sequence alignment with a 100% bootstrap value and 99% confidence probability when compared with those from the National Centre for Biotechnology Information database.
CONCLUSION:
This study demonstrated that M. zeyheri is a host of C. capitata. Therefore, C. capitata from infestation reservoirs of M. zeyheri fruit trees could be a major threat to the tropical and subtropical fruit industries in South Africa owing to the fruit-bearing nature of the new host.

International agreements mandate the expansion of Earth's protected-area network as a bulwark against the continued extinction of wild populations, species, and ecosystems. Yet many protected areas are underfunded, poorly managed, and ecologically damaged; the conundrum is how to increase their coverage and effectiveness simultaneously. Innovative restoration and rewilding programmes in Costa Rica's Area de Conservacion Guanacaste and Mozambique's Parque Nacional da Gorongosa highlight how degraded ecosystems can be rehabilitated, expanded, and woven into the cultural fabric of human societies. Worldwide, enormous potential for biodiversity conservation can be realized by upgrading existing nature reserves while harmonizing them with the needs and aspirations of their constituencies.

Seed dispersal constitutes a pivotal process in an increasingly fragmented world, promoting population connectivity, colonization and range shifts in plants. Unveiling how multiple frugivore species disperse seeds through fragmented landscapes, operating as mobile links, has remained elusive owing to methodological constraints for monitoring seed dispersal events. We combine for the first time DNA barcoding and DNA microsatellites to identify, respectively, the frugivore species and the source trees of animal-dispersed seeds in forest and matrix of a fragmented landscape. We found a high functional complementarity among frugivores in terms of seed deposition at different habitats (forest vs. matrix), perches (isolated trees vs. electricity pylons) and matrix sectors (close vs. far from the forest edge), cross-habitat seed fluxes, dispersal distances, and canopy-cover dependency. Seed rain at the landscape-scale, from forest to distant matrix sectors, was characterized by turnovers in the contribution of frugivores and source-tree habitats: open-habitat frugivores replaced forest-dependent frugivores, whereas matrix trees replaced forest trees. As a result of such turnovers, the magnitude of seed rain was evenly distributed between habitats and landscape sectors. We thus uncover key mechanisms behind 'biodiversity-ecosystem function' relationships, in this case, the relationship between frugivore diversity and landscape-scale seed dispersal. Our results reveal the importance of open-habitat frugivores, isolated fruiting trees, and anthropogenic perching sites (infrastructures) in generating seed dispersal events far from the remnant forest, highlighting their potential to drive regeneration dynamics through the matrix. This study helps to broaden the 'mobile link' concept in seed dispersal studies by providing a comprehensive and integrative view of the way in which multiple frugivore species disseminate seeds through real-world landscapes.

Thursday, June 15, 2017

Plants and climate change

Plants provide us with food, pastures for livestock, and places for recreation and wellbeing. They also directly and indirectly provide numerous invaluable ecosystem services such as water regulation, carbon sequestration and flood prevention. As a result, it is imperative that we understand how plant populations are responding to climate constraints now, and use that information to predict how they are likely to respond to climatic changes in the future.

In fact it might be very important to assess the persistence strategies of plants in any given habitat. Noting its mere presence does not paint a very useful picture as a species may be found in a particular area but that doesn't mean it is making much of a living there; it may, just, be making ends meet for the time being. An international group of ecologists tested the links between climate suitability and persistence strategies for nearly 100 populations of over 30 species of trees and herbs growing on 3 continents and 16 countries across the globe. Some of these data were gathered over the duration of a decade, allowing the researchers to identify emergent patterns linked to climate change with greater confidence.

What they found is that while many species are able to persist in less favourable climate conditions, those same species often do so by adopting last-stand strategies such as shrinking in size and temporarily suspending reproductive and vegetative growth. This merely helps them to survive and makes them more vulnerable to further changes and to disturbances such as wildfires or pest outbreaks. Many such disturbances are more likely today due to changing climates.

Not all plants have the life strategies to persist for extended periods of time in less favourable climates but our research is already helping to pinpoint those that do. One of the next steps is to design management strategies to help support these species and to safeguard the ecosystem services that they provide us.