Chris Hadfield's farewell

Awesome!

The Plague of Justinian

In 541 AD, eight centuries before the Black Death, a deadly infectious disease hit the Byzantine Empire, reaching Constantinople in 542 and North Africa, Italy, Spain, and the French-German border by winter 543. The so called “Plague of Justinian”, named after the contemporaneous emperor, led to mass mortality in Europe similar to that of the Black Death. It persisted in the territory of the Roman Empire until the middle of the 8^th century and likely contributed to its decline, shaping the end of antiquity.

Based on historic records it had been assumed this Justinian plague was similar to the bubonic plague that struck Europe eight centuries later. However, some discrepancies between historical accounts and the progression of infections with the bacterium that causes the plague (Yersinia pestis) caused considerable debate among scientists about whether it is the same disease or a completely different infection. This was further complicated by the fact that the origin of the disease was unknown, although it is thought to have arrived from Egypt through trade ships.

A new study now confirmed unambiguously that Yersinia pestis was indeed the causing agend of this first pandemic. The researchers used ancient DNA analyses on samples obtained from an early medieval cemetery in Achheim in Bavaria, Germany. By using both quantitative Real-Time PCR and a conventional PCR approach they amplified and sequenced a 70 bp portion and a 133 bp fragment of the Yersinia pestis-specific plasminogen activator gene (pla). This gene, which is specific to Yersinia pestis, has been used in previous studies to test samples from plague skeletons dating to the time of the Black Death. The group was also able track down the origins of this plague. As for the second and third pandemic, the original sources of the bacillus were in Asia.

The question remains if at Justinian times only one strain or several were introduced to Europe. The latter was the case for the Black Death in the 14th century. 

Amazing what a couple of bones are able to tell us more than 1400 years after they were buried.

A new bass

Micropterus haiaka (Choctaw bass)

Florida Fish and Wildlife Conservation Commission researchers say they've discovered a new species of fish in the southeastern U.S. They  first noticed a new DNA profile (unfortunately they don't say which gene region they've used) while testing a bass specimen from the Chipola River in 2007 as part of a broader genetic study of bass. After confirming the initial discovery the researchers searched for similar DNA profiles in bass caught in nearby rivers to determine the fish's range. They found the Choctaw bass in coastal rivers in Alabama and along the western Florida panhandle, including Choctawhatchee River.

The Choctaw bass is morphologically very similar to the spotted bass (Micropterus punctatus), and that's why no one had previously distinguished the two different species, in spite of decades of bass research. Have a look at both images and see for yourself. Only by counting scales, fin rays and gill rakers one will perhaps be able to tell them apart - or simply by using DNA Barcoding.

Micropterus punctatus (Spotted bass)

The new fish's name was chosen because its range overlaps with  the historic range of the Native American Choctaw. "Haiaka" is a Choctaw word meaning "revealed" or "manifest".

School Malaise project leaps forward

All samples are back. The traps of our School Malaise Trap program were filled with lots of bugs and our amazing collection team broke pretty much every record. We can't thank them enough for their tireless effort! 

22 000 specimens ready for DNA Barcoding in 35 hours. 

The team counted more than 95 000 individuals in total. Given that not very long ago we still had lots of snow covering the ground this number becomes even more impressive.

Maybe the sample with the most individuals (one week catch)

Samples bottles from the schools

Jenny Gleason happily counting and sorting

Plates ready for DNA extraction

DNA extraction, Paul Janetta keeps a close eye on  the precious samples.

Jayme Sones labels specimens...

...that were sorted and pinned by Crystal Sobel

Know your enemy

The wheat curl mite, Aceria tosichella (Eriophyoidea), is widely distributed worldwide and has a broad host range that includes most cereals and several native and introduced grasses. Unless found in extremely high numbers, wheat curl mites generally cause little direct damage in the field other than the characteristic leaf curling and the occasional trapping of the flag leaf. However, both immature and adult wheat curl mite transmit Wheat Streak Mosaic Virus. 

The majority of eriophyoid species are actually known to be highly host-specific; thus the wide host range exhibited by Aceria tosichella (more than 80 species) has long been regarded as an anomaly. More recent research in Australia showed that there are actually at least two local lineages with overlapping geographical distributions and that only one of them is implicated in Wheat Streak Mosaic Virus transmission. 

Now a group of reasearchers from Poland collected morphologically similar Aceria tosichella populations from only five host plants in a small area of western Poland. They used DNA Barcoding and the nuclear D2 region of 28S rDNA to assess genetic lineages and test if Aceria tosichella really is a single, highly polyphagous species. 

Their study reveals that the wheat curl mite is composed of several discrete genetic lineages with variable host ranges and therefore variable pest potential, indicating not only the likely existence of a cryptic species complex, but also the potential for more genetic and host-range diversity if populations are sampled over a broader area on more of the approximately 80 recorded host plants for this species. Only two lineages in the present study appear to have high pest potential on cereals (one specifically for barley), whereas several others appear to specialize on wild grass species.

There is a lot left to do in order to find out which lineage is harmful and which not. At least we have a good idea on how to do it.

Old fish bones

In 1996 a shipwreck was discovered during a survey of the Dor lagoon on the Israeli Mediterranean coast, south of  Haifa. Based on some metal objects and Carbon14 tests of some organic materials, the so called Tantura F shipwreck was dated to the 7-8th centuries AD which is known to be the region’s Early Islamic period.

Among the findings were eight amphorae made of Nile Delta silt with resinous linings. The 6-7-liter amphorae contained bones  from all parts of the fish skeleton, indicating that the amphorae once contained whole fish. Preliminary morphological analysis of the bones at the University of Haifa assigned the fish to the genus Tilapia but a group of researchers wanted to confirm the species identities and used short DNA Barcodes (mini-barcodes) to find out which load the ship had carried 1400 years ago.

Given the age of the samples they could only retrieve a 140bp fragment which didn't allow a full species designation but the fact that on this length there was only one bp difference to the two Tilapia species Oreochromis aureus and Sarotherodon galilaeus (transition from G to A) certainly confirms the intitial identification. The authors speculate that the ancient fish belonged to an extinct species or sub-species closely related to the two contemporary species. I find that a bit of a stretch given the short length of the sequences. One nucleotide difference on a length of 140bp. That makes perhaps 5 on the entire DNA Barcode region assuming equal distribution of mutations (unlikely, but for this little exercise it will do). That is probably half a percent divergence. Among fishes that rarely qualifies for different species.

That should not divert from the results as such. I find it pretty cool that DNA Barcoding can help with archeology. Let's not forget that the amphorae contained all parts of the fish skeleton which makes identification by morphology possible. Imagine you only have one little fragment.

C for Colombia

With coastlines on the Pacific and Atlantic Oceans, Andean mountains, and Amazon basins, Colombia’s landscapes are vast and vastly diverse. Here, where the Pacific, Amazonian, Caribbean, and Orinoquian lowland regions meet, the landscapes are a patchwork of mangroves, snow-capped peaks, grasslands, deserts, wetlands, rainforests, dry forests, cloud forests, and other habitats. While world-renowned for its richness in bird species, Colombia also has an extraordinary diversity of amphibians and mammals, as well as orchids and butterflies.

Colombia became a member of the iBOL family at the end of 2011. It is the the second most biodiverse country in the world only topped by Brazil. It is perhaps the country with the most bird species in the world. 

However, human induced deforestation has already substantially changed the Andean landscape in Colombia. It is also linked to the conversion of lowland tropical forests to palm oil plantations. However, compared to neighboring countries rates of deforestation in Colombia are still relatively low. Other challenges are caused by natural factors such as the geological instability related to Colombia's position along the Pacific Ring of Fire. Colombia has 15 major volcanoes, the eruptions of which have on occasion resulted in substantial loss of life. Geological faults that have caused numerous devastating earthquakes. Heavy floods both in mountainous areas and in low-lying watersheds and coastal regions regularly occur during the rainy seasons with varying rainfall intensities due to the El Niño-Southern Oscillation.

Reason enough to engage in a global DNA Barcoding program such as iBOL but this is certainly not the only initiative to catalog the country's life.

Colombian researchers have been part of DNA Barcoding studies e.g. on amphibians, mosquitoes, or plants. They are leads of important initiatives to help build the global library of DNA Barcodes (e.g. ArBOL, ColdCode). It is estimated that Colombia might be the home to 150,000 to 200,000 species. About 1000 of them are barcoded (mostly lepidoptera, amphibians, and birds). A lot left to do but I am sure Colombia will catch up very quickly.