Fleshing out Yersinia pestis

Up until a few months ago there were a few representative samples of the Yersinia pestis genome. Important windows into its secrets, but windows none the less. In January a Chinese group remedied this situation by expanding the number of fully sequenced genomes from 15 to 133 (Cui et al, 2013).  China supplied 107 genomes selected from over 900 genotyped specimens collected since 1955 to represent bacterial and host diversity. To these, 11 additional isolates from Mongolia, Myanmar (Burma), the former Soviet Union, and Madagascar were fully sequenced. For the analysis, the previously sequenced 15 genomes were added bringing the total up to 133 including the ancient specimens from 14th century London.

The Core-Genome and the Pan-Genome

Even for a bacterium like Yersinia pestis that is considered to have little genetic diversity, its genome is more elastic than any eukaryote (everything but bacteria). The bacterial genome can be divided into its core genome, found in all members of the species, and the accessory genome, sequences found only in some strains. Plasmids are part of the accessory genome but not all of it. Extra genes are also found on the bacterial chromosome. The core genome is 3.53 Mb long with 3450 genes; the accessory genome has 1.92 Mb with 1249 genes (including 451 on the six known plasmids) (Cui et al, 2013, Table S1). So the accessory genome contains 26% of genes found in the species. This may seem like a lot, but more promiscuous species like Escherishia coli (E. coli) have many more accessory genes than core genes. With E. coli the more specimens that are sequenced, the larger the accessory genome gets with no end in sight.

Combining all of the genes found in Yersinia pestis (core and accessory genome), we have the pan-genome. The pan-genome is 5.46 Mb with 4699 genes (Cui et al, 2013).  No one strain has all of these genes. So different strains do have significant differences in their functions but, as far as I know, there are no significant differences in human prognosis. Hopefully, there will be more study in the future that cross-references strain type  or particular genes with human prognosis, transmission routes (% bubonic vs pneumonic), hosts etc.

Branching Out

Using known and new SNPs, the phylogenetic tree has finally been fleshed out into a healthy looking tree . We couldn’t keep the sickly looking Charlie Brown tree of the past forever! Even so, the tree below represents only the main branches.

Click to enlarge, (Cui et al, PNAS, 2013)

To my mind, the most important aspect of the new tree is that nodes of increased diversity are much more apparent. The authors are the most excited by node 7 where there is a four-way branch, adding two new branches  (3.ANT1 and 4.ANT1) to the main stem of the tree. They refer to this diversity point as the ‘big bang’. This node gains the most attention because the 14th century London genomes are just one step off of node 7 down the 1.ANT1 branch. So it stands the reason that node 7 represents a period of diversity that produced the second pandemic. Yet, looking at their diagram, other locations like node 12 have greater diversity. The 1.IN strains are intermediary on the same lineage between the second the third pandemic. Node 14 is the initial diversity that produced the third pandemic.  Calling node 7 a ‘big bang’ seems to me to have more to do with it producing the second pandemic rather than the diversity at the node itself. The new third and fourth branch (3.ANT and 4.ANT) are concentrated in Mongolia, putting emphasis on the importance of doing such deep sequencing in other Central Asian regions. It is impossible to tell which host species these bursts of diversity occurred within, almost certainly not humans. It’s not that diversity can’t be generated in humans especially during a pneumonic plague, but since it is not endemic in humans,  it must make it back to a reservoir to be preserved anywhere other than in ancient DNA.

Biogeography shows clustering of related strains in regions as would be expected, though they are fairly well mixed within the circled zone in the map above. Samples seem to follow ancient roads, although keep in mind all of these strains have been isolated within the last 60 years.   I do wonder why they were not able to identify a route for the eastern branch two isolates. All of the branch two isolates appear to be running along a fairly straight line from southwest to northeast China (extending trade route III to Manchuria). The 107 Chinese specimens were chosen from > 900 strains identified from 5000 isolates for their diversity revealed by genotyping, host diversity and geography (Cui et al, 2013). It would have been interesting to see a map with all 5000 on it as a measure of abundance (with or without typing).

The oldest strain 0.PE7 is found only on the Qinghai-Tibet plateau in China, an area framed by the ancient trade routes along which most of the western strains are found. This has led Cui et al, 2013 to postulate that the  Qinghai-Tibet plateau as the origin of  Yersinia pestis.

Unsteady Molecular Clocks

Estimating ages from genetics can be a very risky business. To estimate years since the last common ancestor, it requires a steady molecular clock , measured in base changes per unit of time. In theory all of the genes from the core genome should have changed to the same degree from the common ancestor, but that is not the case at all. The number of SNPs in the Yersinia pestis core genome varies greatly. Even excluding the most divergent Angola (0.PE3) strain, there is “a nearly 40 fold difference between the slowest and the fastest evolving branches” (Cui et al, 2013). An unsteady molecular clock was also suggested by previous data from Madagascar, though the discussion was buried in the supplementary material (Morelli et al, 2010, p. S10-s18). Mutator phenotypes do occur (Rajanna et al, 2013), though Cui et al, 2013 assure us that none of these strains are mutators.  On the other hand, a Georgian group suggest that the mutator phenotype, a single point mutation, could naturally reverse (back mutate) altering the predictability of the lineage age (Rajanna et al, 2013). The Chinese group concluded that the faster clock rates for some branches are due to a higher reproduction rate, probably due to more or larger epidemics in the lineage (Cui et al, 2013). The types of genetic changes (SNPs) indicate neutral selection, so the increased reproduction rate is not due to the genetic changes.

While I understand that calculating divergence dates an important exercise to people who focus on phylogenetics, for the understanding of historical plague it is not useful. It is not solid or specific enough to base historical events upon alone. Predictions are just that; all of these groups have been proven wrong, sometimes later by themselves, too often.  Most importantly, it appears that it will eventually be trumped by ancient DNA analysis with an archaeological and/or documentary context. As far as I’m concerned, the Angola strain is a genetic and geographic outlier of uncertain provenance. We don’t know important factors like how long it was kept in active culture before it was made into a stock or the conditions of storage. Both of these can effect mutation rates and the molecular clock (Rajanna et al, 2013).  I’m sure the Angola strain’s story is interesting but unlikely to be useful for understanding the whole species unless it turns up in ancient DNA.

Gaining and Loosing Diversity

Returning to these starburst points on the tree, called polytomys, where multiple lineages share the same ancestor, we have some of the most valuable information in the new phylogenetic tree. Epidemics (and presumably epizootics) are believed to have an increased reproduction rate over enzootic plague. Since the mutation rate is directly tied to the reproduction rate, increased reproduction rates predict an increased mutation rate and, therefore, production of genetic diversity.  The team predicts that “higher clock rates are an indicator of epidemic disease, even in the absence of historical evidence” (Cui et al, 2013). It is unclear how an epidemic can be differentiated from an epizootic by genetics alone. We know from modern observations that not all epizootics spill over into the human population. Yet, major polytomys can at least be used to estimate how many bursts of growth the bacterium has gone through in China. We should see other polytomys with increased sequencing of other Central Asian regions.

While these polytomys show a starburst of new lineages, there is also a loss of diversity during every epidemic. Most of the new lineages produced during an epidemic (or epizootic) will die out (become extinct) when the epidemic ends. If the changes are truly neutral, then which lineage survives to endure in the reservoir will be completely random (as will be the number of surviving lineages). We should also remember that clinical isolates  during an epidemic and ancient DNA can preserve lineages that become extinct (and this is normal). In the four individuals they sequenced from 14th century East Smithfield, they found two different clones, with the second being derivative of the first. Both of these clones may only be found in ancient DNA, not in any living specimen. The more time that passes the greater the likelihood that the minor lineages will become extinct. This tends to make the earlier sections of the pylogenetic tree look cleaner by stripping off side branches.

Another recent study by Vogler et al (2013), supports their scenario on a finer scale during the 9 year epidemic in a port town of Mahajana,  Madagascar from 1991 to 1999. Over a decade we can compare the incidence of plague vs. the genetic diversity. Yersinia pestis evolution can be plotted with great precision. In the lower diagram, clones are color coded to the year of isolation. From 1995 to 1999 it is possible to see the next year’s primary clone emerge in the previous year’s epidemic, which supports local cycling within the city. At the same time, most of the diversity generated is not represented in later outbreaks.

Vogler et al, 2013

Vogler et al, 2013

Host Diversity

Host genus vs Y. pestis strain collected (Cui et al, 2013).

The hosts of these 107 strains give us a glimpse into the host diversity for Yersinia pestis within China (Cui et al, 2013). The figure to the right gives an indication of strain diversity within each host but does not tell us abundance or location within China. What jumps out at me, is that humans and marmots have the most strain diversity. The high strain diversity in humans including 0.PE7, the strain closest to the most recent common ancestor, suggests to the Chinese team that Yersinia pestis has been pathogenic to humans since it evolved (Cui et al, 2013). Thus, at no point in its evolution did it gain the ability to infect humans. The few strains that can not infect humans are hypothesized to have lost their ability to infect humans possibly as a function of purifying selection for voles as hosts. It is interesting that the 1.ORI strains of the third pandemic are only found in humans, rats and mice.  We have to be careful about taking this figure to represent abundance or importance of a particular host. The great gerbil, Rhombomys opimus, is a primary host throughout central Asia is is represented by only one strain in this figure.

Studies published this winter have moved us significantly down the road to fleshing out Yersinia pestis. The genetic survey of Y. pestis in China provides a firm foundation to build on as more ancient DNA becomes available and extensive sequencing is done in other regions. Madagascar continues to be the best laboratory for plague ecology and epidemiology, while the Georgian study begins to address unintended intra-laboratory evolution that may shed light on Y. pestis in the wild. I’ll return to these papers again soon as I continue to examine Y. pestis from different perspectives and ruminate on answers to other questions.

References:

Cui, Y., Yu, C., Yan, Y., Li, D., Li, Y., Jombart, T., Weinert, L., Wang, Z., Guo, Z., Xu, L., Zhang, Y., Zheng, H., Qin, N., Xiao, X., Wu, M., Wang, X., Zhou, D., Qi, Z., Du, Z., Wu, H., Yang, X., Cao, H., Wang, H., Wang, J., Yao, S., Rakin, A., Li, Y., Falush, D., Balloux, F., Achtman, M., Song, Y., Wang, J., & Yang, R. (2013). Historical variations in mutation rate in an epidemic pathogen, Yersinia pestis Proceedings of the National Academy of Sciences, 110 (2), 577-582 DOI: 10.1073/pnas.1205750110

Morelli G, Song Y, Mazzoni CJ, Eppinger M, Roumagnac P, Wagner DM, Feldkamp M, Kusecek B, Vogler AJ, Li Y, Cui Y, Thomson NR, Jombart T, Leblois R, Lichtner P, Rahalison L, Petersen JM, Balloux F, Keim P, Wirth T, Ravel J, Yang R, Carniel E, & Achtman M (2010). Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity. Nature genetics, 42 (12), 1140-3 PMID: 21037571

Rajanna C, Ouellette G, Rashid M, Zemla A, Karavis M, Zhou C, Revazishvili T, Redmond B, McNew L, Bakanidze L, Imnadze P, Rivers B, Skowronski EW, O’Connell KP, Sulakvelidze A, & Gibbons HS (2013). A Strain of Yersinia pestis With a Mutator Phenotype from the Republic of Georgia. FEMS microbiology letters PMID: 23521061

Vogler, A., Chan, F., Nottingham, R., Andersen, G., Drees, K., Beckstrom-Sternberg, S., Wagner, D., Chanteau, S., & Keim, P. (2013). A Decade of Plague in Mahajanga, Madagascar: Insights into the Global Maritime Spread of Pandemic Plague mBio, 4 (1) DOI: 10.1128/mBio.00623-12

Toward a Molecular History of Yersinia pestis (AHA)

This post a resource for the presentation I gave at the AHA meeting in New Orleans on January 5, 2013. A color handout of the slides can be downloaded here.

This map will be continually updated as new finds are published. Some of the balloons mark sites with multiple studies. Click on the balloons for citations.

View Larger Map

References:

Achtman, M. (2012). Insights from genomic comparisons of genetically monomorphic bacterial pathogens. Philosophical Transactions of the Royal Society B: Biological Sciences, 367(1590), 860–867. doi:10.1098/rstb.2011.0303

Bos, K. I., Schuenemann, V. J., Golding, G. B., Burbano, H. A., Waglechner, N., Coombes, B. K., et al. (2011). A draft genome of Yersinia pestis from victims of the Black Death. Nature, 1–5. doi:10.1038/nature10549

Bos, K. I., Stevens, P., Nieselt, K., Hendrik N Poinar, DeWitte, S. N., & Krause, J. (2012). Yersinia pestis: New Evidence for an Old Infection. PLoS ONE, 7(11), e49803.

Drancourt, M., & Raoult, D. (2005). Palaeomicrobiology: current issues and perspectives. Nature Reviews Microbiology, 3(1), 23–35. doi:10.1038/nrmicro1063

Drancourt, M., Houhamdi, L., & Raoult, D. (2006). Yersinia pestis as a telluric, human ectoparasite-borne organism. The Lancet Infectious Diseases, 6(4), 234–241. doi:10.1016/S1473-3099(06)70438-8

Haensch, S., Bianucci, R., Signoli, M., Rajerison, M., Schultz, M., Kacki, S., et al. (2010). Distinct Clones of Yersinia pestis Caused the Black Death. (N. J. Besansky, Ed.)PLoS Pathogens, 6(10), e1001134. doi:10.1371/journal.ppat.1001134.t001

Houhamdi, L., Lepidi, H., Drancourt, M., & Raoult, D. (2006). Experimental model to evaluate the human body louse as a vector of plague. The Journal of Infectious Diseases, 194(11), 1589–1596. doi:10.1086/508995

Little, L. K. (2011). Plague Historians in Lab Coats*. Past & Present, 213(1), 267–290. doi:10.1093/pastj/gtr014

Malou, N., Tran, T.-N.-N., Nappez, C., Signoli, M., Le Forestier, C., Castex, D., et al. (2012). Immuno-PCR – A New Tool for Paleomicrobiology: The Plague Paradigm. (S. Bereswill, Ed.)PLoS ONE, 7(2), e31744. doi:10.1371/journal.pone.0031744.g006

Morelli, G., Song, Y., Mazzoni, C. J., Eppinger, M., Roumagnac, P., Wagner, D. M., et al. (2010). Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity. Nature Genetics. doi:10.1038/ng.705

Nguyen-Hieu, T., Aboudharam, G., Signoli, M., Rigeade, C., Drancourt, M., & Raoult, D. (2010). Evidence of a Louse-Borne Outbreak Involving Typhus in Douai, 1710-1712 during the War of Spanish Succession. PLoS ONE, 5(10), e15405. doi:10.1371/journal.pone.0015405

Parkhill, J., Wren, B. W., Thomson, N. R., Titball, R. W., Holden, M. T., Prentice, M. B., et al. (2001). Genome sequence of Yersinia pestis, the causative agent of plague. Nature, 413(6855), 523–527. doi:10.1038/35097083

Pusch, C. M., Rahalison, L., Blin, N., Nicholson, G. J., & Czarnetzki, A. (2004). Yersinial F1 antigen and the cause of Black Death. The Lancet Infectious Diseases, 4(8), 484–485. doi:10.1016/S1473-3099(04)01099-0

Raoult, D., Dutour, O., Houhamdi, L., Jankauskas, R., Fournier, P.-E., Ardagna, Y., et al. (2006). Evidence for louse-transmitted diseases in soldiers of Napoleon’s Grand Army in Vilnius. The Journal of Infectious Diseases, 193(1), 112–120. doi:10.1086/498534

Schuenemann, V. J., Bos, K., Dewitte, S., Schmedes, S., Jamieson, J., Mittnik, A., et al. (2011). PNAS Plus: Targeted enrichment of ancient pathogens yielding the pPCP1 plasmid of Yersinia pestis from victims of the Black Death. Proceedings of the National Academy of Sciences, 1–22. doi:10.1073/pnas.1105107108

Tran, T., Forestier, C., & Drancourt, M. (n.d.). Brief communication: Co‐detection of Bartonella quintana and Yersinia pestis in an 11th–15th burial site in Bondy, France. American Journal of ….

Tran, T.-N.-N., Signoli, M., Fozzati, L., Aboudharam, G., Raoult, D., & Drancourt, M. (2011). High throughput, multiplexed pathogen detection authenticates plague waves in medieval venice, Italy. PLoS ONE, 6(3), e16735. doi:10.1371/journal.pone.0016735

Wiechmann, I., & Grupe, G. (2004). Detection ofYersinia pestis DNA in two early medieval skeletal finds from Aschheim (Upper Bavaria, 6th century A.D.). American Journal of Physical Anthropology, 126(1), 48–55. doi:10.1002/ajpa.10276

Wiechmann, I., Harbeck, M., & Grupe, G. (2010). Yersinia pestis DNA Sequences in Late Medieval Skeletal Finds, Bavaria. Emerging Infectious Diseases, 16(11), 1806–1807.

On Giants Shoulders #54: A Sleigh Load of History

Welcome to On Giant’s Shoulders #54, the history of science blog carnival! Here, we celebrate the history of science with all its oddities, and modern science delves into the past. I can’t think of a better way to spend my third blogoversary (of regular blogging) here at Contagions. Just a few days away from the winter solstice, I managed to fill my sleigh with a load of science history links. Cuddle up with a warm mug of hot chocolate (or whatever warms you) and settle in for some good reading.

Festive Science and the Holiday Season

Since the culture war between science and religion heated up, there has been friction between science and religious holidays like Christmas. Rupert Cole of Notes & Theories reminds us that this was not always so. In Victorian England, the popularity of science and Christmas festivities peaked with the public at the same time and reveled in each other. Victorian Christmas plays and pageants were followed by science lectures to explain the featured science and technology! Public Christmas trees were decorated with scientific instruments that were given to children. Those were the days. Though some science folks still know how to mix up the traditions. In a throw back to at least the sixteenth century, Diane Mcllmoyle of Esmeralda’s Cumbrian History and Folklore writes about the holiday tradition of mummer’s plays with its requisite quack doctor.

History of Pseudoscience

Let’s kick this carnival off with a stimulating discussion on, of all things, the omnipresence and worth of (what we call today) pseudoscience. Rebekah Higgitt of The H Word addresses claims that pseudoscience is on the rise with a history lesson, and ThonyC of Renaissance Mathematicus goes one step further asserting that pseudoscience has sometimes been helpful to the development of science. Faye Flam of Lightning Rod writes on Michael Gordin’s recent research on pseudoscience. Continuing with the supernatural, Lindsey Fitzharris of The Chirurgeon’s Apprentice discusses Abraham Lincoln’s conversations with the dead.

Darwin and Evolution

As always posts on Charles Darwin must be featured in On Giant’s Shoulders. Suvrat Kher of Rapid Uplift writes about Darwin’s slow, deep-thinking methods. Michael Barton of The Dispersal of Darwin calls out more quote mining of Darwin by anti-Darwinists. James Randerson writes of the private life of Charles Darwin. The Alfred Russel Wallace Correspondence Project also launched this month to coincide with the centenary anniversary of his death in 2013. Tim Jones of Zoonomian celebrated the birthday of the other famous Darwin, the polymath Erasmus Darwin (d. 12.12.1731). He also visits Annie Darwin’s grave and reviews Dr Gully’s water cures.

Joachim D of Mousetrap posted on Herbert Spencer’s synthetic philosophy and the centrality of evolution in his thinking.

Archaeology

Kristina Killgrove of Powered by Osteons summarized Nutrition and Well-Being in the Roman World: The Evidence of Human Bones, a conference this fall in Rome. Katy Myers of Bones Don’t Lie discusses how isotope data from bones informs on the social structure of an Anglo-Saxon settlement. In another post she discusses skeletal weapon trauma in medieval Ireland confirming the violence in Irish medieval records. In her most recent post she discusses the discovery and analysis of the graves of victims of the attempted mutiny of The Batavia off the coast of Australia in 1628.

Epidemiology

Katy Meyers of Bones Don’t Lie discusses a new study examining osteological and molecular evidence of TB at three neolithic sites in Germany at the transition to farming. I have a post on the Black Death Network reviewing the molecular evidence of the Black Death. If you have any interest in the 14th century crises — plague, famine, cattle murrain etc. — check out the Black Death Network. Spirochetes Unwound discusses the latest theory on the mysterious epidemic of 1616-1619 that decimated native Americans along the New England coast. Here on Contagions, I posted on the isolation of smallpox DNA from 17th century Siberia. The History of Vaccines blog posted a sketch of smallpox vaccine production in a cow, along with a discussion of vaccine production in 1872. Bringing us up to the 20th century, Rebecca Kreston of Body Horrors brings us the story of the first case of HIV in a 1961 Norwegian teenager who brought an unusual strain of HIV (group O) to his family and seeded it across in Europe.

Genomics

Genomics can help unravel the history of peoples who have left little documentary record. History of the Ancient World Blog has a post on a new study examining Scythian genetic admixture. Katherine Harmon of Observations covers a new study showing Gypsy or Roma origins in India about 500 CE/AD. This places the movement of the Roma out of India into Central Asia during the Great Migrations period that occurred when the Western Roman Empire fell in the fifth century. Interesting to think of the Roma as the last of the 1500 year old Great Migration peoples. Also covered on Past Horizons.

Mike Drout and his team at Wheaton have been applying DNA analysis and statistics software to Old English texts to determine authorship. They call it Lexomics — check them out.

Medical Practice and Public Health

Early modern medical practice was in the spotlight this month. Mike Rendell, The Georgian Gentleman puts a spotlight on contemporary views of 18th century medical practice. Home remedies were not any more successful, as ThonyC of Renaissance Mathematicus writes about in George Boole’s death from his wife’s homeopathy. Jai Virdi of From the Hands of Quacks explores the motivations of Dr Curtis‘ founding of the Royal Dispensary for Diseases of the Ear. The Secret Histories Project brings us a biography of the unconventional Dr. James Barry, child genius, military surgeon, and annoyance of Florence Nightingale. Venessa Heggie of The H Word, writes on the 70th anniversary of the Beveridge Report, that founds the modern British welfare state, about earlier attempts to build a social safety net in Britain with Elizabethan Poor Laws and the infamous Victorian workhouses. New blogger Jennifer Evans of Early Modern Medicine writes about the rhetoric of men pushing through the pain. Lisa Smith’s of the Sloane Letter project, she looks at the problem of bed wetting in the 18th century. Lindsey Fitzharris of The Chirurgeon’s Apprentice got ready for the holiday season by picking 12 (medical) instruments of Deathmas; most are sure to make you squirm. Caro of The Quack Doctor writes about the fun and games at Illinois Pharmacological Association meetings for traveling salesmen near the turn of the 20th century. Lynsey Shaw of the History of Military Aviation Hospitals writes on The Oxford Military Hospital, 1939-45.

Efforts to figure out the brain were popular this month. Michael Finn of Asylum Science wrote about the use of ophthalmoscope to view the living brain in asylums. The Public Domain Review reprinted “The Brain of Charles Babbage” (1909), the ‘father of the computer’. Darin Hayden wrote about a phrenological examination of Andrew White (who played a role in igniting the friction between science and religion).

On chemicals we are better off without, Marieke Hendriksen of the Medicine Chest writes about how mercury was viewed by early medical practitioners. Deborah Blum of Elemental writes about how early the US FDA knew about radiation dangers in cigarette smoke.

Pharmacy and Diagnostic Texts

Christina Agapakis of the Oscillator writes about the medieval Urine Wheel to diagnose metabolic diseases.

Michelle DiMeo of the Recipe Project writes about Dr Crawford Long’s exploration of the uses of ether for insect bites. Lisa Smith at the Recipe Project writes about a treatise claiming coffee cures the plague. In the area of hard to find reagents, Chelsea Clark of The Recipe Project shines light on the wonders of unicorn horns, bezoars and bones of a stag’s heart for poisoning. Alas, black markets for animal products like Rhino’s horn (a unicorn substitute) and bear gal bladder is still very active and taking its toll on increasingly rare animals. A little easier to resource, Jonathan Cey of the Recipe Project, shows us that feces-containing remedies were common in the early modern pharmacopoeia. So patients were more right than they knew when they said their medicine tasted like crap! Pamela Dangle also of The Recipe Project writes about some really “fishy” remedies for Melancholy (that seem rather unlikely to help, to me). Thinking of odd remedy names, Tim Jones of Zoonomian writes about medical misnomers of the past.

Physics, Astronomy, and Earth Sciences

ThonyC of Renaissance Mathematicus writes about the astronomical and medical roots of the first pocket diary (calendars). I’ll never look at those moon symbols on my calendar the same way again. Sorry Dad, the phases of the moon are not on the calendar to tell you when the fish are biting. Along similar lines of finding practical solutions to scientific dilemmas, Rebekah Higgit of The H Word writes about the catching and keeping of spiders to spin eyepiece filaments for astronomical observations. On the Royal Society blog, Rupert Baker writes about Thomas Hardy’s historical fiction on early astronomers and the royal society.

Let’s get a little textual with our astronomy, starting with Jenny Weston of Medieval Fragments who writes about medieval star-gazing. Astrolabes and Stuff discusses how to construct a medieval equitorium of Mercury and also for the Moon. Katy Barret of the Longitude blog writes about use of Cook’s journals and her longitude book collection. Sarah Werner of The Collation writes about volvelles (movable wheels) on folios of science and pseudoscience books.

Harald Sack at Yovisto writes about the golden-nosed astronomer Tycho Bahre and on Werner Heisenberg and the uncertainty principle. Alberto Vanzo of Early Modern Experimental Philosophy writes about the contributions Geminiano Montanari and the Italian academy. Matt Wisnioski guest posted on American Science about the motto “Change or Die!”

David Bressan of History of Geology writes about how philosophies of the nature of the world effected the study of the history of the Earth, and early efforts to measure its age. BibliOdyssey posts some of the original sketches and paintings of the discovery of Australia and its wildlife and then on Plant atlas from 1878-1783.

Dr SkySkull of Skulls in the Stars sets the record straight on Benjamin Franklin’s kite electricity experiments, outlines Priestly’s 1767 account of Franklin’s experiments and writes of the dangers of experimental ballooning in 19th century. Moving on from riding aloft to the winds on the plains, Carol Clark of Wonders & Marvels writes about the role of wind power in settling the arid American west.

Christian Hansen of Hummus and Magnets writes about the analytical programming of Babbage’s early calculating machines.

Lisa Smith will be hosting the next On Giant’s Shoulders carnival on the Sloane Letter Project in January. So watch for Lisa’s posts on twitter (@historybeagle) for more information.

I hope you found something enlightening and entertaining for a long winter’s night. Watch out for sleighs this holiday season, reindeer get spooked with all the holiday traffic!

Remodeling the Plague Phylogenetic Tree

Understanding the molecular history of any organism requires fitting together ancient DNA with the phylogenetic tree constructed with living exemplars. Constructing a bacterial phylogenetic tree is a snapshot of a moving target because its impossible to sample all of the strains.  A recent study by the East Smithfield group ( Bos et al, 2012 [2]) seeks to fit the recent near complete genomic sequence of Yersinia pestis from the Black Death cemetery at East Smithfield into the current phylogenetic tree.

They pooled their SNP database with those used by Morelli et al [3] for a total of 311 strains, plus the parental species Yersinia pseudotuberculosis as its foundation.  The East Smithfield group expect that the SNP comparison “could provide a qualitative indication of phylogenetic signals that were lost via our original, more conservative analytical approach based strictly on complete genomes.” [2]

New phylogeny of Yersinia pestis (Bos et al, 2012)

Their analysis confirmed that the Black Death strain settles into the base of split between branch 1 & 2. This matches what Haensch et al [4] found in 14th century sites at Hereford and Saint-Laurent-de-Cabrerisse. This indicates that the split occurred after the Black Death, probably due to microevolution in geographically distinct regions. Branch 2 is localized primarily along the Silk Road route in Central Asia, while branch 1 is far more widely distributed  and produced the third pandemic strain [3].  Bos et al further identified two living strains, designated 3.ANT, with SNP profiles that match their East Smithfield Black Death SNP profile [2]. These strains have not been completely sequenced and the plasmid profiles of these strains and the Black Death strain have not been characterized, so we can not yet say that these strains are genetically identical in sequence or genomic architecture to the Black Death strain [2]. Note that genomic architecture (placement of genes in chromosome) will mostly likely effect gene expression and therefore function of the microbe.

The East Smithfield group  observed that a small group of three strains diverged from the main descent line immediately before the Black Death, designated here as 0.ANT3, were all isolated from China [2]. They suggest that these strains may have been produced during a diversifying event that produced the main Black Death strain, possibly in Asia before it reached Europe.

They also observed 11 strains of Yersinia pestis clumped at the 0.ANT1 branch point [2]. By their calculations this split would have occurred between the 8th and 10th century (732-980 AD) overlapping with the documented period of the Plague of Justinian. They suggest that these strains represent genetic radiation that occurred during the Justinian expansion. This is a change from their observations based solely on comparisons of complete genomes [1].

The East Smithfield genomic group still have not incorporated ancient DNA data from any other group in their analysis.

References:

[1] Bos KI, Schuenemann VS, Golding GB, Burbano HA, Waglechner N, et al. (2011) A draft genome of Yersinia pestis from victims of the Black Death. Nature 478: 506.510.

[2] Bos KI, Stevens P, Nieselt K, Poinar HN, DeWitte SN, et al. (2012) Yersinia pestis: New Evidence for an Old Infection. PLoS ONE 7(11): e49803. doi:10.1371/journal.pone.0049803

[3] Morelli G, Song Y, Mazzoni CJ, Eppinger M, Roumagnac P, et al. (2010) Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity. Nat Genet 42: 1140.1143.

[4] Haensch S, Bianucci R, Signoli M, Rajerison M, Schultz M, et al. (2010) Distinct Clones of Yersinia pestis Caused the Black Death. PLoS Pathog 6(10): e1001134. doi:10.1371/journal.ppat.1001134

Leprosy in Medieval Scandinavia

Medieval leper’s bell from Denmark.

Leprosy is an ancient disease. References to leprosy and the social stigma attached to it go back to 600 BC from India and in the Old Testament. However, like the plague, it was not until relatively late (1873) that the term leprosy became attached to a particular microbe, Mycobacterium leprae. Although some medieval descriptions suggest M. leprae,  it can be very difficult to sort true leprosy from other skin conditions in medieval texts. This is where paleomicrobiology and biological anthropology come in.

Bioarchaeologists have been able to identify skeletal changes suggestive of M. leprae for some time. These changes only occur in the most severe cases making it unclear how common true leprosy was in ancient and medieval times.  It takes many years, if not decades, for leprosy to cause skeletal changes. As with many chronic infectious diseases, it is likely that more people died with the disease than from it. Another way to assess the level and origins of ancient and medieval leprosy is by looking at ancient DNA.

Like the plague, leprosy is considered a monomorphic pathogen that has very little genetic diversity. Four single nucleotide polymorphism (SNP)* types have been characterized for M. leprae. These SNP types are defined by three sites in each type. SNP typing can be technologically challenging with degraded ancient DNA (aDNA) because the typing is based on a single base position at each site. These four SNP types define regional types of M. leprae with type 2 found in Asia and type 3 found in Europe and the Mediterranean today.

A Swedish group led by Christos Economou investigated the M. leprae aDNA of ten skeletons, eight with osteological signs of leprosy,  from Sigtuna, Sweden, dating from the 10th to 14th centuries. DNA analysis revealed that nine of the ten were positive for M. leprae aDNA, including all eight with osteological signs. Leprosy often does not have a high bacterial load so they took nine samples from each skeleton. For each skeleton ruled positive for leprosy DNA, there are two to nine positive samples. However, only three of these nine produced readable results at all three SNP sites: two SNP type 2 (G) and one SNP type 3 (I). This is the first discovery of SNP type 2 in Europe. SNP subtype 2G had previously only been found in Nepal near Uzbekistan. The SNP subtype 3I found in one skeleton is consistent with other samples found in Europe of similar date, according to Economou et al (2013).

Map showing the M. leprae SNP types in Europe and Asia. Purple lines show trade routes. Economou et al, 2013.

Although this is the first discovery of SNP type 2 in Europe, it is not terribly surprising. Sweden borders Asia and was tied to Eastern and Central Asia through trade routes from the early medieval period. Economou et al (2013) note that Sigtuna was an economic and administrative center in 10th-14th Sweden producing artifacts from the Middle East. Missing data from Poland and Russia is a significant gap in the map above.

We are left to hypothesize how an Asian strain of M. leprae got to Sweden. Ultimately we can never know for sure. Leprosy takes so many years to manifest disability or outwards signs that infected individuals could travel from the Middle East or Central Asia to Sweden at least once without sign of infection. These two individuals were unlikely traders: a 20-30 year old female and a 11-12 year old child. It is possible that they either traveled with traders or were slaves, but it is more likely that they contracted leprosy in Sweden. (There is no indication that they were related or died even in the same century.) Economou et al (2013) indicate that grave goods and practices from this cemetery suggest a multi-ethnic population.

Studies like this from Economou et al (2013) are just the first step in our understanding of the rise and fall of leprosy in Europe and Asia. Like plague, it is hard to imagine an environment where leprosy flourished in Europe or Asia, but we know it did. These ancient DNA studies offer some of the best evidence of a pathogenic landscape that seems so foreign to us.

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Note and Reference:

*The difference between a SNP and a point mutation is the functional effect on the gene. A mutation causes an observable or measurable change in the function of a gene product. Most mutations are harmful, but not all. A polymorphism is a neutral change, as far as can be determined at the time of identification. Polymorphisms are usually found in a significant percentage of individuals or strains. It is not uncommon for human polymorphisms to be found in 10% or more of the populations. SNP typing can be thought of as a type of micro-genetic fingerprinting, based on the smallest possible change between people (or organisms).

Economou, C., Kjellström, A., Lidén, K., & Panagopoulos, I. (2013). Ancient-DNA reveals an Asian type of Mycobacterium leprae in medieval Scandinavia Journal of Archaeological Science, 40 (1), 465-470 DOI: 10.1016/j.jas.2012.07.005

Insights from Plague Genomics, Part 1: The Chromosome

Most of the news lately has been about the plague phylogenetic tree produced by looking at single nucleotide polymorphisms (SNPs). The plague tree is remarkably simple and can lead to the mistaken impression that the rest of plague genomics are/will be simple. Michel Drancourt has recently compiled an array of genomic information that shows that SNPs are only part of the story.

A more broad view of plague genomics illustrates why the four biovars will continue to be used in scientific and clinical work. The four biovars are easily distinguished by their phenotype (traits that you can see or measure), the most common and easiest way for plague to be typed in clinical settings. It is important to note that the biovars/phenotypes tell clinicians most of what they need to know to treat the patient(s), their only real goal. Naturally, the biovars reflect genomic clusters beyond the metabolic skills measured in the standard phenotype.

Table and figure from Drancourt, 2012.

Chromosomal rearrangements have been the primary evolutionary mechanism of Yersinia pestis. The figure above shows clones representing the four biovars illustrating rearrangements (follow the lines) and inversions (shown underneath the center line representing each clone’s chromosome). These rearrangements are important for two reasons. First, this is a primary mechanism for DNA loss. Recombination errors can cause  sections of the chromosome to be lost. If the section does not contain vital genes, it will make the clone a leaner specialist. This makes sense of the 13% of parental Yersinia pseudotuberculosis genome lost by Y. pestis, while only gaining two coding sequences among eight new loci. Therefore, other Y. pestis specific genes are all contained on plasmids or other mobile elements.   Second, gene rearrangements can change control of gene expression. Although bacteria do not control their genes individually like eukaryotes, they are controlled in sets called operons. Presumably, genomic rearrangements, that do not respect gene or operon  structure, could change the gene compliment of an operon or destroy the operon control regions deregulating its genes. It can also destroy gene function resulting in pseudogenes (relics or wrecks of former genes). Natural selection will eliminate any damaging rearrangements and favor rearrangements that enhance efficient control. Natural selection works so well on operons that they often contain only genes related to specific metabolic pathways and functions.

Genomic rearrangements continue today. The North American strains provide a datable short-range evolutionary history. In only about 100 years the North American clones have gained one genome rearrangement, six inversions, and several SNPs. Despite all the rearrangements shown in the figure above and the loss of Y. pseudotuberculosis sequences, sequenced clones from all the biovars represented above have similar sized genomes. With the current set of hosts, this suggests that the genome is pared down to near its optimal size. For all the little extras that make Y. pestis an effective pathogen, the plasmids take center stage, and I’ll cover those in part 2.

Drancourt, M (2012). Plague in the genomic era Clinical Microbiology and Infection, 18, 224-230

When Yellow Fever Came to the Americas

“Yellow Jack”, Cornhill Mag., 1892

In the early Americas, nothing scared people more than when Yellow Jack came knocking at the door of their city. Yellow Jack, or as we know it better today Yellow Fever, has rightly been called the plague of the Americas.

It has long been assumed that yellow fever came to the Americas with its vector, Aedes aegypti, in the hold of slave ships. These ships would have been an irresistible feast to the mosquito. Yet, little was known about the origin, locations, and dates of transmission to South America. Juliet Bryant, Edwarld Holmes and Alan Barrett (2007) looked to DNA analysis of yellow fever virus (YFV) strains from 22 countries ( 14 African and 8 South American) to resolve and date the phylogentic tree for YFV. They analyzed 133 isolates from humans and animal hosts collected over a 75 year period.

Bryant, Holmes and Barrett (2007: e75) made four clear observations.

1. The American strains represent a single clade (monophyletic).
2. There are two distinct sub-clades in east and west South America respectively.
3. The South American clade is most similar to the West African isolates.
4. The East African clade is the most distinctive.

These observations support an east or central African origin for the Yellow Fever Virus dominated by enzootic transmission. Its development parallels the transmission of its vector Aedes aegypti.

The split between the east and west African clades has been calculated to an average distance of 723 years (roughly 1284 AD). The West African isolates are the most diverse in Senegal, suggesting this was an early focus for West African YSF. From West Africa Yellow Fever was transmitted to Brazil a calculated average of 470 years ago (roughly 1537 AD). Early Portuguese seamen frequented this part of Africa and Brazil was their largest colony, founded in 1500. This suggests that Yellow Fever was transmitted to Brazil virtually from the beginning of the Portuguese colony. It is possible that Yellow Fever was one of the imported diseases brought by the Portuguese that decimated native Brazilians before large-scale importation of Africa slaves. The South American clade split into eastern and western populations when it was transmitted to Peru a calculated average of 306 years ago (roughly 1700). There is no evidence of transmission back to Africa or other areas where Aedes aegypti have spread in Asia. Byrant, Holmes and Barrett (2007) argue that sylvatic transmission is the primary means of maintaining YSF in South America. They note that there hasn’t been an urban epidemic of YSF in South America since 1928, unlike the annual urban outbreaks in West Africa.

Auguste et al (2010) confirmed the overall structure of the YSF phylogenetic tree in the Americas, including its Brazilian origin in the Americas. Their analysis of strains collected over the last decade also confirm that Brazil is the reservoir and origin for most strains in the Americas today with the Peruvian strains remaining primarily localized in Peru and neighboring Bolivia. The analysis of Auguste et al (2010) also supports enzootic maintenance and local evolution in areas of spread from Brazil such as Trinidad and Columbia.

What I find most surprising about the YSF tree is its relative youth. This all suggests that Yellow Fever originated in the Middle Ages and probably did not circulate outside of local areas of central Africa until the late medieval period. We still have a lot of learn about the landscape epidemiology of yellow fever including possible vertical transmission among mosquitoes and the importance of difference primate species as reservoirs. Although we have had an effective vaccine for decades, yellow fever is still a very clear and present danger in both the Americas and Africa.

References:

J E Bryant, E C Holmes, & A D T Barrett (2007). Out of Africa: A Molecular Perspective on the Introduction of Yellow Fever Virus into the Americas PLOS Pathogens, 3 (5) : doi:10.1371/journal.ppat.0030075

Auguste, A.J., Lemey, P., Pybus, O.G., Suchard, M.A., Salas, R.A., Adesiyun, A.A., Barrett, A.D., Tesh, R.B., Weaver, S.C. & Carrington, C.V.F. (2010). Yellow Fever Virus Maintenance in Trinidad and Its Dispersal throughout the Americas, Journal of Virology, 84 (19) 9977. DOI: 10.1128/JVI.00588-10