Applying phylogenetics: Did the California H1N1 swine flu come from Ohio?

Just as we (in Biol 105) finish up studying how phylogenetic trees are estimated, and how they might be used to answer interesting questions, comes this highly topical example - microbiologist and science blogger Sandra Porter spent a happy afternoon applying phylogenetic analyses to try and answer the health scare du jour:

This afternoon, I was working on educational activities and suddenly realized that the H1N1 strain that caused the California outbreak might be the same strain that caused an outbreak in 2007 at an Ohio country fair. Here's the data.

Once I realized that the genome sequences from the H1N1 swine flu were in the NCBI's virus genome resources database, I had to take a look.

And, like eating potato chips, making phylogenetic trees is a little bit addictive. Or maybe it was just the adrenaline rush that hit when I realized that every tree was telling me the same thing.

What did those trees say?

Read the full blog post to study the results yourself, and see what you think of the remarkable concordance between the trees, providing a plausible answer to the question of where this virus may have originated.

In the process, Dr. Porter has also given us all a glimpse at the working product of a fresh analysis - raw results hot off the computer before they are published in a peer-reviewed journal! Is this a first for the blogosphere? I don't know, but given the high level of public interest, I can see why one might want to get the results out quickly. Surely some top science journal would be interested in publishing this quickly as well?

Thanks to Porter's blog, we all get to see how genomic data available in the public domain can be used to help address problems that might affect us in real time! How cool is that?! As I try to impress upon my students every time we discuss the subject: Phylogenies are not just static graphic depictions of inferred relationships between organisms long gone - trees of dead wood, so to speak: they also serve as working models of ongoing evolutionary processes! And often enough, they help us pinpoint the origins of new diseases, in turn helping us develop treatment strategies before the outbreak gets too far out of hand. And how is that for putting those phylogenetic trees to work?

Meanwhile, Tara Smith, of Aetiology (also on ScienceBlogs) following up on Porter's big discovery, notes that the peer-reviewed paper describing the Ohio swine flu strain came out only recently. And here's the bit that really raises the eyebrow, if not the hair on your head:

I also assume this is where the human-avian-swine reassortant claim came from. The authors note that:

The H1N1 viruses contain the HA and NA from the classical swine virus and the internal genes from the triple reassortant H3N2 viruses (rH1N1); the H1N2 viruses contain the HA from the classical swine virus and the NA and internal genes from the triple reassortant H3N2 viruses (Karasin et al., 2002; Webby et al., 2004). Contemporary triple reassortant viruses were demonstrated to have acquired a PB1 gene of human virus origin; PA and PB2 genes of avian virus origin; and the remaining internal genes, M, NS, and NP, of swine virus origin, thus giving rise to the triple reassortant designation (Zhou et al., 1999).

So what it looks like to me is that this isn't a *new* reassortant virus, but is closely related to one that had already been identified in swine--and that had already caused an outbreak in humans right here in the US.

So why is the virus getting so much more media attention this time around? Is the strain in Mexico really the same or different? And if it is the same (or close) how did it get from Ohio to Mexico City and back to Texas and California? Gotta love that globalization, eh!

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Phylogenomics suggest ratites lost flight multiple times

Rebekah Wukits discusses recent findings about ratite evolution for Bio 135.

Ratite evolution has been debated for centuries. Some of the earliest evolutionary biologists questioned whether or not ratites had a linear evolution or if the major groups had had independent origins. Richard Owen proposed that living ratites had much more in common with other flight capable groups while being united by the “arrested development of wings unfitting them for flight”. In 1951, two ornithologists, Mayr and Amadon, stated that, “the present consensus is that the main groups of these birds are of independent origins”.

Traditionally, ratites have been considered to be monophyletic, or ascending from a common ancestor. They are placed in the major group Noegnathae, with the flight-capable tinamous as a sister group. Since the extinct tinamous were capable of flight, it has been thought that the ratites lost flight once in their history, then diversified. Unfortunately, simple geography contradicted this theory. All living ratites (rheas, cassowaries, emus, ostriches and kiwis) are isolated on different southern continents.  Rheas are found in South America. Ostriches reside in Africa. Emus and cassowaries are found only in Australia and kiwis can be found in New Zealand. Extinct species of ratites follow the same pattern. Moas were also found in New Zealand, and elephant birds lived in Madagascar. The question became that if flight was lost once early in ratite evolution, how did they become so spread out and isolated? The perfect answer seemed to reside in the theory of continental drift. Ratites came from a single ancestor, lost flight and were then isolated when Gondwana broke up.

Though most of the recent studies of morphological and molecular ratite characteristics have supported the monophyletic theory, many still debate it. Rarely challenged is the fact that adaptations to a cursorial lifestyle, one that is adapted to running, can lead to convergent evolution, and can be misleading when basing phylogeny on morphology. This led scientists to do further phylogenomic studies in order to test the prevailing theories. These studies include data taken from genetic loci that represent the entire avian genome. In this particular study, data was taken from 20 loci that are dispersed widely throughout the avian genome. The data set included all living ratites and eight outgroup taxa. Previously done similar genetic tests have supported ratite monophyly, however these tests were more sophisticated and advanced and supported a different conclusion.

The results are as follows: analysis of the data strongly supports placing the flight capable tinamous within ratites and ostriches as the sister group. If this new phylogeny is correct, the single loss of flight in ratites is unlikely. In order for all ratites to have lost flight in a common ancestor, the tinamous would have had to regain flight at a later time. It is much more likely that flight was lost multiple times do to convergent evolution than to have gained flight in the earliest ancestors, lost flight in the common ancestor of ratites, than gain flight again in tinamous.

It seems more likely that ratites descended from a single ancestor, than diversified when gondwana broke up. Flight was lost in each family and convergent evolution occurred due to similar environmental conditions. Flight is very costly both energetically and morphologically. Ratites had little pressure to fly and since these features are costly to maintain, they became reduced over time.  The theories of this paper seem concrete however more study is needed. Their own genetic studies produced conflicting results. Placing tinamous within ratites has great implications for their evolution and dispersal. This idea needs to be further developed and supported.

Reference:

J. Harshman, E. L. Braun, M. J. Braun, C. J. Huddleston, R. C. K. Bowie, J. L. Chojnowski, S. J. Hackett, K.-L. Han, R. T. Kimball, B. D. Marks, K. J. Miglia, W. S. Moore, S. Reddy, F. H. Sheldon, D. W. Steadman, S. J. Steppan, C. C. Witt, T. Yuri (2008). Phylogenomic evidence for multiple losses of flight in ratite birds Proceedings of the National Academy of Sciences, 105 (36), 13462-13467 DOI: 10.1073/pnas.0803242105

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The role mtDNA plays in the evolutionary differentiation of species

Bob Koons shares his reflections on a Biogeography class discussion from some weeks ago. I've been unable to upload many student submissions to this blog due to severe tendonitis which limited my computer use for some time, but I'm beginning to catch up and hope to have the remaining student submissions uploaded before the semester ends!

Neotropical diversification of montane populations have been studied mainly in the lowlands of geographical regions simply due to the fact that there is a much larger diversity of species inhabiting the lowlands compared to the highlands. Studies use multiple approaches of statistical methods to get their data to agree. Which test is the best one depends upon the question being asked?

Species can be traced back to their origins using mtDNA, which is directly passed down from the mother. A species that has genetic ties to an ancestor and all its descendant taxa is called monophyletic and a species that has an ancestral taxon and some, but not all, of its descendant taxa; an artificial taxon. (Lomolino et al 2006) Geography plays a role in how a species diversifies over time as was demonstrated by the Finch scenario. The finches migrated south from Mexico to the Northern Andes Mountains of South America. Some finches traversed the Andes and migrated south along the east side of the Andes. The geographic isolation separating the two groups allows for natural selection to run its course allowing for the distinct differences we see in the finches today.

So does this apply to humans also? Can human mtDNA show this geographical divergence differentiating our species? An article entitled, “Geographic origin of human mitochondrial DNA: Accommodating phylogenetic uncertainty and model comparison” by John Huelsenbeck and Nikita Imennov compare the two main theories of the origin of the humans, which are the “out of Africa” and the “regional continuity hypothesis. The “out of Africa” hypothesis relates that modern humans all came from a common ancestor in Africa. Humans spread from there to all parts of the globe, and subsequently wiping out other “homos” that were encountered. The “regional continuity hypothesis” says a single species of homo originated throughout the old world connected through gene flow, after any migration from Africa occurred. Statistics using mtDNA show that the out of Africa scenario is the most possible origin for modern humans. A Bayesian inference statistical analysis was used to accommodate phylogenetic uncertainty from all trees then comparing the probabilities. Bayesian statistics is defined as, “Of or pertaining to statistical methods that regard parameters of a population as random variables having known probability distributions.”In their article Huelsenbeck and Imennov 2002 state, “In this study, we point out how Bayesian inference can be used to accommodate phylogenetic uncertainty when comparing five different models for the origin of modern human mtDNA.” 200 sequences of mtDNA were analyzed, each sequence was 428 sites long, from the hypervariable region I (HVRI) of the mitochondrial region of modern humans and an out group sequence from Neanderthal mtDNA. They used 40 sequences from each geographical region of the globe in their analysis; Africa, Europe, Asia, Americas, and Australia were represented. As discussed in class, and in this paper, a statistical analysis can be modified in many ways. This study used a uniform prior on all possible trees, another way to analyze the data would be to perform a coalescence prior, or to chose another method reconstructing the ancestral geographic area of human mtDNA. Another way of statistical modifications could include a stochastic two-stage model or a coalescence process with different populations connected by variable levels of migration. Still other ways exist that can modify an analysis; the trees could be reconstructed using a molecular clock restraint and incorporated into a Bayesian or maximum likelihood framework. (Huelsenbeck and Imennov 2002) A DNA sequence from Neanderthals may give a clearer answer to the out of Africa hypothesis. MtDNA can be useful to determine human geographic origin after all. Whew! From this we can clearly see that data can and is modified in many different ways to suit a desired outcome.

References:

Huelsenbeck, J. and Imennov, N., 2002. Geographic origin of human mitochondrial DNA: Accommodating phylogenetic uncertainty and model comparison. In Systematic Biology Vol. 51, No 1 pp.155-165.

Lomolino, M.V et al. 2006. Biogeography. MA: Sinauer Associates.

Dictionary.com, Bayesian Statistics. Retrieved October 5,2008.

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How would you like to knit Darwin's Tree?

Into your shorts? Like so:

And if you know how to make/modify patterns, you might want to make it more authentic: add "I think" at the top of the tree and label some of those branches! Here's a photo I was lucky enough to take of the original several years ago:

[Hat-tip: John Wilkins]

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Obligatory reading of the day: Phylogenetic Fallacies

Go read Genomicron on: Phylogenetic fallacies: "early branching equals primitive". It should clarify your thinking and might even help you on the finals! And don't complain that I only serve up links and commentary on non-evolutionary fluff like the brouhaha over next week's events on campus!

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