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Published: November 20, 2011

Answers and mysteries from DNA sequences

John Bates, Curator and Section Head, Life Sciences, Negaunee Integrative Research Center

Before Post-doctoral fellow Michel Valim returned to Brazil several weeks ago there was one of those days that illustrated to me, once again, why molecular data are so special.  They are one big part answers and can still harbor mysteries unsolved.  The answers came from Josh Engel who has been working hard gathering data on genetic structure in birds of the Albertine Rift for our MacArthur Foundation grant.

Before Post-doctoral fellow Michel Valim returned to Brazil several weeks ago there was one of those days that illustrated to me, once again, why molecular data are so special. They are one big part answers and can still harbor mysteries unsolved. The answers came from Josh Engel who has been working hard gathering data on genetic structure in birds of the Albertine Rift for our MacArthur Foundation grant.  From our own work and that of colleagues, we now have some really exciting data sets on genetic structure in birds and small mammals of the Albertine Rift based on tissue samples collected over the last 20 years. A part of the project is to get data from toepads of historical samples taken from study skins. That is always harder, and the samples Josh has been working with from Mountain Yellow Warblers (Chloropeta similis) and African Hill Babblers (Psuedoalcippe abyssinica) have been giving him some trouble. He had done everything right in terms of trying to avoid any possibility of contamination when he extracted DNA from these samples. Contamination means you have sequenced DNA, but it is DNA that is not what you targeted; the most likely thing is that it is DNA from something you have sequenced previously that has gotten somehow gotten into the chemicals you are using.

Even when you do get successful sequencing, you have a DNA sequence, but you still worry that it might not be what you think it is, meaning contamination. You also worry if the sequences are good enough to detect differences, which are going to be few in population studies (then again, if your sequences are identical to sequences from tissue, you would worry again about contamination). Today, he wanted to show me something. He had gotten toepad samples from some of the Hill Babblers to work. So, were they good sequences? They were, but he was not sure until he ran an analysis to see how they related to the fresh tissues samples for which he already had sequence. That is what Josh wanted to show me.  Some of the sequences from toepads were identical to modern samples but they agreed with geography.  By that I mean toepad sequences from the Rwenzori Mountains were identical to sequences from modern individuals from the Rwenzoris and these are different from sequences from other sites.  This makes sense and is independent evidence that these sequences are from the toepads and not something else. 

The analyses were even more exciting because several of the toepad sequences grouped with a single sequence of a modern bird that we had been wondering about. This sequence comes from a bird from Kahuzi-Biega National Park in the Democratic Republic of Congo, but it was notably different from other sequences from the same area.  When you find a single sequence like that your first thought is that maybe something is wrong with the sequence, but we could not find anything. It was a Hill Babbler, just one genetically a little different from others in the same region (and all other regions in the Albertine Rift). Now we had some other sequences 100 years older that clustered with it. These samples were from birds collected at a site in the next set of mountains to the south of Kahuzi-Biega. So we have some more work to do and more samples to study, but Josh is feeling pretty good about his ability to get DNA from toepads and we may have found something interesting about the evolutionary history of Hill Babblers in this part of the Albertine Rift. 

The mystery of molecules came later in the afternoon when I stuck my head into Jason and Michel’s office to hear whether Michel’s new sequences of feather lice were good. They were looking at the computer screen and editing sequence. The results looked good for all but one individual. It was not that the sequence they obtained for this individual was not readable, it was just readily apparent when they compared it to other louse sequences that it was far too different from all the other sequences to be a feather louse. So what was it? The first thing you can try when you get sequence like this is to go to the GenBank web site and use a program called BLAST to see if your sequence matches something in the massive GenBank database of sequences of everything that has been sequenced and submitted to this incredible database. 

Jason and Michel had BLASTED their sequence and it had not matched anything in GenBank. So there is the mystery, a good sequence that they know is not from the thing whose DNA they intended to isolate and study and it does not match anything in GenBank. A mystery, and one not likely to be solved anytime soon, but we have the sequence. There is still much more undocumented DNA sequence across the world’s biodiversity than there is DNA sequence we know something about.

John Bates
Curator and Section Head, Life Sciences

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The tropics harbor the highest species diversity on the planet.  I am most intrigued by evolution at the tips of the tree of life.  My students and I study genetic structure in tropical birds and other organisms to address how this diversity evolved and how it continues to evolve as climates change and humans continue to alter landscapes.

We study comparative genetic structure and evolution primarily in the Afrotropics, the Neotropics, and the Asian tropics.  I am an ornithologist, but students working with me and my wife Shannon Hackett and other museum curators also have studied amphibians and small mammals (bats and rodents) and more recently internal, external and blood parasites (e.g., Lutz et al. 2015, Block et al. 2015, Patitucci et al. 2016).  Research in the our lab has involved gathering and interpreting genetic data in both phylogeographic and phylogenetic frameworks. Phylogenetic work on Neotropical birds has focused on rates of diversification and comparative biogeography (Tello and Bates 2007, Pantané et al 2009, Patel et al. 2011, Lutz et al. 2013, Dantas et al. 2015).  Phylogeographic work has sought to understand comparative patterns of divergence at level of population and species across different biomes (Bates et al 2003, Bates et al. 2004, Bowie et al. 2006, I. Caballero dissertation research, Block et al. 2015, Winger and Bates 2015, Lawson et al. 2015).  We also have used genetic data to better understand evolutionary patterns in relation to climate change across landscapes (e.g., Carnaval and Bates 2007) that include the Albertine Rift (through our MacArthur Grants, e.g., Voelker et al. 2010, Engel et al. 2014), the Eastern Arc Mountains (Lawson dissertation research, Lawson et al. 2015), the Philippines (T. Roberts and S. Weyandt dissertation research) and South America, particularly the Amazon (Savit dissertation research, Savit and Bates 2015, Figueiredo et al. 2013), and we are entering into the genomic realm focusing initially on Andean (Winger et al. 2015) and Amazonian birds (through our NSF Dimensions of Diversity grant). Shane DuBay is doing his dissertation research in the Himalayas on physiological plasticity in Tarsiger Bush Robins.  Nick Crouch, who I co-advise at U. Illinois, Chicago with Roberta Mason-Gamer, is studying specialization in birds from a modern phylogenetic perspective.  We seek to create a broader understanding of diversification in the tropics from a comparative biogeographic framework (Silva and Bates 2002, Kahindo et al, 2007, Bates et al. 2008, Antonelli et al. 2009).  João Capurucho (U. Illinois, Chicago, co-advised with Mary Ashley)  is studying phlylogeography of Amazonian white sand specialist birds and Natalia Piland (Committee on Evolutionary Biology, U. Chicago) is studying the impact of urbanization on Neotropical birds.  New graduate student Valentina Gomez Bahamon (U. Illinois, Chicago) is also working Boris Igic and me, after doing her Master Degree in her native Colombia on genomics and the evolution of migrating Fork-tailed Flycatchers (Tyrannus savana).  Jacob Cooper (Committee on Evolutionary Biology, U. Chicago) is studying the diversification of birds in Afromonte forests

Josh Engel and I are working up multi-species phylogeographic studies of birds across the Albertine Rift, based the Bird Division's long term research throughout the region.  We are working up similar data sets for Malawian birds.  Our current NSF Dimensions of Diversity grant on the assembly of the Amazonian biota and our NSF grant to survey birds and their parasites across the southern Amazon are generating genomic data for analysis in collaboration with paleoecologists, climatologists, geologists, and remote sensing experts from the U.S. and Brazil.  These large collaborative projects are providing new perspectives on the history of Amazonia.

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