Kari's latest paper on Hawaiian Diptera is out!  This one is a phylogeny of the endemic Hawaiian Campsicnemus (Diptera: Dolichopodidae), with some very interesting analyses on the biogeography and ecological adaptations in the group.  Our coauthors were Neal Evenhuis at the Bishop Museum and Pavla Bartosova-Sojkova, a former visiting scholar in the lab.  We have one more paper on Hawaiian dolis in the works and are excited to publish on this very cool radiation of about 350 endemic Hawaiian species.

The lab has been funded as part of a large grant (led by Rosie Gillespie) to examine the origins of Hawaiian biodiversity.  Here's a link to the announcement on the ESPM web page.  

Which genomic changes underlie rapid adaptation? Do these adaptations come from new mutations or from genetic variation already existing in ancestral populations? Are the genomic regions found in protein coding or regulatory regions? This list of questions reads like the intro to a Trends in Ecology and Evolution article on hot questions in evolutionary biology, and is what Jones et al (including David Kingsley) approached in 7 pages of awesome, detailed work on the genome biology of sticklbacks.

Threespine sticklebacks are famous in the evolution world as a study system for rapid adaptation and speciation. In separate populations all over the world, they invaded from the ocean to adapt to the new freshwater environments created after the Pleistocene glaciers retreated about 11,000 years ago (evolutionarily speaking, this was very recent). This created naturally replicated marine/freshwater population pairs that still hybridize in nature. They even can be raised in a lab, which means they can also be experimented on. We know that all plants and animals have adapted to changing conditions at some point or another in their history, but the process is difficult to study in many organisms, and often the genomic signatures of such change are often obscured by the effects of too much time having passed. The sticklebacks have a perfect storm of attributes that make them great for studying these sorts of questions.

In a paper that begins by presenting the first threespine stickleback genome (which is exactly as far as many first genome papers go), Jones and collegues then go deeper into the system, using that genome to look in detail at how it responded to such recent and drastic environmental change. They leverage the power of the naturally replicated freshwater invasions by generating 20 additional genomes from marine/freshwater population pairs all over the world. In order to assess parallel changes occurring across the entire genome, they looked for regions in the genomes that were similar among all the freshwater animals worldwide but different from the marine ones. Using two complimentary approaches, they found 147 regions (0.2% of the whole genome) that were divergent among the ecotypes.

The researchers then focused in on one marine/freshwater population pair with an active hybrid zone to ask if these globally shared variants were the main ones involved or if there were also a lot of variants contributed by the local populations. They found of the divergent changes between the two populations, 35.3% contained these global variants, suggesting that there is a substantial contribution from local variants in each population in addition to what is shared across populations.

An outstanding question in biology asks whether adaptive changes occur because of changes in protein coding genes or regulatory regions. Evidence has been accumulating from a variety of systems about specific adaptations, which are typically restricted to relatively narrow regions within a genome.  This study allowed a look at what is going on across an entire genome. The authors found that of all of the freshwater variants that were shared across all populations, 17% were located within protein coding regions, while 41% were found in non-coding regions and presumed to be regulatory. An additional 43% were more ambiguous, and the authors speculate that they also primarily fall into the regulatory category. More work needs to be done to classify and verify these variants, but the results are already suggestive that a significant amount of adaptive change across the genome is due to changes in the regulatory regions.

While we are not quite at a stage of being able to write a how-to manual on adapting to a novel environment, this series of studies provides a lot of new detail on how it works in nature in one particularly well-suited system – a system truly powerful and special for its ability to give us insight into the dynamics of rapid adaptation. Even though the et al on this paper is a long list of contributors that render this approach way beyond what is possible to do by a single researcher, it is still inspirational to picture how these approaches could illuminate the biology of other natural systems.

Kari Goodman

Jones, F.C. et al 2012. The genomic basis of adaptive evolution in threespine sticklebacks, Nature, vol 484, pp. 55-61. doi:10.1038/nature10944.

Postdoc Kari Goodman's paper on Nesosydne divergence is out in Evolution.  Here's the link.  Congratulations!!  And happy National Postdoctoral Appreciation Week!

How do new species form? This pervasive question in evolutionary biology has its roots in Darwin (and let’s not forget the common man’s evolutionist – Wallace) and natural history observation, but has flourished over the last couple of decades with modern molecular and computational techniques. Birds, fish, lizards and arthropods get most of the attention on this subject, while an incredibly diverse member of the eukaryotes, the fungi, has received very little. 

How diverse are the fungi? Educated guesses are variable, and currently range between 1.5 million and 5.1 million. With all that diversity, and so many examples of fungi that intersect with our lives (for some great stories on this, see the Cornell Mushroom Blog) it is incredible how little attention they have received as the subjects of speciation studies. Why? I could chalk it up to the charismatic macrofauna effect, but c’mon – there is a fungus that turns ants into zombies! And then there’s another fungus that prevents that zombie fungus from spreading out of control! The world is full of charismatic fungi. Alternatively, the reason is that as humans we can more or less picture what an animal species is while this is not necessarily so with the fungi - we typically can’t even picture an entire fungal individual.

Among folks who study how species form, there has been a particular lot of attention focused on the role that adaptation to different resources plays in the fracturing of species. It is now being suggested that fungal plant pathogens are incredible model systems for this area of research, as one of the primary ways new plant fungal pathogen species may emerge is by shifting onto new host plant resources. This is interesting for at least two reasons. First, the large amount of theory and research that exists on speciation may be able to help guide plant pathogen researchers at understanding the internal factors controlling host switches in the fungal pathogens. Second, it points speciation researchers towards a myriad of new study systems on which experiments can be done. Tatiana Giraud and colleagues point out in a 2010 article that plant pathogens are full of characteristics that make them great for studying rapid ecological speciation (their hosts provide strong selection, they have lots of offspring which increases both their survival and mutation rate, they mate entirely within the host, they have only a few genes that control host specificity and they can clone themselves to keep themselves going for long periods between mating with another individual).

How rapid is rapid? In one example, a rust fungal species emerged by hybridization IN 1997 to infect a poplar tree that itself is a hybrid (Newcombe et al 2000). Wow! In another recent example, researchers studied a pathogen that infects green coffee berries, and found that it diverged approximately 2200 yrs ago. Although ages longer than the first example, this is still very recent in the realm of speciation examples, and leads me to wonder what else is going on out there in this fast-paced world of fungal speciation. From the perspective of an insect researcher, where experiments can be done but lab rearing is tricky, this is fascinating stuff. Stay tuned, and especially to the Giraud Lab (Ecologie, Systematique et Evolution, Universite Paris-Sud) for more neat work in this area!

Kari Goodman

Newcombe, G, Stirling, B., McDonald, S., and Bradshaw, H.D., Jr. (2000) Melampsora x columbiana, a natural hybrid of M. medusae and M. occidentalis.  Mycological Research 104(3): 261-274.