Not many people get paid to be twelve years old, at least not as adults, so I feel I’m one of the lucky ones. I’ve been working on a project that lets me go to so some beautiful rivers and streams, flip over rocks, and look for aquatic insects. It kindles the fun and curiosity that I remember while doing that kind of thing when I was a kid. Now, of course, I have a research question in mind while I’m out there. Our lab has been conducting surveys of aquatic insects in a few representative Northern California watersheds to establish the composition of aquatic insect communities, create a DNA barcoding (see this blog, too) database of Norcal aquatics for more efficient biomonitoring in the future, link taxa to characteristics of the habitat, and, using landscape genetics, make predictions about how global change biology may affect our local rivers and streams.

Aquatic insects have been used in biomonitoring for about a century as a way to assess the health of riparian areas. Biomonitoring adds informative data to chemical testing of water. Chemical testing provides valuable information about a particular component, such as dissolved oxygen or the concentration of a pollutant, at one moment in time. Biomonitoring is a way to assess whether all of the components of a system are such that they support the surveyed organisms over their entire lifespan. Both chemical and biological surveys can be combined to give a fuller picture of ecosystem health. Biomonitoring of aquatic insects is now being used not only to assess current and past ecosystem health, but also to predict future changes, for example in response to climate change.

In recent years, concerns about the effects of human-driven climate change on riparian ecosystem have increased. Climate change is projected to alter precipitation patterns, the timing of seasonal transitions, and extremes of both heat and cold, among other effects. These changes will affect different members of biotic communities differently according to their ability to adapt to changing conditions or disperse to more favorable habitat. We can use species distribution modeling to identify key characteristics of favorable habitat, and use patterns we find today using landscape genetics to identify potential obstacles that could prevent taxa from shifting ranges.

We are fortunate to be doing this as part of a larger consortium on campus, the Berkeley Initiative in Global Change Biology, or BIGCB. With funding from the Vice Chancellor’s Office, the Moore Foundation and the Keck Foundation, the BIGCB is focused on global change forecasting for California ecosystems, using analyses of fossil, historic and current data to better understand California ecosystems responses to environmental change and make predictions of future ecosystem changes.

Brian Ort

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.

When we want to visualize biogeographical distributions we usually create maps. When we want to visualize phylogenetics we often build taxonomic trees. What if we want to visualize phylogeography? Typically we use maps and phylogenetic trees side-by-side. There is a relatively new tool called GeoPhyloBuilder that joins the two. It is available in ArcGIS 9.3 and later versions and was created by David Kidd and Xianhua Liu of The National Evolutionary Synthesis Center (2008).  GeoPhyloBuilder builds a 3D spatiotemporal, phylogenetic GIS data model by attaching the phylogenetic tree tips to the geographical locations of the samples. The geographical locations can be points, lines, or polygons. The 3D dimension comes from the node depths of the phylogenetic tree.  Longer, older branches are elevated further above the map.  The model can be visualized in 2D or 3D in ArcMap, ArcScene, or other Earth Browsers. Examples of images and movies as well as the download are available at: https://www.nescent.org/sites/evoviz/GeoPhyloBuilder.  Although some of these images make the phylogenetic tree look like spaghetti hanging over a map, you can color code different branches to see how they relate geographically. You can also visualize the 3D images in a movie, rotating the image so that you can get varying perspectives. Passing information on is easiest when you have powerful visuals and this may be helpful for some phylogeographical results.

Lisa Marrack

Phylogenies of the freshwater fish family Goodienae: (purple; Webb et al., 2004) and genera Poeciliopsis (green; Mateos et al., 2002) and Notropis (blue; Schonhuth & Doadrio, 2003) with modern elevation and drainage. Pliocene and Miocene drainage and palaeolakes from de Cserna & Alvarez (1995). [In Kidd and Ritchie (2006): Journal of Biogeography].


 

This paper was a convincing argument for the promise of DNA barcoding taking over the world, basically. DNA barcoding of aquatic macroinvertebrates  is gaining backing as an extremely useful tool for taxonomic identification and research, and in turn,  application in bioassessment programs.  Some have argued that DNA barcoding is an unreliable way to identify aquatic macroinvertebrates, but this paper shoots those ideas down; (!!!) as it found that the average intraspecific divergence  was 12.5%, while the average intraspecific divergence was 1.97%. While there were some complications in identification, caused mainly by polyphyly and species complexes (which still need to be further studied and resolved,) in general these results indicate that DNA barcoding is, in general, a promising tool in aquatic macroinvertebrate taxonomy and bioassessment programs. 

Aside from the intra and interspecific  divergences being accurate, for the most part, this paper further points out that DNA barcoding is particularly useful for other reasons.  In addition to helping streamline the identification, delimitation, and discovery of species, DNA barcoding also gives consistent results across life stages, which is particularly important in aquatic ecology applications, as a large majority of benthic macroinvertebrates are immature. In many cases, taxonomy is based on adult male morphology, and identification of immatures, particularly early instars, is exceedingly time-consuming and requires substantial training. Additionally, specimens are often very tiny, and delicate, which can lead, in many cases, to missing gills, caudal filaments or even legs, which can in turn further complicate accurate identifications.  Furthermore, the use of DNA barcoding allows for data standardization, and thus a broader, more accurate  comparison of results.

This paper also suggested that much more work on North American Ephemeroptera  taxonomy and classification is required, as many currently recognized species are  highly divergent. Most of these confused species have complex histories of synonymy and reflect  the 60 year trend in North American mayfly systematics towards inclusive species concepts. Further taxonomic work that synthesizes a variety of identification and classification methods including morphological, biogeographic, ecological, behavioral and molecular techniques is required to test current species hypotheses, particularly of those unusually divergent Ephemeroptera species. DNA barcoding is one of the techniques that will be useful in this aim of achieving stable, supported species hypotheses. Re-examined and updated species hypotheses will allow us to identify aquatic insects more accurately and more efficiently, which will in turn allow us to determine and communicate the ecological characteristics of a species, such as phenology and tolerance to pollutants, and thus  improve our ability to utilize these organisms in bioassessment programs. 

Natalie Stauffer

Mike, Brian and I traveled to Angelo Coast Reserve on the 19th to do some collecting.  Our goals were to collect some aquatic insects in the Eel River and look for Scaptomyza species in the surrounding riparian zones.  We didn't see any Scaptomyza but we got a great sample of aquatics, including lots of Dicosmoecus, Neophylax and Calineuria.  

This week we made two short field trips to collect aquatic insects.  On Tuesday we worked northwest of Sebastapol. Brian and I visited several sites we had collected last fall. Our first stop was Pyrrington Creek on Graton Road, followed by Dutch Bill Creek along the Occidental Highway.  We stopped for lunch at Stumptown Brewpub in Guerneville.  After lunch we drove north of the Russian River to Austin Creek near the town of Cazadero. Our last stop of the day was Salmon Creek, northwest of the town of Bodega.  

Thursday we did a half day trip to two streams in Marin County, Lagunitas Creek and Pine Gulch Creek in Bolinas.  Thanks to Sarah Hake for allowing us access to Pine Gulch Creek!  We collected Neophylax here, as well as three species of Scaptomyza!!

The lab was just awarded a $3500 grant to do barcoding of aquatic insects in Northern California. Congrats to Brian for all his hard work on this project.