2019 was actually a pretty intense year for me. I tried to publish. And to survive. I made a collection of the happiest moments on photo. Now we are taking off. Driving south.
A few weeks ago, I was asked what my proudest career moment was. Here you go:
I am having a hard time to be proud of myself. But my husband just reminded me that I had 3 first-author manuscripts accepted about a month ago – all on the same day! One was about frog demographies. We modeled abundances of individual frogs at different life stages for that paper. (We even accounted for their detection probabilities!) It all started as a side-project when I was still in Stephanie Carlson’s lab at UC Berkeley. Sébastien Nusslé had started analyzing this dataset but he left because he founded a company with his very successful wife Semira Gonseth. GenKnowMe. Hence, I adopted another orphan project. Kathleen Matthews, a friend and mentor of Stephanie’s had collected data on frog demographies in Kings Canyon National Park. She hiked out to Dusy Basin every summer for 18 years to count Rana sierrae. The Sierra Nevada Mountain Yellow-legged Frog. Kathleen and her team counted frogs at different life stages throughout the summer. From when the ice melted at this high elevation habitat in spring, until winter came back in early fall. I convinced Zack Steel, a graduate student at UC Davis (now postdoc at UC Berkeley) with great experience in population modeling, to help me analyze this dataset after Sébastien had left. We investigated which biotic and environmental factors affected frog demographies before this local population went extinct in 2013.
Find the paper here, it is all open access.
Abstract: The Sierra Nevada yellow-legged frog (Rana sierrae) was once an abundant and widely distributed amphibian in California’s alpine ranges. Rana sierrae is adapted to high-elevation, fishless habitats. Its adaptions are reflected in a unique life cycle that involves a flexible, extended juvenile phase due to the short growing season typical of its alpine habitat. However, today this species is critically endangered, and most populations have been extirpated from their native range. Here, we present an 18-yr-long demographic study of a R. sierrae population in 15 lakes at Dusy Basin in Kings Canyon National Park. We focused on the period leading up to the arrival of the pathogenic chytrid fungus, Batrachochytrium dendrobatidis (Bd), and the subsequent local extinction of R. sierrae. We used N-mixture abundance modeling, which accounts for detection probabilities, to quantify factors affecting frog abundance at different life stages. The abundance of subadult and adult frogs was negatively associated with the presence of introduced trout (Oncorhynchus mykiss and O. aquabonita). Frog abundance in all life stages was positively associated with lake surface area. The propensity of lakes drying correlated negatively with abundance of eggs, subadults, and adults in the following year. Moreover, drought years, characterized by longer summers and less winter snowpack, led to higher rates of lakes drying. Finally, our results suggest that the frequency of such droughts in the region has increased since 1937. Increased frequency or severity of droughts is expected to decrease the value of shallow lakes for Sierra Nevada yellow-legged frogs because these habitats are prone to drying. We discuss our results in terms of future restoration strategies, including reintroduction and probiotic treatment, in this changed and changing ecosystem.
The second paper that was published on my lucky day was an invited perspective about the implications of host hybridization for microbial symbioses. I wrote this paper on my own but I got support from Cassie Ettinger and Jonathan Eisen. I really enjoyed writing this piece because it let me muse about my greatest interests including speciation, hybridization, evolution of microbial symbioses, and clams. Lots of clams. I also want to mention Shana Goffredi at Occidental College, Perrine Cruaud at Laval University in Québec, and people at the Monterey Bay Aquarium Research Institute (MBARI) who all provided nice images to me to create a nice figure.
Also open access!
Check it out here: https://onlinelibrary.wiley.com/doi/full/10.1111/mec.15262
Abstract: Evolutionary adaptation is the adjustment of species to a new or changing environment. Engaging in mutualistic microbial symbioses has been put forward as a key trait that promotes the differential, evolutionary success of many animal and plant lineages (McFall-Ngai 2008). Microbial mutualists allow these organisms to occupy new ecological niches where they could not have persisted on their own or would have been constrained by competitors. Vertical transmission of beneficial microbial symbionts from parents to the offspring is expected to link the adaptive association between a given host and microbe, and it can lead to coevolution and sometimes even co-speciation (Fisher et al. 2017). Vertical transmission also causes bottlenecks that strongly reduce the effective population size and genetic diversity of the symbiont population. Moreover, vertically transmitted symbionts are assumed to have fewer opportunities to exchange genes with relatives in the environment. ‘In a From the Cover article in this issue of Molecular Ecology, Breusing et al. (2019) investigated whether hybridization among different host species could lead to inter-species exchange of otherwise strictly vertically transmitted symbionts. Hybridization of divergent lineages can potentially cause intrinsic and extrinsic incompatibilities, swamp rare alleles, and lead to population extinctions. In some cases, however, it might also create novel trait combinations that lead to evolutionary innovation (Marques et al. 2019). Breusing et al. (2019) linked the concept of hybridization to symbiont transmission, and their findings have significant implications for the study of evolution of vertically transmitted symbionts and their hosts.
Figure 1: Chemosynthetic bacterial symbionts of vesicomyid clams.
A.1) Phreagena soyoae gills; photo generously provided by Professor Shana Goffredi (ORCID: 0000-0002-9110-9591), Occidental College, Los Angeles, CA, USA. A.2) Transverse section of gill fixed for fluorescent in situ hybridization (FISH). A.3) Symbionts hybridized with bacterial probe in orange and DAPI-stained frontal ciliated host cells in blue. A.4) Same specimen and coloring, at higher magnification. Each host cell (bacteriocyte; grey highlighting) contains hundreds; i.e., a population of bacterial symbiont cells. Images A.2, A.3, and A.4 were kindly provided by Dr. Perrine Cruaud (ORCID: 0000-0001-8628-3600) at the Laboratory of Microbiology of the Extreme Environments (LMEE), Ifremer, Brest, France. B) Breusing et al. (2019) constructed haplotype networks for host genes (mitochondrial: mtCOI; nuclear: ANT, H3), as well as symbiont genes (16S rRNA gene: sym16S) of two host species (light green = P. soyoae, dark green = Archivesica gigas). Each circle represents a haplotype with circle size showing its frequency in the dataset. Mixed haplotypes are shown as pie charts of light and dark green. C.1, C.2) Deep sea hydrocarbon seep collection site at Pescadero Basin in the Gulf of California, Mexico from the expedition in 2015 when Breusing et al. (2019)’s samples were collected in their natural habitat. An image-use agreement was provided by the Monterey Bay Aquarium Research Institute (MBARI).
And the third one was a whitepaper that resulted from a workshop I organized together with Matt Leray and Jarrod Scott a year ago. That one is my personal gem because it was just such a unique experience to organize a workshop, meet new people and make new friends, and then write a paper with everybody. Here we discuss how host-associated microbiomes contribute to ecosystem structure and function in marine systems. We highlight the rise of the Isthmus of Panama as a great (if not the greatest) natural experiment to study the ecology and evolution of marine microbial symbioses and host-associated microbiomes.
Of course open access as well: https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3000533
Abstract: The significance of symbioses between eukaryotic hosts and microbes extends from the organismal to the ecosystem level and underpins the health of Earth’s most threatened marine ecosystems. Despite rapid growth in research on host-associated microbes, from individual microbial symbionts to host-associated consortia of significantly relevant taxa, little is known about their interactions with the vast majority of marine host species. We outline research priorities to strengthen our current knowledge of host–microbiome interactions and how they shape marine ecosystems. We argue that such advances in research will help predict responses of species, communities, and ecosystems to stressors driven by human activity and inform future management strategies.
Today was Linnea’s first day of first grade at school. As it turns out, she is in her favorite classroom with her favorite teacher. Miss Eagle!
When this summer break started, I was concerned. Not sure how that would play out with my husband watching the kids the whole summer without a break for him. I traveled a lot. I had to let go. Let him do his own thing. Let him feed them what he thinks is right. Let him decide how much screen time they would get and how much play time.
It worked very well. Linnea had a super creative summer. The most creative girl I know. I am proud of my husband. He supports her dance. He lets her create.
I am not too concerned about Buddha. The two of them are living in a symbiosis where both partners benefit.
I know that she ate too many popsicles and slept with the dog when she missed me at night. But that is OK.
There might be a bit of a bias towards marine creatures. But that is OK, too.
Today, Cassie’s and my article on metagenome-assembled genomes in two hot springs of Kamchatka, Russia was published in Scientific Reports. Cassie and I only analyzed the data. The whole story is much older and involves many more people, including Elizabeth Burgess who originally collected the samples as a graduate student in Jürgen Wiegel’s lab. Or Russell Neches, who went to Kamchatka himself and had played with this dataset before us. And Ray Keren who encouraged and distracted me with his fascination for arsenic biochemical pathways.
Laura Hug led the way in the beginning and Chris Brown provided the tools when we got stuck.
We are all working really hard and sometimes don’t even find the time to celebrate or to be proud. I had a hard time today to enjoy. Now it is sinking in slowly. I am incredibly proud of Cassie. Working on this project with Cassie cheered me up, it motivated me to do things right, and it gave me a strong feeling of peace.
We learned a lot and we tried to do it right. In every aspect. Guillaume showed us many tricks. And Jonathan believed in us.
And A. Murat Eren was very important too. A bright star on the horizon. And the Banfield lab. We got a lot of inspiration. Obscure archaea are awesome.
At some point, when we are all a bit less busy, Jonathan might write a blog post about the background and history of our article…
I did not think I could work so much like I did lately. I did not think I could be involved in so many things. It feels like a landslide. Like free fall. I am dancing free-style.
My two little anchors are small but strong. Keeping me grounded.
And then there was this one about public data sharing. Posted on The Molecular Ecologist blog a few days ago.
Check out my recent blog post on the istmobiome website about my recent clam lab work. Just an every day blog post.
Elizabeth Crone, Tufts University
Live blogging from UC Berkeley Wildlife Seminar, January 25th 2019. (Still my favorite University. Still my favorite seminar.)
Monarch butterflies had the lowest population sizes ever in 2018! Shocking news on Thursday January 17, 2019 in the San Francisco Chronicle. What is going on??? Here is the link: https://www.sfchronicle.com/news/article/California-s-most-famous-butterfly-nearing-13539657.php#photo-16782648
Elizabeth Crone from Tufts University came to UC Berkeley today and gave a talk at the Wildlife Seminar about the three following points:
- How much has the whole population declined?
- Why are they declining?
- What can we do about it?
There is a global insect Armageddon. Art Shapiro at UC Davis says: ‘No. We don’t know why.’
Western Monarch butterfly populations are much smaller and less studied than the ones at the East Coast. They spend several generations at California coasts and move then inland towards Rocky Mountains. Monarch butterflies are just awesome because their migrations include several generations. While the grandparents might have been born at the coast, their grandgrandchildren decide to fly somewhere else. The same cycle repeats many generations later.
In Central California there are volunteers, CITIZEN SCIENTISTS, who count butterflies every year around Thanksgiving. In 1997, there was a very high count, then only smaller numbers. Had numbers before 1997 been consistently higher? There were no citizen scientist projects back then. Elizabeth had to collate data from different research groups. She found quite a lot but nothing was standardized. Everybody had used different approaches. Hence, Elizabeth had to apply some statistical models to account for all this variation. She did MARSS modeling and analyzed a very long time series. This model assumes that monarchs function as a single large population in the west, with a single growth rate. For each site she estimated a rate of proportionality compared to the total population. MARSS also allows to include an observation error. –> Estimate of historic abundance. 1980s millions of butterflies, 2000 only thousands. Something happened in the 90s. Population decline is ~7% per year.
In 2018 counts dropped again. We have never had anything close to this low. Yet, it might just be ordinary fluctuations in the environment. If we loose a few hundred butterflies in a population of several millions, the population will persist. However, if we loose a few hundreds in a population of a few thousands, this population might eventually go extinct due to the extinction vortex. So Elizabeth applied for emergency funding from the NSF. Is anybody looking for an awesome postdoc position???
What caused decrease: Climate (temperature, precipitation)? Everybody always thinks first it is climate change. Pesticides. Habitat loss. Overwintering habitats along the coast have become smaller due to housing development and dryland farming. How do we know which factors really drove the population decline? Don’t do linear modeling with so many correlated variables. Instead: PLSR: Partial Least Square Regression. This analysis can handle a large set of variables. Retains uncertainty about which variable is correlated with outcome. Similar to PCA. Relative importance of different variables for 1st and 2nd components (axes). What did the model spit out? Summary: Land development, glyphosate, and nicotinoids all correlated negatively with butterfly numbers. With regard to the drop in 2018, it could be attributed to the cold and wet months of February and March. They had been bad for butterfly recruitment.
Not just climate change – land use matters. And use of pesticides by everybody, farmers and hobby gardeners. This is a large landscape scale problem. Not just butterflies. Many other insects are suffering from the same problem.
During the questioning session in the end: Some monarchs don’t migrate. They sit on perennial milk weed their whole life. These populations are common in Southern California and Mexico. In Central and Northern California, populations are migratory. Don’t buy perennial milkweed in the store and plant them in the garden. They might invite butterflies to become stationary and then infected by parasites. Indeed, stationary populations have higher parasite loads! Buy endemic milkweed to support Western butterflies and plant them early in the season. Thanks.
And a little side note: Elizabeth is an awesome presenter. She must be a really great teacher. Thanks for entertaining us.
I have been busy writing articles on science topics at the Molecular Ecologist!
Check out my guest blog post on the website of the Research Coordinated Network for Evolution in Changing Seas!