My proudest career moment

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.

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