Research

Here you can find information about some of my past and current research projects. Check out the links to papers and recorded talks for more information and please email me (ilichtermarck at berkeley.edu) if you would like to collaborate!

Can next generation sequencing (NGS) be used at shallow taxonomic scales to study systematics in the sunflower family (Asteraceae)?

I focus my systematics research on the sunflower family (Asteraceae) for their incredible diversity and fascinating ecology. One in ten flowering plants is a member of the sunflower family and they are the dominant group in most extratropical regional floras. For most of the history of synantherology (the study of Asteraceae), floral and fruit traits have formed the basis for classification. In the present age of molecular systematics however, new forms of data have radically changed our understanding of the sunflower family. Now, NGS approaches promise to extend the molecular revolution to shallower taxonomic scales where poor resolution has long impeded our understanding of evolutionary relationships. In my dissertation research, I tested the promise of NGS approaches by carrying out one of the first densely sampled species-level phylogenomic analyses of a tribe of sunflowers, the rock daisies (Perityleae). The rock daisies are a diverse group of ~ 85 spp. found on mountains in western North America that had never been the subject of a densely sampled molecular study. Over three years, I visited dozens of herbaria and carried out rough terrain field work to make collections of rock daisies. I applied an experimental target capture approach to these collections and the experiment yielded hundreds of orthologous nuclear loci. I analyzed these data in an integrative framework with morphology and chromosome numbers, radically rewriting the evolutionary story of the rock daisies and putting morphological traits emphasized in past taxonomy into new context. This study was recognized with a best paper award from JSE because it produced the most comprehensive dataset available for any tribe in the sunflower family. Resolution of phylogenetic uncertainty in the rock daisies has also formed the basis for reclassification of the tribe,setting the stage for new species descriptions and new combinations that will inform an innovative, collaborative, and ‘open-source’ monograph.

What are the processes underlying floristic assembly in the North American Deserts?

Understanding where and when endemic elements of regional floras assembled is important for understanding the effects of future climate change on biodiversity. The sunflower family is not only megadiverse, but also an ecologically important part of many biomes, especially deserts, grasslands, mountains, and islands. Understanding the biogeographic and evolutionary origins of Asteraceae can therefore help us understand the assembly of these biomes. Rock daisies are one of the most diverse clades of North American desert sunflowers and an ideal group in which to tease apart the contributions of dispersal and adaptation to past shifts into the desert biome. In a recent research project, I synthesized diverse lines of evidence from my comprehensive clade-based study of the rock daisy tribe, including extrinsic (ecological) and intrinsic (trait) data gathered from museum specimens, to infer the timing of adaptation and biome-shifts into deserts. The results were surprising and showed that desert rock daisies stemmed from ancestors that were already exapted to arid conditions through their habitat (edaphic) endemism on bare, rocky outcrops before they shifted into the desert biome. These results refute the notion that plants rapidly adapted to deserts. Instead, it reveals pre-adaptation (exaptation) and dispersal as important processes guiding assembly in deserts and raises concerns about the potentially limited organismal responses to climate change.

How does ecological specialization evolve?

The framework of ecological specialization is useful for understanding the forces that generate adaptation and narrow endemism. My interest in ecological specialization stems from my first major research endeavor, my master’s thesis in Ecology on the causes and consequences of narrow diet breadths in larval Lepidoptera (caterpillars) in eastern deciduous forests. In this work I showed that specialization in caterpillars (narrow diet breadths), was strongly associated with heightened defense strategies, and lower attack rates from bird predators, suggesting that natural enemies drive ecological specialization. I also uncovered community wide effects of caterpillar specialization. For example, variation in the proportion of specialists to generalist caterpillars across tree species explained variation in the strength of trophic cascades, and influenced the abundance of other predatory and herbivorous insect guilds. This research made me excited to test hypotheses about the drivers of ecological specialization in my studies on plants with more robust phylogenetic approaches. This was one of the reasons why I chose to study rock daisies, which get their name because many are edaphic specialists that grow only on bare rock outcrops and cliffs. During my PhD, I collected geological data for rock daisies and inferred the timing of edaphic specialization across their phylogeny. I found that ecological specialization onto bare rock evolved early in the group and has had cascading effects influencing the radiation of the entire tribe. To contextualize these data and lay the groundwork for more detailed analyses of the causes and consequences of edaphic specialization onto bare rock outcrops, I recently wrote a synthesis paper on this topic for American Journal of Botany.

Where does variation, the raw material for evolutionary radiation, come from?

Comprehensive phylogenomic data for the rock daisy tribe is the basis for my NSF postdoctoral research fellowship, which aims to study how hybridization furnished the variation for morphological differentiation and niche evolution during the recent radiation of rock daisies at three scales of organization. Hybridization can provide the raw material for evolution through two pathways: by seeding variation via hybridization at the onset (the hybrid origins hypothesis) and by generating variability through reticulation among members of a radiating clade (the syngameon hypothesis). I will test these competing hypotheses using rock daisy radiations in mountains, islands, and deserts of North America and Chile (Fig.1).

Further reading: check out the abstract for my NSF DBI-PRFP award.

Figure 1: Two hypotheses for how hybridization generates variation during evolution. (A) The hybrid origins hypothesis (HOH): hybridization at the onset boosts genetic and morphological variation prior to shifts into new niches. (B) The syngameon hypothesis (SH): hybridization among members of a radiation leads to concurrent accumulation of morphological, genetic, and environmental variability.

What are the processes underlying floristic assembly of the Hawaiian flora?

Hotspot archipelagos offer a unique geological chrono-sequence ideal for pinpointing when and where evolutionary events of particular importance occurred. In my post-doctoral work with Dr. Felipe Zapata (UCLA), I have been leveraging this fact to reconstruct the floristic assembly of the endemic Hawaiian flora. Thus far, I have used herbarium specimens at the National Tropical Botanical Garden in Kaua’i to generate phylogenomic scale data for twelve lineages of endemic Hawaiian plants, including wild coffees (Rubiaceae), palms (Arecaceae), grasses (Poaceae), and others. To decode signals of historical biogeography and diversification in these phylogenomic datasets, I am be collaborating with Fabio Mende, Sarah Swiston, and Michael Landis (Wash. U.) to develop innovative statistical biogeographic models of island growth and decay using Bayesian statistical inference in the coding language RevBayes.

What is the genomic basis of budding speciation?

Layia glandulosa (pictured on the right) is the most geographically widespread self-incompatible annual in the tarweed and silversword tribe (Madieae Jeps.). It has been the subject of evolutionary studies of speciation in the past for its peripatric progenitor-derivative species relationship with the narrowly endemic serpentinite specialist species Layia discoidea D.D. Keck. It turns out that L. discoidea is nested within L. glandulosa in phylogenetic analyses, suggesting that despite being so morphologically distinct that it was previously placed in a separate tribe, L. discoidea is the recent derivative of a presumably extreme natural selection event. In a collaboration with my Ph.D. advisor Bruce Baldwin funded by the California Conservation Genomics Project, we are investigating in greater detail the evolutionary history of this fascinating species complex and using whole genome data to understand the dynamics of budding speciation.

To read more about this project and the harrowing field work involved, check out this write up for Capitulum, the journal of the International Compositae Alliance (TICA).