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Ecology and Evolution of Symbioses




I'm a Ph.D. student in the Lutzoni lab at Duke University. My research focuses on the ecology and evolution of symbioses. I am particularly interested in how mutualistic interactions are structured at different spatial scales and along landscape gradients.

I address these questions using cyanolichens as a model system and within a robust phylogenetic framework. 

I always enjoy engaging in conversations about my research or any related topics. I'm also committed to making all resources from my studies available to anyone interested. Please feel free to contact me if you'd like to chat or have any data requests!



Phylogenomic conflict in nostocalean cyanobacteria: traces of an ancient radiation

The cyanobacterial symbionts that are found in the lichens that I study are from the genus Nostoc, in the order Nostocales. To study how symbiosis has evolved in these cyanobacteria, it is very important to have a good idea of their evolutionary history. In trying to figure out the phylogenetic position Nostoc within Nostocales, I realized that previous phylogenomic studies of this order recover different relationships when using different datasets (i.e., phylogenetic conflicts; Fig. 1). What is the cause of these conflics? Because these are bacteria, my initial hypothesis was that these conflicts could be the result of widespread horizontal gene transfers (HGTs). However, my findings indicate that an ancient radiation at the origin of some of the major lineages of Nostocales is the main cause of the phylogenetic conflicts. Stay tuned for the upcoming paper!


Fig 1. Examples of conflicts among published phylogenies of Nostocales. Schematic representation of relationships among major lineages of Nostocales inferred from different sets of concatenated loci across four different studies: a) Gagunashvili and Andrésson (2018), b) Warshan et al. (2018), c) Sánchez-Baracaldo (2015), and d) Nelson et al. (2019). A: Cylindrospermum stagnale PCC7417, NI: Trichormus variabilis ATCC 29413, NII: Nostoc sp. cyanobiont of Peltigera aphthosa JL23, No: Nodularia sp. NIES 3585, F: Fortiea contorta PCC 7126, Fi: Fischerella sp. PCC 9605, Ri: Rivularia sp. PCC7116, S: Scytonema sp. HK 05 v2, and T: Tolypothrix sp. NIES 4075.

New approach to study phylogenetic specialization in ecological networks

A species that interacts with two partners is often considered more specialized than a species that interacts with five. But what if the two partners of the first species are distantly related, and the five partners of the second species are closely related? How do we characterize specialization then? I developed an approach that integrates phylogenetic structure and partner availability to detect three different patterns of specialization in ecological networks (Fig 2).

Check out the paper and the R package for computing PSS!


Fig 2. Schematic representation of three possible patterns (a–c) of phylogenetic structure (random, clustered, and overdispersed) of partners (guild A) associated with one species from guild B. The size of the orange circles represents the relative availability of each member of guild A in an interaction matrix. Our approach measures the Phylogenetic Structure of Specialization (PSS) to characterize these different types of specialization.

Eco-evolutionary drivers of cyanolichen network structure

I am sequencing over 3000 cyanolichen specimens collected by the ABMI in Alberta, Canada, to study the spatial structure of the interaction network between lichen-forming fungi from the genus Peltigera and their Nostoc cyanobionts. Preliminary results show that at least 28 species of Peltigera are found in Alberta (Fig 3A). In contrast, only six Nostoc phylogroups are found in most thalli. The distribution of these Nostoc phylogroups seems to be spatially structured (Fig 2 B-G). My goal is to study the network properties at different spatial scales and within a robust macroevolutionary framework for both partners.


Fig 3. Association patterns and spatial distribution of the six most common Nostoc phylogroups associated with Peltigera in Alberta based on 157 thalli from 61 ABMI sampling sites. A) Phylogeny of exemplar species representing the eight sections of the genus Peltigera, including 28 species found in association with the six most common Nostoc phylogroups in Alberta. Colored circles in the columns show the Nostoc phylogroups found in association with each species. B-G) Spatial distribution of Nostoc phylogroups found in Peltigera thalli at 61 ABMI sampling sites (circles). Roman numerals correspond to Nostoc phylogroups. Colored circles represent sites where the Nostoc phylogroups associated with Peltigera were found. The size of the colored circles denotes the number of thalli in which a Nostoc phylogroup was found at a given site. “n” is the total number of thalli in which a Nostoc phylogroup was found.

Phylogenetics and interaction patterns in the Peltigera-Nostoc symbioses

During my undergraduate research, I studied lineages of Peltigera that form trimembered thalli, i.e., a symbiosis between a mycobiont (Peltigera), a cyanobacteria (Nostoc) and a green alga (Coccomyxa). I found that two closely related lineages of Peltigera show contrasting patterns of specialization towards their cyanobacterial partners (Fig 4). Species from section Chloropeltigera can associate with up to seven Nostoc phylogroups, while species from section Peltidea associate only with two. I also found evidence that this difference in association patterns might be driven by the type of photobiont transmission. In Peltidea, it is likely that most of the photobiont transmission is vertical, favoring specialization. In Chloropeltigera, photobiont transmission might be mostly horizontal, favoring acquisition of new partners through time.


Fig 4. Phylogenetic relationships among the three Peltigera sections that include trimembered thalli. Thick branches represent ≥70% bootstrap support. Bars on the right indicate the proportion of Peltigera specimens associating with Nostoc phylogroups, Coccomyxa species, and inhabiting various geographic regions. The distribution ranges of the samples are divided into ten broad geographic regions based on latitudinal, oceanic and orographic conditions: Alaska (ALA), Alberta (ALB), Arctic (ARC), Central Europe (CE), Eastern North America (ENA), Mid-Western North America (MWNA), Northern Europe (NE), Pacific North West (PNW), Russia (RUS), and South East Asia (SEA). From Pardo-De la Hoz et al. (2018).




Pardo-De la Hoz, C. J., Magain, N., Piatkowski, B., Cornet, L., Dal Forno, M., Carbone, I., Miadlikowska, J., and Lutzoni, F. (2023). Ancient Rapid Radiation Explains Most Conflicts Among Gene Trees and Well-supported Phylogenomic Trees of Nostocalean Cyanobacteria. Systematic Biology, syad008. PDF



Pardo-De la Hoz, C. J., Medeiros, I. D., Gibert, J. P., Chagnon, P. L., Magain, N., Miadlikowska, J., and Lutzoni, F. (2021). Phylogenetic structure of specialization: A new approach that integrates partner availability and phylogenetic diversity to quantify biotic specialization in ecological networks. Ecology and Evolution, 12, e8649. PDF




Medeiros, I. D., Mazur, E., Miadlikowska, J., Flakus, A., Rodriguez-Flakus, P., Pardo-De la Hoz, C. J., Cieślak, E., Śliwa, L., and Lutzoni, F. (2021). Turnover of lecanoroid mycobionts and their Trebouxia photobionts along an elevation gradient in Bolivia highlights the role of environment in structuring the lichen symbiosis. Frontiers in microbiology, 12, 774839. PDF 



Stone, D. F., McCune, B., Pardo-De la Hoz, C. J., Magain, N., and Miadlikowska, J. (2021). Sinuicella denisonii, a new genus and species in the Peltigeraceae from western North America. The Lichenologist, 53, 185–192. PDF 



Miadlikowska, J., Magain, N., Buck, W. R., Vargas Castillo, R., Barlow, G. T., Pardo-De la Hoz, C. J., LaGreca, S., and Lutzoni, F. (2020). Peltigera hydrophila (Lecanoromycetes, Ascomycota), a new semi-aquatic cyanolichen species from Chile. Plant and Fungal Systematics, 65 (1), 210-218. PDF 


Miadlikowska, J., Magain, N., Pardo-De la Hoz, C.J., Niu, D., Goward, T., Sérusiaux, E. and Lutzoni, F., 2018. Species in section Peltidea (aphthosa group) of the genus Peltigera remain cryptic after molecular phylogenetic revision. Plant and Fungal Systematics, 63(2), pp.45-64. PDF 



Pardo‐De la Hoz, C.J., Magain, N., Lutzoni, F., Goward, T., Restrepo, S. and Miadlikowska, J., 2018. contrasting symbiotic patterns in two closely related lineages of trimembered lichens of the genus Peltigera. Frontiers in Microbiology, 9, 2770. PDF 



Rojas, P., Pardo-De la Hoz, C.J., Calderón, C., Vargas, N., Cabrera, L.A., Restrepo, S. and Jiménez, P., 2018. First Report of Colletotrichum kahawae subsp. ciggaro Causing Anthracnose Disease on Tree Tomato in Cundinamarca, Colombia. Plant Disease, 102(10), pp.2031-2031. PDF 



​Cabrera, L., Rojas, P., Rojas, S., Pardo‐De la Hoz, C.J., Mideros, M.F., Danies, G., Lopez‐Kleine, L., Jiménez, P. and Restrepo, S., 2018. Most Colletotrichum species associated with tree tomato (Solanum betaceum) and mango (Mangifera indica) crops are not host‐specific. Plant Pathology, 67(5), pp.1022-1030. PDF 




Vargas, N., Pardo-De la Hoz, C.J., Danies, G., Franco-Molano, A.E., Jiménez, P., Restrepo, S. and Grajales, A., 2017. Defining the phylogenetic position of Amanita species from Andean Colombia. Mycologia, 109(2), pp.261-276. PDF  




Pardo‐De la Hoz, C.J., Calderón, C., Rincón, A.M., Cárdenas, M., Danies, G., López‐Kleine, L., Restrepo, S. and Jiménez, P., 2016. Species from the Colletotrichum acutatum, Colletotrichum boninense and Colletotrichum gloeosporioides species complexes associated with tree tomato and mango crops in Colombia. Plant Pathology, 65(2), pp.227-237. PDF  



Mailing address

Department of Biology

Duke University

130 Science Dr.

Durham, NC, USA





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