I’m a data scientist at Phylagen, a startup in San Francisco committed to harnessing the unseen world of microbes to improve our daily lives. Every day I get to work with large sequencing datasets, combining my love for bioinformatics, big data, and biodiversity.
I was born in Bogotá, Colombia, where I grew up. Beginning my major in biology at the Universidad de los Andes in Bogotá, with a specialization in botany, I discovered the amazing world of molecular biology and learned about the phylogenetic tools available. I joined the Systematic Botany Lab where I focused my undergraduate honors thesis on the phylogeny of the Colombian species of Bartsia and Castilleja with Dr. Santiago Madriñán as my advisor and Dr. Sarah Mathews from the Harvard University Herbarium as my co-advisor. I took part in a yearlong exchange at the Johannes Gutenberg Univesität in Mainz, Germany, where I worked at the Institut für Spezielle Botanik with Prof. Dr. Joachim Kadereit on the phylogeny and reciprocal hybridization of Senecio flavus and S. glaucus.
During the summer of 2008, I interned at the New York Botanical Garden (NYBG) with Dr. Amy Litt working on the phylogeny of Vochysiaceae. In August 2009, I started my Ph.D. at the University of Idaho where I worked with Dr. David Tank on the evolution of Neobartsia and the development of novel high-throughput sequencing methods to generate large amounts of genomic data quickly and cost effectively. I spent two years as a postdoctoral research fellow working on phylogenomics of the genus Burmeistera (Campanulaceae) with Dr. Nathan Muchhala at the University of Missouri – St. Louis and as a research associate at the Missouri Botanical Garden. Finally, I was a postdoctoral fellow working on genomics and bioinformatics with Dr. Stephen Smith at the University of Michigan. Specifically, I was improving large scale phylogenetic methods and analyses with a special emphasis on angiosperms.
Genomics and Phylogenomics
I have developed two approaches to generate genomic data quickly and cost effectively. The first approach is based on microfluidic PCR and benefits from the high-throughput of the Fluidigm Access Array System—an instrument capable of amplify ~2300 PCRs simultaneously. For this method, I designed 96 primer pairs that were used to amplify 48 nuclear and 48 chloroplast loci in over 500 samples of Neobartsia. This resulted in a molecular matrix with multiple individuals per species and almost no missing data, ideal for coalescent-based species tree methods (Uribe-Convers et al., 2016).
The second approach uses 16 universal overlapping primer combinations and long-PCR to amplify complete chloroplast genomes. These amplicons are then sequenced on a high-throughput sequencer (e.g., Illumina) and the reads assembled into complete plastomes. We tested this method in 12 orders of angiosperms and one order of gymnosperms showing the universality of the primers and the efficiency of the method (Uribe-Convers et al., 2014).
I have also worked with sequence capture, designing baits (capture probes) for over 800 nuclear loci that were used in studies in Burmeistera and the Centropogonid clade in Campanulaceae. My work included designing the baits from transcriptome data and shotgun libraries, to process the raw sequence data, and to analyze it in a phylogenomic and coalescent context.
Lastly, I’m working with raw Genotyping by Sequencing (GBS) data as part of my collaboration in the Tanager Bird project. This includes cleaning and filtering the data and conducting the phylogenetic, biogeographic, and population genetic studies.
Systematics and Evolution
For most of my academic career (undergraduate and Ph.D.) I’ve worked on the genus Bartsia (Orobanchaceae), doing extensive fieldwork in the Andes in South America, molecular systematics and phylogenetics, and genomics and phylogenomics. One of the results in this group showed that the genus is not monophyletic and that led to a new taxonomic classification in which the new genus Neobartsia was described. Furthermore, I showed that the Andean species are diversifying much faster than other species in the Rhinantheae clade—a group of ~500 species—and that this is associated with the biogeographic movement from the Mediterranean Region and the colonization of the páramo ecosystem ~1.5 million years ago. I’m currently using coalescent-based species tree methods to elucidate the relationships in Neobartsia and to study the accumulation of lines of evidence for speciation in the group. This is in collaboration with Dr. David Tank.
I’m studying the phylogeographic patterns and population dynamics of Tanager birds (Thraupidae) in the Greater and Lesser Antilles. We are particularly interested in the gene flow between islands and in the expansion and contraction of population sizes over macroevolutionary time. This is in collaboration with Dr. Robert Ricklefs.
Finally, I’ve also worked on the genus Burmeistera (Campanulaceae) for my postdoc at UMSL. I was interested in the interspecific relationships among the ~120 species in the genus, their pollination syndromes, and the possible barriers (pre- or post-zygotic) that prevent hybrids to occur in nature. By hand-pollinating different species of Burmeistera in the greenhouse, I investigated what type of barriers exist and if they were associated with how closely related the species are. This was in collaboration with Dr. Nathan Muchhala.
Ancient DNA from the Clarkia Fossil Bed
I have been working on extracting, amplifying, and sequencing DNA from Miocene (~15 MA) plant tissue. The Clarkia fossil bed, located in Clarkia, Idaho, has the perfect conditions needed to preserve unoxidized plant tissue that is suitable for molecular techniques.
You can watch a video of how we lift the tissue below and the episode of “Plants Are Cool, Too!” where this work got featured. Super Cool!
* Denotes mentored undergraduate student co-author
Randle CP and Uribe-Convers S. 2019. Bartsia. In: Flora of North America Editorial Committee, eds. 1993+. Flora of North America North of Mexico. 20+ vols. New York and Oxford. Vol. 17, pp. 488-489. [link]
Jacobs SJ, Kristofferson C*, Uribe-Convers S, Latvis M, Tank DC. 2018. Incongruence in molecular species delimitation schemes: what to do when adding more data is difficult. Molecular Ecology. [pdf] [link]
McKain MR, Johnson MG, Uribe-Convers S, Eaton D, Yang Y. 2018. Practical considerations for plant phylogenomics. Applications in Plant Sciences 6(3): e1038. *All authors contributed equally. [link to Open Access]
Klein, LL, Miller AJ, Ciotir C, Hyma K, Uribe‐Convers S, Londo J. 2018. High‐throughput sequencing data clarify evolutionary relationships among North American Vitis species and improve identification in USDA Vitis germplasm collections. American Journal of Botany 105(2): 215–226. [pdf] [link]
Latvis M, Mortimer SME, Morales-Briones DF, Torpey S*, Uribe-Convers S, Jacobs SJ, Mathews S, Tank DC. 2017. Primers for Castilleja and their Utility Across Orobanchaceae: I. Chloroplast Primers. Applications in Plant Sciences 5 (9): 1700020. [link to Open Access]
Uribe-Convers S, Carlsen M, Lagomarsino L, Muchhala N. 2017. Phylogenetic relationships of Burmeistera (Campanulaceae)—combining whole plastome and Sanger data to improve resolution in a recent group. Molecular Phylogenetics and Evolution 107: 551-563. [pdf] [link]
Uribe-Convers S and Tank D.C. 2016. Phylogenetic Revision of the genus Bartsia (Orobanchaceae), disjunct distributions correlate to independent lineages. Systematic Botany 41(3): 672-684. [pdf] [link]
Uribe-Convers S, Settles ML, Tank DC. 2016. A Phylogenomic Approach Based on PCR Target Enrichment and High Throughput Sequencing: Resolving the Diversity within the South American Species of Bartsia L. (Orobanchaceae). PLoS ONE. 11(2): e0148203. doi:10.1371/journal.pone.0148203 [link to Open Access]
Uribe-Convers S and Tank DC. 2015. Shifts in diversification rates linked to biogeographic movement into new areas: an example of disparate continental distributions and a recent radiation in the Andes. American journal of Botany 102:1854–1869 [pdf][link]
…….Featured by the editor of the American Journal of Botany in the “Highlights Section” http://goo.gl/pAvqmH
Nürk NM, Uribe-Convers S, Gehrke B, Tank DC, Blattner F. 2015. Oligocene niche shift, Miocene diversification – cold tolerance and accelerated speciation rates in the St. John’s Worts (Hypericum, Hypericaceae). BMC Evolutionary Biology 15:80 [link to Open Access]
Uribe-Convers S, Duke JR*, Moore JM, Tank DC. 2014. A long-PCR based method for chloroplast genome enrichment and phylogenomics in angiosperms. Applications in Plant Sciences 2 (1): 1300063 [link to Open Access]
…….Featured in EurekAlert!: http://goo.gl/C4rAeh and in ScienceDaily: http://goo.gl/zdFuZ4
Goldberg CS, Tank DC, Uribe-Convers S, Bosworth WR, Marx HH, Waits LP. 2012. Species designation of the Bruneau Dune tiger beetle (Cicindela waynei) is supported by phylogenetic analysis of mitochondrial DNA sequence data. Conservation Genetics 13: 373-380. [pdf] [link]
Kadereit JW, Uribe-Convers S, Westberg E, Comes HP. 2006. Reciprocal hybridization at different times between Senecio flavus and Senecio glaucus gave rise to two polyploid species in North Africa and Southwest Asia. New Phytologist 169: 431 – 441. [pdf] [link]
In Preparation or in Review
Malagon MDP, Mendoza-Cifuentes H, Gómez-Parra S, Uribe-Convers S. In prep. A new species of Neobartsia (Orobanchaceae) from the Colombian Andes. To be submitted to Phytotaxa.
Uribe-Convers S, Settles ML, Tank DC (2016) Data from: A phylogenomic approach based on PCR target enrichment and high throughput sequencing: resolving the diversity within the South American species of Bartsia (Orobanchaceae). Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.fh592.
Uribe-Convers S and Tank D.C. (2015) Data from: Shifts in diversification rates linked to biogeographic movement into new areas: an example of disparate continental distributions and a recent radiation in the Andes. American Journal of Botany http://dx.doi.org/10.5061/dryad.7v1f8.
Nürk NM, Uribe-Convers S, Gehrke B, Tank DC, Blattner FR (2015) Data from: Oligocene niche shift, Miocene diversification – cold tolerance and accelerated speciation rates in the St. John’s Worts (Hypericum, Hypericaceae). BMC Evolutionary Biology http://dx.doi.org/10.5061/dryad.4tm8j.
Uribe-Convers S, Duke JR, Moore MJ, Tank DC (2014) Data from: A long PCR based approach for DNA enrichment prior to next–generation sequencing for systematic studies. Applications in Plant Sciences http://dx.doi.org/10.5061/dryad.kc75n.
Pre-Prints (Not Peer Reviewed)
Uribe-Convers S, Settles ML, Tank DC. 2015. A targeted subgenomic approach for phylogenomics based on microfluidic PCR and high throughput sequencing. bioRxiv 021246; doi:http://dx.doi.org/10.1101/021246.
Uribe-Convers S and Tank DC. 2015. Shifts in diversification rates linked to biogeographic movement into new areas, an example of disparate continental distributions and a recent radiation in the Andes. bioRxiv 019554; doi: http://dx.doi.org/10.1101/019554.
Uribe-Convers S. 2008. Molecular Phylogeny for the Colombian species of páramo, for the genera Bartsia and Castilleja (Orobanchaceae). Honors Thesis B.Sc. Biology, Universidad de los Andes, Bogotá – Colombia. [pdf] [link]