Dr. Tiago Simões | Simões Lab

Bio:
Dr. Tiago Simões started his career in his home city (Rio de Janeiro, Brazil), where he obtained his BSc and MSc in Biological Sciences- Zoology at the Federal University of Rio de Janeiro and the National Museum of Brazil. He obtained his PhD at the University of Alberta, Canada, in 2018 working with Dr. Michael Caldwell. Between 2019 and 2023 he was a Postdoctoral Fellow at the Museum of Comparative Zoology & Dpt. Organismic and Evolutionary Biology, Harvard University, working with Dr. Stephanie Pierce, and since 2022 a Research Associate in the Division of Vertebrate Zoology at the American Museum of Natural History. Since 2024, he has been an Assistant Professor in the Dpt. Ecology and Evolutionary Biology at Princeton University.

Dr. Simões’s research integrates data from living and extinct species, as well as morphological and genomic data, to investigate deep time problems in vertebrate evolution, with a special focus on the origin and early evolution of lizards and snakes. He has created several new morphological and total-evidence datasets employing state-of-the-art techniques in Bayesian phylogenetics and phylodynamics that helped bridging gaps between morphological and molecular hypothesis of reptile evolution. These studies, along with new technical advances in phylogenetics have been published in several peer-reviewed scientific articles creating, including in Nature, Nature Ecology & Evolution, and Science Advances. 

:
The history of life on Earth is marked by complex interactions between species genomes and phenotypes across constantly changing environments. Therefore, it is necessary to investigate these interactions across deep evolutionary time to understand the processes responsible for the construction of both past and modern biological diversity. However, this line of research has historically faced several logistic and methodological limitations, such as the lack of quantitative methods for combining various data types sampled across vastly different organismal and temporal dimensions. Fortunately, the past decade has been testimony to several advances in Bayesian evolutionary analyses that have fostered the integration of data types towards more sophisticated inferences of evolutionary trees and macroevolutionary dynamics. Here, I will illustrate how I have used and expanded this class of techniques to integrate molecular and phenotypic data from living and fossil species to understand the patterns and processes operating across major evolutionary transitions in vertebrates, with a special focus on reptiles. These results have overhauled the structure of key areas of the reptile tree of life, including the origin of lizards and turtles, the interplay between phenotypic and molecular innovations during evolutionary transitions, and how these events have been impacted by climate change across deep time. I conclude by highlighting how a new omics era, integrating whole genomes and phenomes, can conciliate historical challenges in understanding organismal evolution and the interplay between genomes and phenotypes with their surrounding environments across broad taxonomic and time scales.

Watch the seminar here!

Dr. Tiago Simões | Simões Lab

Bio:
Dr. Tiago Simões started his career in his home city (Rio de Janeiro, Brazil), where he obtained his BSc and MSc in Biological Sciences- Zoology at the Federal University of Rio de Janeiro and the National Museum of Brazil. He obtained his PhD at the University of Alberta, Canada, in 2018 working with Dr. Michael Caldwell. Between 2019 and 2023 he was a Postdoctoral Fellow at the Museum of Comparative Zoology & Dpt. Organismic and Evolutionary Biology, Harvard University, working with Dr. Stephanie Pierce, and since 2022 a Research Associate in the Division of Vertebrate Zoology at the American Museum of Natural History. Since 2024, he has been an Assistant Professor in the Dpt. Ecology and Evolutionary Biology at Princeton University.

Dr. Simões’s research integrates data from living and extinct species, as well as morphological and genomic data, to investigate deep time problems in vertebrate evolution, with a special focus on the origin and early evolution of lizards and snakes. He has created several new morphological and total-evidence datasets employing state-of-the-art techniques in Bayesian phylogenetics and phylodynamics that helped bridging gaps between morphological and molecular hypothesis of reptile evolution. These studies, along with new technical advances in phylogenetics have been published in several peer-reviewed scientific articles creating, including in Nature, Nature Ecology & Evolution, and Science Advances. 

:
The history of life on Earth is marked by complex interactions between species genomes and phenotypes across constantly changing environments. Therefore, it is necessary to investigate these interactions across deep evolutionary time to understand the processes responsible for the construction of both past and modern biological diversity. However, this line of research has historically faced several logistic and methodological limitations, such as the lack of quantitative methods for combining various data types sampled across vastly different organismal and temporal dimensions. Fortunately, the past decade has been testimony to several advances in Bayesian evolutionary analyses that have fostered the integration of data types towards more sophisticated inferences of evolutionary trees and macroevolutionary dynamics. Here, I will illustrate how I have used and expanded this class of techniques to integrate molecular and phenotypic data from living and fossil species to understand the patterns and processes operating across major evolutionary transitions in vertebrates, with a special focus on reptiles. These results have overhauled the structure of key areas of the reptile tree of life, including the origin of lizards and turtles, the interplay between phenotypic and molecular innovations during evolutionary transitions, and how these events have been impacted by climate change across deep time. I conclude by highlighting how a new omics era, integrating whole genomes and phenomes, can conciliate historical challenges in understanding organismal evolution and the interplay between genomes and phenotypes with their surrounding environments across broad taxonomic and time scales.

Watch the seminar here!

Dr. Tiago Simões | Simões Lab

Bio:
Dr. Tiago Simões started his career in his home city (Rio de Janeiro, Brazil), where he obtained his BSc and MSc in Biological Sciences- Zoology at the Federal University of Rio de Janeiro and the National Museum of Brazil. He obtained his PhD at the University of Alberta, Canada, in 2018 working with Dr. Michael Caldwell. Between 2019 and 2023 he was a Postdoctoral Fellow at the Museum of Comparative Zoology & Dpt. Organismic and Evolutionary Biology, Harvard University, working with Dr. Stephanie Pierce, and since 2022 a Research Associate in the Division of Vertebrate Zoology at the American Museum of Natural History. Since 2024, he has been an Assistant Professor in the Dpt. Ecology and Evolutionary Biology at Princeton University.

Dr. Simões’s research integrates data from living and extinct species, as well as morphological and genomic data, to investigate deep time problems in vertebrate evolution, with a special focus on the origin and early evolution of lizards and snakes. He has created several new morphological and total-evidence datasets employing state-of-the-art techniques in Bayesian phylogenetics and phylodynamics that helped bridging gaps between morphological and molecular hypothesis of reptile evolution. These studies, along with new technical advances in phylogenetics have been published in several peer-reviewed scientific articles creating, including in Nature, Nature Ecology & Evolution, and Science Advances. 

:
The history of life on Earth is marked by complex interactions between species genomes and phenotypes across constantly changing environments. Therefore, it is necessary to investigate these interactions across deep evolutionary time to understand the processes responsible for the construction of both past and modern biological diversity. However, this line of research has historically faced several logistic and methodological limitations, such as the lack of quantitative methods for combining various data types sampled across vastly different organismal and temporal dimensions. Fortunately, the past decade has been testimony to several advances in Bayesian evolutionary analyses that have fostered the integration of data types towards more sophisticated inferences of evolutionary trees and macroevolutionary dynamics. Here, I will illustrate how I have used and expanded this class of techniques to integrate molecular and phenotypic data from living and fossil species to understand the patterns and processes operating across major evolutionary transitions in vertebrates, with a special focus on reptiles. These results have overhauled the structure of key areas of the reptile tree of life, including the origin of lizards and turtles, the interplay between phenotypic and molecular innovations during evolutionary transitions, and how these events have been impacted by climate change across deep time. I conclude by highlighting how a new omics era, integrating whole genomes and phenomes, can conciliate historical challenges in understanding organismal evolution and the interplay between genomes and phenotypes with their surrounding environments across broad taxonomic and time scales.

Watch the seminar here!

Dr. Susana Magallón Puebla

Bio:
Dr. Susana Magallón Puebla is the Director of the Biology Institute at the Universad Nacional Autónoma de México. She is an evolutionary biologist who focuses on understanding macroevolutionary processes associated to the evolution of flowering plants, including their floral structure, the timing and dynamics of their diversification, and the mechanisms of acquisition of species richness in diverse Mesoamerican lineages. She obtained her B.Sc. and M.SC. degrees from UNAM, and a Ph.D. from the University of Chicago. She held a postdoctoral fellowship at the University of California, Davis. Her research is characterized by a deep understanding and integration of paleobiology and of phylogenetic comparative methods, involving the combination of morphological and molecular data from extant and fossil species. Dr. Magallón was inducted as a member of the National Academy of Sciences (USA)  and the Royal Society (UK) in 2024 because of the quality of her research and contributions to the scientific community.

Abstract:
Integration of molecular data, to provide a general phylogenetic framework, and morphological data, to allow incorporation of fossils, represents a cardinal approach to investigate evolution in deep time. We assembled a morphological matrix for 1201 extant species representing all angiosperm families, and 121 well-preserved fossil flowers, and in combination with a molecular database for extant species based on exemplar representation, used it to investigate methodological issues relating to integration of extant and fossil taxa in phylogenetic estimation; divergence time estimation in a full Total Evidence approach; and estimation of the theoretical floral morphospace. Phylogenetic analyses used different optimization criteria and kinds of data to estimate relationships, as well as uncertainty in fossil placements. We found that the joint use of molecular and morphological data in a parametric context allows to recover a phylogenetic framework in agreement with molecular estimates, and fossils associated to branches in agreement with assessments based on detailed morphological comparisons. Nevertheless, uncertainty associated to fossil placements is usually high. An attempt to estimate divergence times using morphological, molecular and temporal information indicates that, while available models to integrate extant and fossil species in the same diversification process represent significant advances, there are practical difficulties with fossils for which few characters can be scored, and in the free estimation of model parameters. The theoretical morphospace of floral structure was estimated through the construction of a pairwise distance matrix among extant and fossil species, estimation of disparity, and ordination techniques to reduce dimensionality. The area of the theoretical morphospace occupied by extant and fossil species was identified, as well as how morphospace occupation has changed through time and among groups. A decrease in morphospace occupation towards the present and canalization in the of morphospace occupation among derived clades are documented, in agreement with previous independent observations.


How did the first flower in the history of Earth look like?

Dr. Susana Magallón Puebla

Bio:
Dr. Susana Magallón Puebla is the Director of the Biology Institute at the Universad Nacional Autónoma de México. She is an evolutionary biologist who focuses on understanding macroevolutionary processes associated to the evolution of flowering plants, including their floral structure, the timing and dynamics of their diversification, and the mechanisms of acquisition of species richness in diverse Mesoamerican lineages. She obtained her B.Sc. and M.SC. degrees from UNAM, and a Ph.D. from the University of Chicago. She held a postdoctoral fellowship at the University of California, Davis. Her research is characterized by a deep understanding and integration of paleobiology and of phylogenetic comparative methods, involving the combination of morphological and molecular data from extant and fossil species. Dr. Magallón was inducted as a member of the National Academy of Sciences (USA)  and the Royal Society (UK) in 2024 because of the quality of her research and contributions to the scientific community.

Abstract:
Integration of molecular data, to provide a general phylogenetic framework, and morphological data, to allow incorporation of fossils, represents a cardinal approach to investigate evolution in deep time. We assembled a morphological matrix for 1201 extant species representing all angiosperm families, and 121 well-preserved fossil flowers, and in combination with a molecular database for extant species based on exemplar representation, used it to investigate methodological issues relating to integration of extant and fossil taxa in phylogenetic estimation; divergence time estimation in a full Total Evidence approach; and estimation of the theoretical floral morphospace. Phylogenetic analyses used different optimization criteria and kinds of data to estimate relationships, as well as uncertainty in fossil placements. We found that the joint use of molecular and morphological data in a parametric context allows to recover a phylogenetic framework in agreement with molecular estimates, and fossils associated to branches in agreement with assessments based on detailed morphological comparisons. Nevertheless, uncertainty associated to fossil placements is usually high. An attempt to estimate divergence times using morphological, molecular and temporal information indicates that, while available models to integrate extant and fossil species in the same diversification process represent significant advances, there are practical difficulties with fossils for which few characters can be scored, and in the free estimation of model parameters. The theoretical morphospace of floral structure was estimated through the construction of a pairwise distance matrix among extant and fossil species, estimation of disparity, and ordination techniques to reduce dimensionality. The area of the theoretical morphospace occupied by extant and fossil species was identified, as well as how morphospace occupation has changed through time and among groups. A decrease in morphospace occupation towards the present and canalization in the of morphospace occupation among derived clades are documented, in agreement with previous independent observations.


How did the first flower in the history of Earth look like?

Dr. Susana Magallón Puebla

Bio:
Dr. Susana Magallón Puebla is the Director of the Biology Institute at the Universad Nacional Autónoma de México. She is an evolutionary biologist who focuses on understanding macroevolutionary processes associated to the evolution of flowering plants, including their floral structure, the timing and dynamics of their diversification, and the mechanisms of acquisition of species richness in diverse Mesoamerican lineages. She obtained her B.Sc. and M.SC. degrees from UNAM, and a Ph.D. from the University of Chicago. She held a postdoctoral fellowship at the University of California, Davis. Her research is characterized by a deep understanding and integration of paleobiology and of phylogenetic comparative methods, involving the combination of morphological and molecular data from extant and fossil species. Dr. Magallón was inducted as a member of the National Academy of Sciences (USA)  and the Royal Society (UK) in 2024 because of the quality of her research and contributions to the scientific community.

Abstract:
Integration of molecular data, to provide a general phylogenetic framework, and morphological data, to allow incorporation of fossils, represents a cardinal approach to investigate evolution in deep time. We assembled a morphological matrix for 1201 extant species representing all angiosperm families, and 121 well-preserved fossil flowers, and in combination with a molecular database for extant species based on exemplar representation, used it to investigate methodological issues relating to integration of extant and fossil taxa in phylogenetic estimation; divergence time estimation in a full Total Evidence approach; and estimation of the theoretical floral morphospace. Phylogenetic analyses used different optimization criteria and kinds of data to estimate relationships, as well as uncertainty in fossil placements. We found that the joint use of molecular and morphological data in a parametric context allows to recover a phylogenetic framework in agreement with molecular estimates, and fossils associated to branches in agreement with assessments based on detailed morphological comparisons. Nevertheless, uncertainty associated to fossil placements is usually high. An attempt to estimate divergence times using morphological, molecular and temporal information indicates that, while available models to integrate extant and fossil species in the same diversification process represent significant advances, there are practical difficulties with fossils for which few characters can be scored, and in the free estimation of model parameters. The theoretical morphospace of floral structure was estimated through the construction of a pairwise distance matrix among extant and fossil species, estimation of disparity, and ordination techniques to reduce dimensionality. The area of the theoretical morphospace occupied by extant and fossil species was identified, as well as how morphospace occupation has changed through time and among groups. A decrease in morphospace occupation towards the present and canalization in the of morphospace occupation among derived clades are documented, in agreement with previous independent observations.


How did the first flower in the history of Earth look like?

Dr. Susana Magallón Puebla

Bio:
Dr. Susana Magallón Puebla is the Director of the Biology Institute at the Universad Nacional Autónoma de México. She is an evolutionary biologist who focuses on understanding macroevolutionary processes associated to the evolution of flowering plants, including their floral structure, the timing and dynamics of their diversification, and the mechanisms of acquisition of species richness in diverse Mesoamerican lineages. She obtained her B.Sc. and M.SC. degrees from UNAM, and a Ph.D. from the University of Chicago. She held a postdoctoral fellowship at the University of California, Davis. Her research is characterized by a deep understanding and integration of paleobiology and of phylogenetic comparative methods, involving the combination of morphological and molecular data from extant and fossil species. Dr. Magallón was inducted as a member of the National Academy of Sciences (USA)  and the Royal Society (UK) in 2024 because of the quality of her research and contributions to the scientific community.

Abstract:
Integration of molecular data, to provide a general phylogenetic framework, and morphological data, to allow incorporation of fossils, represents a cardinal approach to investigate evolution in deep time. We assembled a morphological matrix for 1201 extant species representing all angiosperm families, and 121 well-preserved fossil flowers, and in combination with a molecular database for extant species based on exemplar representation, used it to investigate methodological issues relating to integration of extant and fossil taxa in phylogenetic estimation; divergence time estimation in a full Total Evidence approach; and estimation of the theoretical floral morphospace. Phylogenetic analyses used different optimization criteria and kinds of data to estimate relationships, as well as uncertainty in fossil placements. We found that the joint use of molecular and morphological data in a parametric context allows to recover a phylogenetic framework in agreement with molecular estimates, and fossils associated to branches in agreement with assessments based on detailed morphological comparisons. Nevertheless, uncertainty associated to fossil placements is usually high. An attempt to estimate divergence times using morphological, molecular and temporal information indicates that, while available models to integrate extant and fossil species in the same diversification process represent significant advances, there are practical difficulties with fossils for which few characters can be scored, and in the free estimation of model parameters. The theoretical morphospace of floral structure was estimated through the construction of a pairwise distance matrix among extant and fossil species, estimation of disparity, and ordination techniques to reduce dimensionality. The area of the theoretical morphospace occupied by extant and fossil species was identified, as well as how morphospace occupation has changed through time and among groups. A decrease in morphospace occupation towards the present and canalization in the of morphospace occupation among derived clades are documented, in agreement with previous independent observations.


How did the first flower in the history of Earth look like?

Dr. Susana Magallón Puebla

Bio:
Dr. Susana Magallón Puebla is the Director of the Biology Institute at the Universad Nacional Autónoma de México. She is an evolutionary biologist who focuses on understanding macroevolutionary processes associated to the evolution of flowering plants, including their floral structure, the timing and dynamics of their diversification, and the mechanisms of acquisition of species richness in diverse Mesoamerican lineages. She obtained her B.Sc. and M.SC. degrees from UNAM, and a Ph.D. from the University of Chicago. She held a postdoctoral fellowship at the University of California, Davis. Her research is characterized by a deep understanding and integration of paleobiology and of phylogenetic comparative methods, involving the combination of morphological and molecular data from extant and fossil species. Dr. Magallón was inducted as a member of the National Academy of Sciences (USA)  and the Royal Society (UK) in 2024 because of the quality of her research and contributions to the scientific community.

Abstract:
Integration of molecular data, to provide a general phylogenetic framework, and morphological data, to allow incorporation of fossils, represents a cardinal approach to investigate evolution in deep time. We assembled a morphological matrix for 1201 extant species representing all angiosperm families, and 121 well-preserved fossil flowers, and in combination with a molecular database for extant species based on exemplar representation, used it to investigate methodological issues relating to integration of extant and fossil taxa in phylogenetic estimation; divergence time estimation in a full Total Evidence approach; and estimation of the theoretical floral morphospace. Phylogenetic analyses used different optimization criteria and kinds of data to estimate relationships, as well as uncertainty in fossil placements. We found that the joint use of molecular and morphological data in a parametric context allows to recover a phylogenetic framework in agreement with molecular estimates, and fossils associated to branches in agreement with assessments based on detailed morphological comparisons. Nevertheless, uncertainty associated to fossil placements is usually high. An attempt to estimate divergence times using morphological, molecular and temporal information indicates that, while available models to integrate extant and fossil species in the same diversification process represent significant advances, there are practical difficulties with fossils for which few characters can be scored, and in the free estimation of model parameters. The theoretical morphospace of floral structure was estimated through the construction of a pairwise distance matrix among extant and fossil species, estimation of disparity, and ordination techniques to reduce dimensionality. The area of the theoretical morphospace occupied by extant and fossil species was identified, as well as how morphospace occupation has changed through time and among groups. A decrease in morphospace occupation towards the present and canalization in the of morphospace occupation among derived clades are documented, in agreement with previous independent observations.


How did the first flower in the history of Earth look like?

Dr. Susana Magallón Puebla

Bio:
Dr. Susana Magallón Puebla is the Director of the Biology Institute at the Universad Nacional Autónoma de México. She is an evolutionary biologist who focuses on understanding macroevolutionary processes associated to the evolution of flowering plants, including their floral structure, the timing and dynamics of their diversification, and the mechanisms of acquisition of species richness in diverse Mesoamerican lineages. She obtained her B.Sc. and M.SC. degrees from UNAM, and a Ph.D. from the University of Chicago. She held a postdoctoral fellowship at the University of California, Davis. Her research is characterized by a deep understanding and integration of paleobiology and of phylogenetic comparative methods, involving the combination of morphological and molecular data from extant and fossil species. Dr. Magallón was inducted as a member of the National Academy of Sciences (USA)  and the Royal Society (UK) in 2024 because of the quality of her research and contributions to the scientific community.

Abstract:
Integration of molecular data, to provide a general phylogenetic framework, and morphological data, to allow incorporation of fossils, represents a cardinal approach to investigate evolution in deep time. We assembled a morphological matrix for 1201 extant species representing all angiosperm families, and 121 well-preserved fossil flowers, and in combination with a molecular database for extant species based on exemplar representation, used it to investigate methodological issues relating to integration of extant and fossil taxa in phylogenetic estimation; divergence time estimation in a full Total Evidence approach; and estimation of the theoretical floral morphospace. Phylogenetic analyses used different optimization criteria and kinds of data to estimate relationships, as well as uncertainty in fossil placements. We found that the joint use of molecular and morphological data in a parametric context allows to recover a phylogenetic framework in agreement with molecular estimates, and fossils associated to branches in agreement with assessments based on detailed morphological comparisons. Nevertheless, uncertainty associated to fossil placements is usually high. An attempt to estimate divergence times using morphological, molecular and temporal information indicates that, while available models to integrate extant and fossil species in the same diversification process represent significant advances, there are practical difficulties with fossils for which few characters can be scored, and in the free estimation of model parameters. The theoretical morphospace of floral structure was estimated through the construction of a pairwise distance matrix among extant and fossil species, estimation of disparity, and ordination techniques to reduce dimensionality. The area of the theoretical morphospace occupied by extant and fossil species was identified, as well as how morphospace occupation has changed through time and among groups. A decrease in morphospace occupation towards the present and canalization in the of morphospace occupation among derived clades are documented, in agreement with previous independent observations.


How did the first flower in the history of Earth look like?

Dr. Celina Juliano | Juliano Lab

Bio:
Dr. Juliano joined the faculty at UC Davis in 2015 as an Assistant Professor in the Molecular and Cellular Biology Department and was promoted to Associate Professor with tenure in 2021. She is a developmental biologist with a long-standing interest in stem cell biology. Her doctoral research, mentored by Dr. Gary Wessel at Brown University, focused on understanding the molecular mechanisms underlying the maintenance of plasticity during sea urchin development. Dr. Juliano completed her post-doctoral work at Yale University in the laboratory of Dr. Haifan Lin with co-mentoring from Dr. Rob Steele at UC Irvine. At Yale, Dr. Juliano began working with Hydra, a small freshwater cnidarian that continually renews all cell types as an adult and has remarkable regenerative abilities. During her post-doctoral work, she discovered a critical role for the PIWI-piRNA pathway in Hydra stem cells. In her own laboratory at UC Davis, Dr. Juliano continues to use Hydra as a model to understand, stem cell function, development, and regeneration, with funding from the National Institutes of Health. Dr. Juliano was a recipient of the Elizabeth D. Hay New Investigator award from the Society for Developmental Biology in 2020 and she was named a UC Davis Chancellor’s fellow in 2024. Dr. Juliano is the founder of the biennial Cnidarian Model Systems Meetings, the founder and director of the annual Hydra Workshop (Marine Biological Laboratory), and a founding board member of the International Society for Regenerative Biology. 

Abstract:
In our laboratory at UC Davis, we use Hydra as a model to understand, stem cell function, development, and regeneration. As a starting point, we subjected the adult Hydra to single cell sequencing, created a molecular map of the entire organism, and built differentiation trajectories to describe each stem cell differentiation pathway. This work now serves as a foundation for our research goals, which include dissecting the molecular mechanisms underlying stem cell differentiation, understanding how the conserved injury program triggers developmental pathways during regeneration, and understanding how the Hydra nervous system is able to continually remove and add neurons into neural circuits.

Watch the seminar here!