About

Professor Tiago R. Simões leads the Simões Lab in the Department of Ecology and Evolutionary Biology at Princeton University, focusing on phylogenetics, macroevolution, and paleobiology. His research investigates the history of life on Earth by integrating genomic and phenotypic data from both living and fossil species. The lab aims to reconstruct deep time evolutionary patterns and processes to understand the origin of major vertebrate groups, with a particular emphasis on reptiles. Key areas of study include evolutionary relationships, the emergence of key innovations during major evolutionary transitions, and the impact of climate change across broad taxonomic and temporal scales. Professor Simões and his lab employ a multidisciplinary approach combining comparative anatomy, phylogenomics, and evolutionary tree construction to explore organismal evolution across extensive taxonomic and temporal ranges.

Research topics

• Computer Science
• Biology
• Artificial Intelligence
• Evolutionary biology
• Ecology
• Medicine
• Physics
• Paleontology
• Genetics
• Computational biology
• Demography

Selected publications

• Supplementary Data for "Evolutionary rate incongruences in squamates reveal contrasting patterns of evolutionary novelties and innovation"

  Open MIND · 2026-02-19

  dataset1st authorCorresponding

  Supplementary Data files S1-S3. See README for detailed data and code structure.

  DOI

• Total-evidence phylogeny reveals recent crown group radiation and biogeographical history of hamsters

  BMC Biology · 2026-04-09

  articleOpen access

  BACKGROUND: The systematics of extant hamsters (Cricetinae) have been increasingly clarified, due to advances in molecular phylogenetics. In contrast, their relationships with their fossil relatives have remained relatively unclear. Furthermore, studies on the biogeographical history and divergence times of the main groups of extant hamsters have so far been limited to molecular phylogenies and node dating approaches. RESULTS: Here, we present the first 'total-evidence' analysis of hamsters that combines extinct and extant taxa, based on a comprehensive dataset covering 82 species (~ 75% of the total known diversity of 109 species). We performed a relaxed-clock Bayesian phylogenetic reconstruction and used the resulting tip-dated tree to estimate ancestral geographic ranges. Our results confirm '†Kowalskia' as a synonym of †Neocricetodon, support the previously suggested non-monophyly of †Allocricetus, †Cricetulodon, and '†Cricetinus' and reveal several fossil taxa as potential close relatives of the crown group. We recover a Pliocene origin of the crown hamsters, considerably younger than previous estimates of a late/middle Miocene origin. Our biogeographic reconstructions suggest a Central and Eastern European origin of the entire group, with crown hamsters emerging in the region around the Black Sea and the Eastern Mediterranean. Subsequent dispersal events into Western Europe and East Central Asia may be linked to the expansion of open vegetation. CONCLUSIONS: Based on a total-evidence phylogenetic reconstruction, we highlight necessary taxonomical revisions for several fossil cricetine taxa and explore the biogeographical evolution of the group. Importantly, our estimated divergence dates reveal a substantially younger group of crown hamsters than previously assumed.

  PublisherDOI

• Osteology and ontogeny of the Permian dicynodont <i>Rastodon procurvidens</i> (Synapsida, Therapsida) based on micro-CT scanning and its phylogenetic and biogeographical implications

  Zoological Journal of the Linnean Society · 2025-08-01 · 1 citations

  article

  Abstract Dicynodonts were a globally distributed group of herbivorous synapsids that first appeared during the middle Permian (Guadalupian) and survived the Permian–Triassic Mass Extinction, until their extinction in the Late Triassic. Their fossil record in South America is almost entirely concentrated in the Triassic, with only two described Permian species. One of these, Rastodon procurvidens, was found in the Rio do Rasto Formation in Rio Grande do Sul, Brazil, and represents one of the best-preserved Permian therapsids from South America. The phylogenetic position of Rastodon within dicynodonts remains debated, with competing hypotheses leading to radically different conclusions regarding the early biogeography of dicynodonts. In this study, we present a detailed description of both the cranial and postcranial skeleton of the R. procurvidens holotype using microcomputed tomography. Phylogenetic analyses under both maximum parsimony and Bayesian criteria support the placement of Rastodon within the emydopoid clade Kingoriidae. These findings provide the first evidence of Emydopoidea and Kingoriidae in South America and underscore the limited knowledge of dicynodonts during the Guadalupian, particularly outside southern Africa. Furthermore, they suggest an earlier origin of Kingoriidae and the possibility that the group originated in west rather than east Gondwana.

  PublisherDOI

• Evolutionary Rate Incongruences in Squamates Reveal Contrasting Patterns of Evolutionary Novelties and Innovation

  Systematic Biology · 2025-09-27

  articleOpen access1st authorCorresponding

  Understanding the rate of phenotypic evolution can reveal fundamental aspects of organismal evolutionary trajectories. Hence, several studies have attempted to detect the tempo of evolution for multiple organisms, although based on different data types (e.g., discrete and morphometric) and methods (phylodynamic vs. comparative methods). Here, we ask whether these competing approaches provide comparable estimates of rate trajectories using an expanded squamate phylogenetic dataset that is matched (to the species-level) with new geometric morphometric data, while also assessing method robustness to fossil sampling. Our new squamate total-evidence time-tree suggests a new placement for several putative stem pleurodontan iguanians (Temujinidae) as stem acrodontans, whereas matching divergence time estimates of recent phylogenomic studies. We show that low fossil sampling inadvertently removes entire regions of the morphospace and leads to contraction of crown clade phenotypic diversity, as morphospace boundaries are frequently delimited by transitional fossils. Critically, different data types produce incongruent rate patterns, which are further exacerbated by methodological differences. We suggest that phylogenetic discrete data (i.e., characters) are strongly influenced by neomorphisms and reveal phenotypic novelties, whereas morphometric data (i.e., shape) reflect changes in phenotypic refinement leading to phenotypic innovation. This conceptual distinction conciliates discrepant macroevolution trajectories across squamates, which we expect to be generalizable to other systems across the Tree of Life.

  PublisherOA PDFDOI

• Supplementary Data for "Total-evidence phylogeny reveals recent crown group radiation and biogeographical history of hamsters"

  Harvard Dataverse · 2025-10-09 · 1 citations

  datasetOpen access

  Supplementary data including input and output files for all analyses

  PublisherDOI

• Origin and Early Evolution of Squamates and Their Kin: From Fossils to Genomes

  Annual Review of Ecology Evolution and Systematics · 2025-09-02 · 2 citations

  articleOpen access1st authorCorresponding

  Squamates (lizards, including snakes) are the most diverse group of terrestrial vertebrates on Earth today and have an evolutionary history dating back to at least the Middle Triassic (ca. 242 Mya). Despite their vast taxonomic, morphological, and ecological diversity, understanding their origin has remained a challenging and controversial topic for over a century. Initial studies focused on their patchy early fossil record using morphological data, yielding strongly contrasting hypotheses on squamate early evolutionary trajectories. The past decade has seen a massive overhaul of the subject, due to rapid advances in the areas studying phylogenomics, comparative genomics, phenotypic evolution, and new fossil discoveries. Here, we review advances across all of these fields and how they have been bridging hypotheses previously considered irreconcilable, providing a renewed and synthetic understanding of early squamate evolution. We conclude by discussing new datasets and methods behind these advances and perspectives on how the field will move forward for the next decade.

  PublisherDOI

• Author response: Cryptovaranoides is not a squamate

  2025-12-23

  peer-reviewOpen accessSenior author
  PublisherDOI

• † <i>Cryptovaranoides</i> is not a squamate

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-04-23

  preprintOpen accessSenior author

  Abstract Accurate reconstruction of the timescale of organismal evolution requires placement of extinct representatives among living branches. In this way, the fossil record has the capacity to revise hypotheses of organismal evolution by producing representatives of clades that far pre-date the age of the clade inferred using phylogenies built from molecular data and previous fossil calibrations. Recently, one fossil with the potential to drastically change current understanding surrounding the timescale of reptile diversification was described from Triassic fissure-fill deposits in the United Kingdom. This taxon, † Cryptovaranoides microlanius , was originally placed deep within the squamate crown clade, suggesting that many lineages of living lizards and snakes must have appeared by the Triassic and implying long ghost lineages that paleontologists and molecular phylogeneticists have failed to detect using all other available data. Our team challenged this identification and instead suggested † Cryptovaranoides had unclear affinities to living reptiles, but a crown-squamate interpretation was later re-iterated by the team that originally described this species. Here, we again challenge the morphological character codings used to support a crown squamate affinity for † Cryptovaranoides microlanius and illustrate several empirical problems with analyses that find this taxon is a crown squamate. Our analyses emphasize the importance of stringency in constructing hypodigms of fossils, particularly when they may be key for proper time calibration of the Tree of Life.

  PublisherOA PDFDOI

• Evolutionary rate incongruences in squamates reveal contrasting patterns of evolutionary novelties and innovation

  2025-05-06 · 1 citations

  preprintOpen access1st authorCorresponding

  Understanding the rate of phenotypic evolution can reveal fundamental aspects of organismal evolutionary trajectories. Hence, several studies have attempted to detect the tempo of evolution for multiple organisms, although based on radically different datatypes (e.g., discrete and morphometric) and methods (phylodynamic vs comparative methods). Here, we ask whether these competing approaches provide comparable rate trajectories using an expanded squamate phylogenetic dataset that is matched (to the species-level) with new geometric morphometric data, while also assessing method robustness to fossil sampling. Our new squamate total-evidence time-tree suggests a new placement for putative stem iguanians while matching divergence time estimates of recent phylogenomic studies. We show that low fossil sampling inadvertently removes entire regions of the morphospace and contraction of crown clade phenotypic diversity, as morphospace boundaries are frequently delimited by transitional fossils. Critically, different datatypes produce radically incongruent rate patterns, which are further exacerbated by methodological differences. We suggest that phylogenetic discrete data (i.e., characters) are strongly influenced by neomorphisms and reveal phenotypic novelties, while morphometric data (i.e., shape) reflects changes in phenotypic refinement leading to phenotypic innovation. This conceptual distinction conciliates discrepant macroevolution trajectories across squamates, which we expect to be generalizable to other systems across the Tree of Life.

  PublisherOA PDFDOI

• Cryptovaranoides is not a squamate

  eLife · 2025-12-04

  articleOpen accessSenior author

  Accurate reconstruction of the timescale of organismal evolution requires placement of extinct representatives among living branches. In this way, the fossil record has the capacity to revise hypotheses of organismal evolution by producing representatives of clades that far pre-date the age of the clade inferred using phylogenies built from molecular data and previous fossil calibrations. Recently, one fossil with the potential to drastically change current understanding surrounding the timescale of reptile diversification was described from Triassic fissure-fill deposits in the United Kingdom. This taxon, †Cryptovaranoides microlanius, was originally placed deep within the squamate crown clade, suggesting that many lineages of living lizards and snakes must have appeared by the Triassic and implying long ghost lineages that paleontologists and molecular phylogeneticists have failed to detect using all other available data. Our team challenged this identification and instead suggested †Cryptovaranoides had unclear affinities to living reptiles, but a crown-squamate interpretation was later re-iterated by the team that originally described this species. Here, we again challenge the morphological character codings used to support a crown squamate affinity for †Cryptovaranoides microlanius and illustrate several empirical problems with analyses that find this taxon is a crown squamate. Our analyses emphasize the importance of stringency in constructing hypodigms of fossils, particularly when they may be key for proper time calibration of the Tree of Life.

  PublisherDOI

Frequent coauthors

• Michael W. Caldwell

  University of Alberta

  58 shared

• Stephanie E. Pierce

  Harvard University

  32 shared

• Oksana Vernygora

  University of Alaska Anchorage

  20 shared

• Alessandro Palci

  University of Adelaide

  19 shared

• Randall L. Nydam

  Midwestern University

  18 shared

• Michael S. Y. Lee

  Flinders University

  11 shared

• Sebastián Apesteguı́a

  Consejo Nacional de Investigaciones Científicas y Técnicas

  11 shared

• Fernando F. Garberoglio

  Universidad Maimónides

  8 shared

Education

• PhD, Biological Sciences

  University of Alberta

  2018

• MSc, Geologia e Paleontologia

  Universidade Federal do Rio de Janeiro Museu Nacional

  2012

• Bachelor, Instituto de Biologia/ Departamento de Zoologia

  Universidade Federal do Rio de Janeiro

  2011