About

Professor Thomas Near leads the Near Lab at Yale University and the Peabody Museum, focusing on the integrative natural history, phylogeny, and organismal biology of fishes. His research aims to discover the mechanisms that generate biodiversity by using phylogenies, or evolutionary trees, inferred from DNA sequence data. This approach allows him to investigate speciation, historical biogeography, and the timing of lineage diversification. A significant aspect of his work involves the discovery of biodiversity through the description of new species. The lab primarily studies ray-finned fishes (Actinopterygii), which comprise nearly half of all living vertebrates. By reconstructing phylogenetic relationships using genomic information from these vertebrates, Professor Near's research explores patterns and mechanisms of diversification, reconstructs historical biogeography, and estimates evolutionary timescales. His work spans systematics, speciation mechanisms, and phylogenetics, contributing to a deeper understanding of the origins and evolution of Earth's rich biota.

Research topics

• Biology
• Computer Science
• Business
• Paleontology
• Fishery
• Evolutionary biology
• Computational biology
• Genetics
• Anatomy
• Earth science
• Geochemistry
• Data science
• Geology
• Ecology
• Database

Selected publications

• Phylogenomics and the origins of sharks

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-02-15 · 1 citations

  articleOpen accessSenior author

  Abstract Genomes have the capacity to drastically modify hypotheses about the relationships of species. Despite the growing availability of non-model organism genome sequences, historically contentious portions of Tree of Life remain untested using genomic data. Here, we infer the phylogeny of sharks, skates, rays, and chimaeras using the genomes of 48 species, targeting different genomic marker types. Although phylogenetic relationships of chondrichthyans are relatively consistent across analyses, different molecular markers yield conflicting results about shark monophyly. Exons support the traditional view that sharks are monophyletic, whereas ultraconserved elements and legacy nuclear markers instead suggest that the frilled and cow sharks ( Hexanchiformes ), which retain the ancestral jaw structure of cartilaginous fishes, is the sister lineage of all other sharks and rays. The resolution of sharks as monophyletic or paraphyletic has little effect on inferences of the timescale of shark evolution or the origins of key traits, such as their ancestral ecology and genome size. We tie the diversification of living cartilaginous fishes to the transformation of marine ecosystems during the middle Mesozoic Era, confirming that living shark diversity is the product of rapid ancient diversification. Consequently, our results suggest that despite uncertainty around whether sharks are monophyletic, consensus can still be reached about major evolutionary events in this iconic vertebrate lineage. Significance Statement Living sharks, skates, rays, and chimaeras form one of the three principal groups of vertebrates. These iconic animals, which include over 1200 species, are key components of marine ecosystems and have helped us reconstruct the evolution of vertebrate genomes and phenotypes. However, much work on this group has assumed that sharks are a natural group. Here, for the first time, we leverage genome-scale data to test this hypothesis. Surprisingly, we show different genome regions reject or support hypothesis that sharks form a natural group to the exclusion of skates and rays. This throws an unexpected wrench into our understanding of the relationships of some of the oldest living vertebrate clades.

  PublisherDOI

• Phylogenomics of Characidae, a hyper-diverse Neotropical freshwater fish lineage, with a phylogenetic classification including four families (Teleostei: Characiformes)

  The Catalogue of Life · 2026-02-16

  datasetOpen access
  PublisherDOI

• Four New Species of Darters Related to Percina evides (Percidae: Etheostomatinae)

  Bulletin of the Peabody Museum of Natural History · 2026-04-24

  articleSenior author
  PublisherDOI

• The subunit composition of the mammalian Mediator complex is not conserved in all vertebrates: Insights from evolutionary plasticity of fish genomes

  Protein Science · 2026-04-11

  articleOpen access

  The Mediator complex is an indispensable, multi-subunit protein transcriptional coactivator with a central role in gene expression in Eukaryotes. Among vertebrates, its molecular structure and subunit composition are well-known only for mammals. Genes encoding fish Mediator subunits remain unknown even for zebrafish that is otherwise the best explored fish species. Here, we first reconstructed genes encoding Mediator subunits from 12 brain transcriptomes of a percid fish, pikeperch (Sander lucioperca). These data revealed two additional fish-specific paralogous genes (med13b and med31l) and a missing paralog (med12l) in comparison to genes of mammalian Mediator subunits. The Med13 subunit is encoded by two paralogs in basal (coelacanth) as well as derived sarcopterygians (mammals), while three paralogs are present in numerous but not all fish lineages. All three med13 paralogs were highly transcribed in the juvenile pikeperch brain. Our molecular-phylogenetic analysis of the three fish med13 paralogs revealed the evolutionary origin of the additional med13b paralog from the teleost-specific genome duplication. The additional paralog med31l encoding the Med31 subunit shows a more limited occurrence among fishes with potentially different ways and times of its origin-tandem duplication on the same chromosome, translocation in the opposite strand of another chromosome or a consequence of whole-genome duplication. The mammalian Mediator complex is not universal to all vertebrates and paralogs encoding subunits of the Mediator complex are not conserved across all vertebrates. Further research is needed to explore fish-specific genes encoding subunits of the Mediator complex and their tissue-specific transcription.

  PublisherDOI

• Phylogeny Reconciles Classification in Antarctic Plunderfishes

  The Catalogue of Life · 2026-02-16

  datasetOpen accessSenior author
  PublisherDOI

• Recognition of Sterletus Rafinesque 1820 as a nomen oblitum and Huso Brandt & Ratzeburg 1833 as a nomen protectum: A response to Kottelat and Freyhof (2025)

  Zootaxa · 2026-02-16

  articleSenior author
  PublisherDOI

• Stable genome structures in living fossil fishes

  Genome Research · 2026-01-13

  preprint

  Genomic evolution can propel and restrict species diversification. Rapid molecular evolution and genomic rearrangement is often associated with increased species diversification, but whether genome structural evolution shows a slow tempo in long-lived, species-poor lineages remains unclear. Here, we present two chromosome-level genomes of gars, a lineage of seven living species of freshwater fishes that are nearly identical in anatomy to extinct species from tens of millions of years ago. Using the new genomes, we show that gars have the slowest rates of genomic structural and sequence evolution of all vertebrates. In species of the two living gar genera Atractosteus and Lepisosteus , 83.35% of the genomes remain identical even though they diverged over 100 million years ago. Genome size variation among gars is almost entirely attributable to single base pair insertions and deletions. Yet, we also detect inflated GC repeat numbers on Chromosomes 14 and 23 of Atractosteus spatula that are absent in Lepisosteus and show that gar microchromosomes and macrochromosomes display different rates of structural evolution. Our analyses suggest that the genomic stability of gars, which may explain the ability of deeply divergent gar species to hybridize and has contributed to their higher structural similarity to tetrapod genomes than those of the far more closely related teleost fishes, may result from very low rates of transposable element origination and high inactivity compared to other vertebrates. Beyond providing a reference point for comparative vertebrate genomic studies, the new gar genomes illuminate a structural component of slow genomic evolution in living fossils and molecular mechanisms that may underlie exceptional genome stability.

  PublisherDOI

• Aquifer-mediated speciation in cave-adapted fishes

  Integrative Organismal Biology · 2026-05-12

  articleOpen accessSenior author

  Abstract The nature of speciation within subterranean ecosystems following invasions from the surface remains poorly understood. Most proposed examples of in situ subterranean speciation instead appear to reflect multiple independent surface invasions, supporting the classic hypothesis that subterranean ecosystems are evolutionary dead ends. Here, we examine the species diversity within the most widespread subterranean vertebrate species, the Southern Cavefish Typhlichthys subterraneus. Phylogenomic analyses reveal that T. subterraneus as currently recognized is paraphyletic with respect to the Missouri Cavefish T. eigenmanni, as a distinct set of populations is resolved as the sister lineage of a clade formed by T. eigenmanni and T. subterraneus sensu stricto. High-resolution computed tomography (CT) scanning reveals skeletal autapomorphies of this lineage, supporting its recognition as a new species: Typhlichthys styx sp. nov. Ancestral biogeographic reconstructions reveal that speciation in Typhlichthys occurred along aquifer boundaries, with lineages dispersing through widespread karstic aquifer systems across southeastern and central North America. This dispersal facilitated secondary sympatry among cavefish species that last shared common ancestry approximately eight million years ago. Together, these results reveal aquifer geology as a driver of allopatric speciation in obligate cave-dwelling vertebrates, with implications for understanding biodiversity in subterranean ecosystems worldwide.

  PublisherDOI

• Systematics of the Stripetail Darter, Etheostoma kennicotti (Putnam), and the Distinctiveness of the Upper Cumberland Endemic Etheostoma cumberlandicum Jordan and Swain

  The Catalogue of Life · 2026-02-16

  datasetOpen access1st authorCorresponding
  PublisherDOI

• Undescribed and imperiled vertebrate biodiversity near an American urban center

  Biology Letters · 2025-04-01 · 2 citations

  articleOpen accessSenior author

  Urban expansion threatens biodiversity hotspots and endemic species. In this study, we describe two imperiled new species of fishes belonging to the vermilion darter ( Etheostoma chermocki ) complex. These new species are restricted to individual stream systems surrounding the city of Birmingham, Alabama, USA, and are at risk of extinction due to anthropogenic development. Genomic species delimitation reveals that members of this species complex, which differ subtly but consistently in meristic counts and coloration, show high levels of genomic divergence and little gene flow among them. These brilliantly coloured species, whose diversification tied to the erosional dynamics of the Black Warrior River basin, exemplify the imperiled, yet undescribed, species diversity within an urban landscape in the southeastern North American biodiversity hotspot.

  PublisherDOI

Recent grants

• Genomic Approaches to Resolving Phylogenies of Antarctic Notothenioid Fishes

  NSF · $491k · 2009–2013

• Collaborative Research: Causes and Consequences of Exceptional Diversity in Spiny-Rayed Fishes

  NSF · $304k · 2011–2015

• DISSERTATION RESEARCH: Linking population genetic patterns of introgressive hybridization to the breakdown of reproductive barriers in Darters (Percidae)

  NSF · $13k · 2010–2013

• Phylogenomic Study of Adaptive Radiation in Antarctic Fishes

  NSF · $397k · 2014–2017

• DISSERTATION RESEARCH: The evolutionary history of beryciforms and the contribution of signal and noise to phylogenetic inference in multi-locus datasets

  NSF · $15k · 2011–2014

Frequent coauthors

• Brant C. Faircloth

  Louisiana State University

  797 shared

• Brian C. O’Meara

  757 shared

• Luke J. Harmon

  University of Idaho

  756 shared

• H. Bradley Shaffer

  California Department of Conservation

  755 shared

• John Trueman

  Australian National University

  754 shared

• Felipe Zapata

  754 shared

• Jonathan C. Banks

  Cawthron Institute

  754 shared

• Shannon Straub

  754 shared

Education

• Ph.D., Ecology, Ethology, and Evolution

  University of Illinois Urbana-Champaign

  2000

• M.S., Biological Sciences

  Northern Illinois University

  1995

• B.A., History

  Northern Illinois University

  1993

• B.S., Biological Science

  Northern Illinois University

  1993