About

Thomas Kocher is a professor in the Department of Biology at the University of Maryland. His research focuses on understanding the evolutionary forces that have caused rapid speciation within Lake Malawi cichlid fishes, with more than 700 species arising within the last million years. He aims to identify the genes responsible for phenotypic traits associated with speciation, such as jaw morphology, color pattern, sex determination, and mate preferences, and to study the geographic distribution of allelic variants among wild populations. Kocher teaches courses including Principles of Genetics and Genetic Research on Cichlid Fishes. His educational background includes a B.A. from Yale University and a Ph.D. from the University of Colorado. His research contributions include elucidating sex chromosome systems in basal Haplotilapiine cichlids, identifying supergenes for sex and color in Lake Malawi cichlids, and investigating the structure and evolution of sex chromosomes across various fish species. His work advances understanding of the genetic mechanisms underlying speciation, sex determination, and biodiversity in fishes.

Research topics

• Statistics
• Ecology
• Paleontology
• Evolutionary biology
• Genetics
• Biology

Selected publications

• Target Trial Emulation in Observational Research—Strengths, Limitations, and Methodological Considerations

  Journal of Periodontal Research · 2026-03-06

  articleOpen access

  Cohort studies are vulnerable to confounding and time-related biases. Recent advances emphasize the importance of emulating a hypothetical target trial to minimize several of these biases. The target trial framework is a critical tool for designing cohort studies. It requires explicit specification of protocol components: eligibility criteria, treatment strategies, outcomes, timing of follow-up (time zero), and the causal contrast to be estimated. Critical to this framework is defining "time zero" when treatment assignment takes place and follow-up begins, which prevents prevalent user and immortal time bias and ensures proper temporal sequencing of confounders, exposure, and outcome. By guiding design, data collection, and analysis, the target trial framework helps align observational studies with the principles of randomized trials, improving the validity and interpretability of their findings. While it cannot eliminate unmeasured confounding, this approach promotes transparent, bias-conscious cohort design, minimizes time-related bias, and supports more robust causal inference with observational data.

  PublisherDOI

• Large inversions in Lake Malawi cichlids are associated with habitat preference, lineage, and sex determination

  eLife · 2025-01-31 · 1 citations

  preprintOpen access

  Abstract Chromosomal inversions are an important class of genetic variation that link multiple alleles together into a single inherited block that can have important e7ects on fitness. To study the role of large inversions in the massive evolutionary radiation of Lake Malawi cichlids, we used long-read technologies to identify four single and two tandem inversions that span half of each respective chromosome, and which together encompass over 10% of the genome. Each inversion is fixed in one of the two states within the seven major ecogroups, suggesting they played a role in the separation of the major lake lineages into specific lake habitats. One exception is within the benthic sub-radiation, where both inverted and non-inverted alleles continue to segregate within the group. The evolutionary histories of three of the six inversions suggest they transferred from the pelagic Diplotaxodon group into benthic ancestors at the time the benthic sub-radiation was seeded. The remaining three inversions are found in a subset of benthic species living in deep waters. We show that some of these inversions are used as XY sex-determination systems but are also likely limited to a subset of total lake species. Our work suggests that inversions have been under both sexual and natural selection in Lake Malawi cichlids and that they will be important to understanding how this adaptive radiation evolved.

  PublisherOA PDFDOI

• Before the East African Radiation: Sex Chromosome Systems in Basal Haplotilapiine Cichlids

  Genome Biology and Evolution · 2025-10-09 · 1 citations

  articleOpen accessSenior author

  Cichlid fishes have undergone an extraordinary diversification in East Africa. They also have a high rate of sex chromosome turnover. This clade provides an opportunity to study the rates and patterns of sex chromosome turnover, and the interactions of sex chromosome turnover with adaptation and speciation. Here we investigate the evolution sex chromosomes in the tribes Tilapiini, Coptodonini, Heterotilapiini, Gobiocichlini, Pelmatolapiini, and Oreochromini. We assembled chromosome-scale genomes of male and female Pelmatotilapia mariae. We then mapped pooled sequencing reads for males and females of P. mariae and 12 additional species on several genome assemblies to identify sex chromosomes. Tilapia sparrmanii and Oreochromis aureus share a ZW system on LG3 that overlaps the ZW system identified in P. mariae. Heterotilapia buettikoferi, Tilapia brevimanus, and Coptodon bakossiorum share an XY system mapping to another region of LG3. Coptodon zilli, Sarotherodon galilaeus, Sarotherodon melanotheron, and Oreochromis niloticus share an XY system on LG1. Finally, Oreochromis mossambicus and O. shiranus share an XY system on LG14 and we find evidence of an XY system on LG20 in Danakilia sp. "shukoray". The phylogenetic distribution of these sex determination systems suggests a long period of polymorphism for the systems on LG1 and LG3 and a generally lower rate of sex chromosome turnover in these lineages compared to the lacustrine lineages of the East African radiation. Our data is not consistent with the recent suggestion of figla and banf2 as candidate genes for the LG1XY and LG3ZW systems. We suggest a possible role for ubiquitination in the XY systems on LG3.

  PublisherOA PDFDOI

• Large inversions in Lake Malawi cichlids are associated with habitat preference, lineage, and sex determination

  eLife · 2025-05-21 · 1 citations

  preprintOpen access

  Abstract Chromosomal inversions are an important class of genetic variation that link multiple alleles together into a single inherited block that can have important e7ects on fitness. To study the role of large inversions in the massive evolutionary radiation of Lake Malawi cichlids, we used long-read technologies to identify four single and two tandem inversions that span half of each respective chromosome, and which together encompass over 10% of the genome. Each inversion is fixed in one of the two states within the seven major ecogroups, suggesting they played a role in the separation of the major lake lineages into specific lake habitats. One exception is within the benthic sub-radiation, where both inverted and non-inverted alleles continue to segregate within the group. The evolutionary histories of three of the six inversions suggest they transferred from the pelagic Diplotaxodon group into benthic ancestors at the time the benthic sub-radiation was seeded. The remaining three inversions are found in a subset of benthic species living in deep waters. We show that some of these inversions are used as XY sex-determination systems but are also likely limited to a subset of total lake species. Our work suggests that inversions have been under both sexual and natural selection in Lake Malawi cichlids and that they will be important to understanding how this adaptive radiation evolved.

  PublisherDOI

• Genome sequencing and identification of candidate variants for a red/black color polymorphism in tilapia (Oreochromis spp.)

  Aquaculture · 2025-03-12 · 1 citations

  articleOpen accessSenior authorCorresponding

  Red tilapia are favored by consumers, but the molecular genetic basis for this color pattern is unknown. Here we report on the genetic and physical mapping of the red locus in two strains of tilapia. We raised ~3000 hybrid individuals to map the red locus to a single bacterial artificial chromosome clone on linkage group 3. Long-read sequencing allowed us to assemble contigs spanning both the black and red haplotypes. The red haplotype contains additional repetitive sequence totaling almost one megabase that includes no obvious candidate genes. We suggest that the red phenotype may arise from substitutions in a protein in the primary cilia (Ccdc149), or changes in the expression of a nearby gene ( nckx2 ). Red mutations in several unlinked loci have now been identified, creating an opportunity to identify the best allelic combinations for aquacultural production. • Consumers prefer red-pigmented tilapia, but the genetic basis for this trait is unknown. • Genetic mapping narrowed the red locus to a small region of linkage group 3. • Long-read genome assembly identified an expansion of repetitive sequences totaling ~1 Mb in the red allele. • Variation in either ccdc149a or nckx2 might be responsible for the red phenotype. • Combinations of several unlinked loci may produce the best red tilapia for aquaculture.

  PublisherDOI

• Author response: Large inversions in Lake Malawi cichlids are associated with habitat preference, lineage, and sex determination

  2025-01-31

  peer-reviewOpen access

  Chromosomal inversions are an important class of genetic variation that link multiple alleles together into a single inherited block that can have important effects on fitness. To study the role of large inversions in the massive evolutionary radiation of Lake Malawi cichlids, we used long-read technologies to identify four single and two tandem inversions that span half of each respective chromosome, and which together encompass over 10% of the genome. Each inversion is fixed in one of the two states within the seven major ecogroups, suggesting they played a role in the separation of the major lake lineages into specific lake habitats. One exception is within the benthic sub-radiation, where both inverted and non-inverted alleles continue to segregate within the group. The evolutionary histories of three of the six inversions suggest they transferred from the pelagic Diplotaxodon group into benthic ancestors at the time the benthic sub-radiation was seeded. The remaining three inversions are found in a subset of benthic species living in deep waters. We show that some of these inversions are used as XY sex-determination systems but are also likely limited to a subset of total lake species. Our work suggests that inversions have been under both sexual and natural selection in Lake Malawi cichlids and that they will be important to understanding how this adaptive radiation evolved.

  PublisherDOI

• Large inversions in Lake Malawi cichlids are associated with habitat preference, lineage, and sex determination

  eLife · 2025-01-31 · 1 citations

  preprintOpen access

  Abstract Chromosomal inversions are an important class of genetic variation that link multiple alleles together into a single inherited block that can have important effects on fitness. To study the role of large inversions in the massive evolutionary radiation of Lake Malawi cichlids, we used long-read technologies to identify four single and two tandem inversions that span half of each respective chromosome, and which together encompass over 10% of the genome. Each inversion is fixed in one of the two states within the seven major ecogroups, suggesting they played a role in the separation of the major lake lineages into specific lake habitats. One exception is within the benthic sub-radiation, where both inverted and non-inverted alleles continue to segregate within the group. The evolutionary histories of three of the six inversions suggest they transferred from the pelagic Diplotaxodon group into benthic ancestors at the time the benthic sub-radiation was seeded. The remaining three inversions are found in a subset of benthic species living in deep waters. We show that some of these inversions are used as XY sex-determination systems but are also likely limited to a subset of total lake species. Our work suggests that inversions have been under both sexual and natural selection in Lake Malawi cichlids and that they will be important to understanding how this adaptive radiation evolved.

  PublisherDOI

• Author response: Large inversions in Lake Malawi cichlids are associated with habitat preference, lineage, and sex determination

  2025-05-21

  peer-reviewOpen access

  Chromosomal inversions are an important class of genetic variation that link multiple alleles together into a single inherited block that can have important e7ects on fitness. To study the role of large inversions in the massive evolutionary radiation of Lake Malawi cichlids, we used long-read technologies to identify four single and two tandem inversions that span half of each respective chromosome, and which together encompass over 10% of the genome. Each inversion is fixed in one of the two states within the seven major ecogroups, suggesting they played a role in the separation of the major lake lineages into specific lake habitats. One exception is within the benthic sub-radiation, where both inverted and non-inverted alleles continue to segregate within the group. The evolutionary histories of three of the six inversions suggest they transferred from the pelagic Diplotaxodon group into benthic ancestors at the time the benthic sub-radiation was seeded. The remaining three inversions are found in a subset of benthic species living in deep waters. We show that some of these inversions are used as XY sex-determination systems but are also likely limited to a subset of total lake species. Our work suggests that inversions have been under both sexual and natural selection in Lake Malawi cichlids and that they will be important to understanding how this adaptive radiation evolved.

  PublisherDOI

• A Chromosome Inversion Creates a Supergene for Sex and Colour in Lake Malawi Cichlids

  Molecular Ecology · 2025-06-10 · 2 citations

  articleOpen accessSenior authorCorresponding

  Cichlid fishes have the highest rates of evolutionary turnover of sex chromosomes among vertebrates. Many large structural polymorphisms in the radiation of cichlids in Lake Malawi are associated with sex chromosomes and may also carry adaptive variation. Here, we investigate the structure and evolutionary history of an inversion polymorphism that includes both a ZW sex locus and an orange-blotch colour polymorphism in the rock-dwelling cichlid fishes of Lake Malawi. We use long-read sequencing to characterise the sequence and breakpoints of the inversion. We quantify allele frequency differences across the inversion in population samples of the genera Metriaclima and Labeotropheus. We also examine expression differences of genes in the inversion. The simple inversion spans 7 Mb and is flanked by CACTA transposons that may have catalysed the rearrangement. The region includes ~600 genes, several of which show large differences in expression. Some of these genes are candidates for the sex and colour phenotypes. This inversion is an accessible model system for studying the role of structural polymorphisms and sex chromosome turnover in the adaptive radiation of cichlids in the lakes of East Africa.

  PublisherDOI

• Mutation of <i>mpv17</i> results in loss of iridophores due to mitochondrial dysfunction in tilapia

  Journal of Heredity · 2024-07-01 · 4 citations

  article

  Mpv17 (mitochondrial inner membrane protein MPV17) deficiency causes severe mitochondrial DNA depletion syndrome in mammals and loss of pigmentation of iridophores and a significant decrease of melanophores in zebrafish. The reasons for this are still unclear. In this study, we established an mpv17 homozygous mutant line in Nile tilapia. The developing mutants are transparent due to the loss of iridophores and aggregation of pigment granules in the melanophores and disappearance of the vertical pigment bars on the side of the fish. Transcriptome analysis using the skin of fish at 30 dpf (days post fertilization) revealed that the genes related to purine (especially pnp4a) and melanin synthesis were significantly downregulated. However, administration of guanine diets failed to rescue the phenotype of the mutants. In addition, no obvious apoptosis signals were observed in the iris of the mutants by TUNEL staining. Significant downregulation of genes related to iridophore differentiation was detected by qPCR. Insufficient ATP, as revealed by ATP assay, α-MSH treatment, and adcy5 mutational analysis, might account for the defects of melanophores in mpv17 mutants. Several tissues displayed less mtDNA and decreased ATP levels. Taken together, these results indicated that mutation of mpv17 led to mitochondrial dTMP deficiency, followed by impaired mtDNA content and mitochondrial function, which in turn, led to loss of iridophores and a transparent body color in tilapia.

  PublisherDOI

Recent grants

• NIH Grant R01HD058635

  NIH · $1.3M · 2012

• Genomic Architecture of an Adaptive Radiation

  NSF · $910k · 2012–2016

• Color, Sex and Speciation of Lake Malawi Cichlid Fishes

  NSF · $586k · 2005–2008

• Genetic Basis of Adaptive Morphological Radiation in Lake Malawi Cichlid Fishes

  NSF · $338k · 1999–2003

• Color, Sex and Speciation of Lake Malawi Cichlid Fishes

  NSF · $169k · 2007–2010

Frequent coauthors

• Matthew A. Conte

  Walter Reed Army Institute of Research

  49 shared

• Jay R. Stauffer

  Pennsylvania State University

  30 shared

• Jean‐François Baroiller

  Centre de Coopération Internationale en Recherche Agronomique pour le Développement

  29 shared

• Hélèna D'Cotta

  28 shared

• Kenneth R. McKaye

  United Nations University World Institute for Development Economics Research

  25 shared

• Deshou Wang

  Southwest University

  25 shared

• Karen L. Carleton

  23 shared

• William Gammerdinger

  Harvard University

  22 shared

Education

• NIH Postdoctoral Fellow, Biochemistry

  University of California Berkeley

  1989

• PhD, EPO Biology

  University of Colorado Boulder

  1986

• BA, Biology

  Yale University

  1981