About

Karen Carleton is a Professor in the Department of Biology at the University of Maryland. Her research focuses on the evolution of visual systems and visual communication, including the genetics of visual system tuning and physical modeling of color signals and visual discrimination. She uses African cichlid fishes as a model to explore how natural and sexual selection drive communication. Her work also involves studying the evolution of rod and cone phototransduction by tuning photoreceptor responsivity through the evolution of protein structure and gene expression, employing a comparative genomic approach across a diversity of vertebrates including mammals, reptiles, amphibians, fish, and agnathans.

Research topics

• Biology
• Evolutionary biology
• Genetics
• Zoology
• Materials science

Selected publications

• Rapid Divergence of Visual Systems and Signaling Traits to Contrasting Light Regimes During Early Speciation of African Crater Lake Cichlid Fish

  Molecular Biology and Evolution · 2025-08-19 · 2 citations

  articleOpen access

  Sensory adaptation is widely hypothesized to drive ecological speciation, yet empirical evidence from natural populations undergoing early stage divergence remains limited. In Lake Masoko, a young crater lake in East Africa, the haplochromine cichlid Astatotilapia calliptera is undergoing early stage sympatric speciation into shallow-water littoral and deep-water benthic ecotypes that experience contrasting light environments. Here, we integrate retinal transcriptomics, phenotypic analyses, and visual modeling to uncover rapid sensory divergence associated with this ecological transition. We find striking shifts in cone opsin expression, with the benthic ecotype exhibiting a switch from short-wavelength sensitive SWS2B to SWS2A and an overall narrowing of cone sensitivity toward the center of the light spectrum, consistent with changes in deep-water light environment. In contrast, coding sequence variation in opsin genes was limited and no significant differences in allele frequencies were detected across nine polymorphic sites, pointing to expression regulation as the primary axis of early divergence in visual systems. In parallel, we observed divergence in male signaling traits, with benthic males displaying deeper red egg-spots, aligning with predictions from visual modeling of signal efficiency in different light environments. These results demonstrate rapid transcriptomic and phenotypic divergence in associated signaling traits-within ∼1,000 years-supporting a potential role for regulatory evolution in sensory adaptation during early ecological speciation.

  PublisherOA PDFDOI

• Whole genome sequencing identifies genetic candidates for high-frequency hearing loss in canaries (<i>serinus canaria</i>)

  The Journal of the Acoustical Society of America · 2025-04-01

  article

  Over hundreds of years, breeders have selectively bred different strains of canaries for plumage and song characteristics. One strain, the Belgian Waterslager canary, has been bred for loud, low frequency song and coincidently has been found to have a high-frequency hearing loss due to damaged and missing hair cells in the basilar papilla. Here, we investigated the possible genetic basis for this hearing loss in the Belgian Waterslager canary by conducting whole-genome Illumina (San Diego, CA) sequencing in three canary strains. We identified a total of 16 Belgian Waterslager male-specific "high-impact" single nucleotide polymorphisms (SNP) variants with three mutations occurring within genes previously identified in mammalian hair cell abnormalities and hearing loss disorders: pericentriolar material 1 (PCM1), p21 (RAC1) activated kinase 3 (PAK3)-like, and protein tyrosine phosphatase receptor type K (PTPRK). Interestingly, we also identified three male-specific "high-impact" SNP variants in one of our control strains: the American Singer canary. One of these mutations occurs within genes previously associated with hearing loss in mammals. Since songbirds rely on hearing to develop a normal vocal repertoire, investigating the role of these genes in hearing loss at the molecular level may provide a valuable animal model for examining the relationship between hearing loss and vocal development in humans.

  PublisherDOI

• Group Active Engagements for Facilitating Principles-Based Learning in Introductory Organismal Biology

  The American Biology Teacher · 2023-08-01 · 1 citations

  article

  Organismal biology (OrgBio) comprises the diversity, structures, and functions of all organisms from bacteria to humans. Arguably, OrgBio is often the most poorly taught and least conceptually rigorous section of the introductory biology sequence offered at most U.S. institutions of higher education. This article reports on the successful implementation of conceptual and pedagogical reforms in an introductory OrgBio course offered at a large public university. Conceptual reforms were based on a theoretical framework consisting of universal physical and chemical laws, deep molecular homologies, and diverse structure–function relationships. Pedagogical reforms involved the development of group active engagements (GAEs) that were designed to encourage students to develop their abilities to engage in principles-based reasoning. A new model for characterizing different approaches toward principles-based reasoning in biology was developed to analyze these GAEs. Two surveys indicated that OrgBio students developed more favorable perceptions about the effectiveness of GAE-based course offerings, as compared to similar lecture-based versions.

  PublisherDOI

• Long‐wavelength‐sensitive (<i>lws</i>) opsin gene expression, foraging and visual communication in coral reef fishes

  Molecular Ecology · 2022-12-23 · 11 citations

  articleOpen access

  Coral reef fishes are diverse in ecology and behaviour and show remarkable colour variability. Investigating the visual pigment gene (opsin) expression in these fishes makes it possible to associate their visual genotype and phenotype (spectral sensitivities) to visual tasks, such as feeding strategy or conspecific detection. By studying all major damselfish clades (Pomacentridae) and representatives from five other coral reef fish families, we show that the long-wavelength-sensitive (lws) opsin is highly expressed in algivorous and less or not expressed in zooplanktivorous species. Lws is also upregulated in species with orange/red colours (reflectance >520 nm) and expression is highest in orange/red-coloured algivores. Visual models from the perspective of a typical damselfish indicate that sensitivity to longer wavelengths does enhance the ability to detect the red to far-red component of algae and orange/red-coloured conspecifics, possibly enabling social signalling. Character state reconstructions indicate that in the early evolutionary history of damselfishes, there was no lws expression and no orange/red coloration. Omnivory was most often the dominant state. Although herbivory was sometimes dominant, zooplanktivory was never dominant. Sensitivity to long wavelength (increased lws expression) only emerged in association with algivory but never with zooplanktivory. Higher lws expression is also exploited by social signalling in orange/red, which emerged after the transition to algivory. Although the relative timing of traits may deviate by different reconstructions and alternative explanations are possible, our results are consistent with sensory bias whereby social signals evolve as a correlated response to natural selection on sensory system properties in other contexts.

  PublisherOA PDFDOI

• Environmental plasticity in opsin expression due to light and thyroid hormone in adult and developing Astatotilapia burtoni

  Hydrobiologia · 2022-08-10 · 9 citations

  articleSenior author
  PublisherDOI

• Testing Wickler’s hypothesis: cichlids are unable to distinguish eggs from egg spots in the wild

  Hydrobiologia · 2022-12-20 · 1 citations

  articleSenior author
  PublisherDOI

• A second locus contributing to the differential expression of the blue sensitive opsin SWS2A in Lake Malawi cichlids

  Hydrobiologia · 2022-10-18 · 5 citations

  articleSenior author
  PublisherDOI

• A novel exome probe set captures phototransduction genes across birds (Aves) enabling efficient analysis of vision evolution

  Molecular Ecology Resources · 2021-10-15 · 6 citations

  article

  The diversity of avian visual phenotypes provides a framework for studying mechanisms of trait diversification generally, and the evolution of vertebrate vision, specifically. Previous research has focused on opsins, but to fully understand visual adaptation, we must study the complete phototransduction cascade (PTC). Here, we developed a probe set that captures exonic regions of 46 genes representing the PTC and other light responses. For a subset of species, we directly compared gene capture between our probe set and low-coverage whole genome sequencing (WGS), and we discuss considerations for choosing between these methods. Finally, we developed a unique strategy to avoid chimeric assembly by using "decoy" reference sequences. We successfully captured an average of 64% of our targeted exome in 46 species across 14 orders using the probe set and had similar recovery using the WGS data. Compared to WGS or transcriptomes, our probe set: (1) reduces sequencing requirements by efficiently capturing vision genes, (2) employs a simpler bioinformatic pipeline by limiting required assembly and negating annotation, and (3) eliminates the need for fresh tissues, enabling researchers to leverage existing museum collections. We then utilized our vision exome data to identify positively selected genes in two evolutionary scenarios-evolution of night vision in nocturnal birds and evolution of high-speed vision specific to manakins (Pipridae). We found parallel positive selection of SLC24A1 in both scenarios, implicating the alteration of rod response kinetics, which could improve color discrimination in dim light conditions and/or facilitate higher temporal resolution.

  PublisherDOI

• Chromosome‐level assembly of southern catfish (<i>silurus meridionalis</i>) provides insights into visual adaptation to nocturnal and benthic lifestyles

  Molecular Ecology Resources · 2021-01-27 · 32 citations

  article

  The Southern catfish (Silurus meridionalis) is a nocturnal and benthic freshwater fish endemic to the Yangtze River and its tributaries. In this study, we constructed a chromosome-level draft genome of S. meridionalis using 69.7-Gb Nanopore long reads and 49.5-Gb Illumina short reads. The genome assembly was 741.2 Mb in size with a contig N50 of 13.19 Mb. An additional 116.4 Gb of Bionano and 77.4 Gb of Hi-C data were applied to assemble contigs into scaffolds and further into 29 chromosomes, resulting in a 738.9-Mb genome with a scaffold N50 of 28.04 Mb. A total of 22,965 protein-coding genes were predicted from the genome with 22,519 (98.06%) genes functionally annotated. Comparative genomic and transcriptomic analyses revealed a rod-dominated visual system which was responsible for scotopic vision. The absence of cone opsins SWS1 and SWS2 resulted in the lack of ultraviolet and blue violet sensitivity. Mutations at key amino acid sites of RH1.1, RH1.2 and RH2 resulted in spectral tuning good for dim light vision and narrow colour vision. A higher expression level of rod phototransduction genes than that of cone genes and higher rod-to-cone ratio led to higher optical sensitivity under dim light conditions. In addition, analysis of the genes involved in eye morphogenesis and development revealed the loss of some conserved noncoding elements, which might be associated with the small eyes in catfish. Together, our study provides important clues for the adaptation of the catfish visual system to the nocturnal and benthic lifestyles. The draft genome of S. meridionalis represents a valuable resource for studies of the molecular mechanisms of ecological adaptation.

  PublisherDOI

• Movement of transposable elements contributes to cichlid diversity

  bioRxiv (Cold Spring Harbor Laboratory) · 2020-02-26 · 4 citations

  preprintOpen access1st authorCorresponding

  Abstract African cichlid fishes are a prime model for studying the mechanisms of speciation. Despite the development of extensive genomic resources, it has been difficult to determine which sources of genetic variation are responsible for variation in cichlid phenotypes. Cichlids have some of the largest known shifts in vertebrate visual sensitivity. These shifts arise mainly from the differential expression of seven cone opsin genes. By mapping expression quantitative trait loci (eQTL) in intergeneric crosses of Lake Malawi (LM) cichlids, we have thus far identified four causative genetic variants that correspond to indels in the promoters of either key transcription factors or of the opsin gene itself. Here we show that these indels are caused by the movement of transposable elements (TEs). These precise indels are not found outside of LM, suggesting that these TEs are recently active and are segregating within the Malawi cichlid lineage. A similar indel has arisen independently outside of LM at one locus, suggesting that some locations are primed for TE insertion and the resulting indels. Increased TE mobility may be associated with interspecific hybridization, which disrupt mechanisms of TE suppression. Overall, our study suggests that TEs may contribute to key regulatory changes, and may facilitate rapid phenotypic change and possibly speciation in African cichlids.

  PublisherOA PDFDOI

Recent grants

• What Do Lake Malawi Cichlid Fishes See?

  NSF · $33k · 2006–2008

• What Do Lake Malawi Cichlid Fishes See?

  NSF · $287k · 2002–2006

• Evolutionary mechanisms controlling opsin gene expression variation

  NIH · $1.9M · 2014–2022

• NIH Grant R15EY016721

  NIH · $218k · 2007

• CAREER: Proximate and Ultimate Causes of Sensory System Evolution

  NSF · $800k · 2009–2014

Frequent coauthors

• Stephen R. Leone

  Lawrence Berkeley National Laboratory

  36 shared

• Bernard Bourguignon

  Université Paris-Saclay

  27 shared

• Sara M. Stieb

  Swiss Federal Institute of Aquatic Science and Technology

  25 shared

• N. Justin Marshall

  University of Queensland

  25 shared

• Thomas D. Kocher

  University of Maryland, College Park

  23 shared

• Matthew A. Conte

  Walter Reed Army Institute of Research

  19 shared

• Fabio Cortesi

  19 shared

• Sri Pratima Nandamuri

  University of Maryland, College Park

  19 shared