@article{brandon_michael_carmona baez_moore_ciccotto_roberts_roberts_powder_2024, title={Distinct genetic origins of eumelanin levels and barring patterns in cichlid fishes}, volume={19}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0306614}, abstractNote={Pigment patterns are incredibly diverse across vertebrates and are shaped by multiple selective pressures from predator avoidance to mate choice. A common pattern across fishes, but for which we know little about the underlying mechanisms, is repeated melanic vertical bars. To understand the genetic factors that modify the level or pattern of vertical barring, we generated a genetic cross of 322 F 2 hybrids between two cichlid species with distinct barring patterns, Aulonocara koningsi and Metriaclima mbenjii . We identify 48 significant quantitative trait loci that underlie a series of seven phenotypes related to the relative pigmentation intensity, and four traits related to patterning of the vertical bars. We find that genomic regions that generate variation in the level of eumelanin produced are largely independent of those that control the spacing of vertical bars. Candidate genes within these intervals include novel genes and those newly-associated with vertical bars, which could affect melanophore survival, fate decisions, pigment biosynthesis, and pigment distribution. Together, this work provides insights into the regulation of pigment diversity, with direct implications for an animal’s fitness and the speciation process.}, number={7}, journal={PLOS ONE}, author={Brandon, A. Allyson and Michael, Cassia and Carmona Baez, Aldo and Moore, Emily C. and Ciccotto, Patrick J. and Roberts, Natalie B. and Roberts, Reade B. and Powder, Kara E.}, year={2024}, month={Jul} }
 @article{moore_ciccotto_peterson_lamm_albertson_roberts_2022, title={Polygenic sex determination produces modular sex polymorphism in an African cichlid fish}, volume={119}, ISSN={["1091-6490"]}, DOI={10.1073/pnas.2118574119}, abstractNote={Significance
          Sex differences in traits can occur when those traits are modified by genetic factors inherited on sex chromosomes. We investigated how sex differences emerge in a species with more than one set of sex chromosomes, measuring a variety of morphological, physiological, and behavioral traits. Rather than exhibiting sexual dimorphism associated with primary sex, the species has higher-order sexual polymorphism in secondary sexual characteristics or more than two phenotypic sexes. Variation in secondary sexual characteristics is modular, involving the interplay of sex-linked and sex-limited traits. Our findings provide implications for how sex determination systems and whole-organism fitness traits coevolve, including that significant creation or loss of variation in diverse traits can occur during transitions among sex chromosome systems.}, number={14}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Moore, Emily C. and Ciccotto, Patrick J. and Peterson, Erin N. and Lamm, Melissa S. and Albertson, R. Craig and Roberts, Reade B.}, year={2022}, month={Apr} }
 @article{conte_joshi_moore_nandamuri_gammerdinger_roberts_carleton_lien_kocher_2019, title={Chromosome-scale assemblies reveal the structural evolution of African cichlid genomes}, volume={8}, ISSN={["2047-217X"]}, DOI={10.1093/gigascience/giz030}, abstractNote={African cichlid fishes are well known for their rapid radiations and are a model system for studying evolutionary processes. Here we compare multiple, high-quality, chromosome-scale genome assemblies to elucidate the genetic mechanisms underlying cichlid diversification and study how genome structure evolves in rapidly radiating lineages. We re-anchored our recent assembly of the Nile tilapia (Oreochromis niloticus) genome using a new high-density genetic map. We also developed a new de novo genome assembly of the Lake Malawi cichlid, Metriaclima zebra, using high-coverage Pacific Biosciences sequencing, and anchored contigs to linkage groups (LGs) using 4 different genetic maps. These new anchored assemblies allow the first chromosome-scale comparisons of African cichlid genomes. Large intra-chromosomal structural differences (∼2–28 megabase pairs) among species are common, while inter-chromosomal differences are rare (<10 megabase pairs total). Placement of the centromeres within the chromosome-scale assemblies identifies large structural differences that explain many of the karyotype differences among species. Structural differences are also associated with unique patterns of recombination on sex chromosomes. Structural differences on LG9, LG11, and LG20 are associated with reduced recombination, indicative of inversions between the rock- and sand-dwelling clades of Lake Malawi cichlids. M. zebra has a larger number of recent transposable element insertions compared with O. niloticus, suggesting that several transposable element families have a higher rate of insertion in the haplochromine cichlid lineage. This study identifies novel structural variation among East African cichlid genomes and provides a new set of genomic resources to support research on the mechanisms driving cichlid adaptation and speciation.}, number={4}, journal={GIGASCIENCE}, author={Conte, Matthew A. and Joshi, Rajesh and Moore, Emily C. and Nandamuri, Sri Pratima and Gammerdinger, William J. and Roberts, Reade B. and Carleton, Karen L. and Lien, Sigbjorn and Kocher, Thomas D.}, year={2019}, month={Apr} }
 @article{johnson_moore_wong_godwin_streelman_roberts_2020, title={Exploratory behaviour is associated with microhabitat and evolutionary radiation in Lake Malawi cichlids}, volume={160}, ISSN={["1095-8282"]}, DOI={10.1016/j.anbehav.2019.11.006}, abstractNote={Encountering and adaptively responding to unfamiliar or novel stimuli is a fundamental challenge facing animals and is linked to fitness. Behavioural responses to novel stimuli can differ strongly between closely related species; however, the ecological and evolutionary factors underlying these differences are not well understood, in part because most comparative investigations have focused on only two species. In this study, we investigate behavioural responses to novel environments, or exploratory behaviours, sampling from a total of 20 species in a previously untested vertebrate system, Lake Malawi cichlid fishes, which comprises hundreds of phenotypically diverse species that have diverged in the past one million years. We show generally conserved behavioural response patterns to different types of environmental stimuli in Lake Malawi cichlids, spanning multiple assays and paralleling other teleost and rodent lineages. Next, we demonstrate that more specific dimensions of exploratory behaviour vary strongly among Lake Malawi cichlids, and that a large proportion of this variation is explained by species differences. We further show that species differences in open field behaviours are explained by microhabitat and by a major evolutionary split between the mbuna and benthic/utaka radiations in Lake Malawi. Lastly, we track some individuals across a subset of behavioural assays and show that patterns of behavioural covariation across contexts are characteristic of modular complex traits. Taken together, our results tie ecology and evolution to natural behavioural variation, and highlight Lake Malawi cichlids as a powerful system for understanding the biological basis of exploratory behaviours.}, journal={ANIMAL BEHAVIOUR}, author={Johnson, Zachary V and Moore, Emily C. and Wong, Ryan Y. and Godwin, John R. and Streelman, Jeffrey T. and Roberts, Reade B.}, year={2020}, month={Feb}, pages={121–134} }
 @article{stuckert_moore_coyle_davison_macmanes_roberts_summers_2019, title={Variation in pigmentation gene expression is associated with distinct aposematic color morphs in the poison frog Dendrobates auratus}, volume={19}, ISSN={["1471-2148"]}, DOI={10.1186/s12862-019-1410-7}, abstractNote={Color and pattern phenotypes have clear implications for survival and reproduction in many species. However, the mechanisms that produce this coloration are still poorly characterized, especially at the genomic level. Here we have taken a transcriptomics-based approach to elucidate the underlying genetic mechanisms affecting color and pattern in a highly polytypic poison frog. We sequenced RNA from the skin from four different color morphs during the final stage of metamorphosis and assembled a de novo transcriptome. We then investigated differential gene expression, with an emphasis on examining candidate color genes from other taxa. Overall, we found differential expression of a suite of genes that control melanogenesis, melanocyte differentiation, and melanocyte proliferation (e.g., tyrp1, lef1, leo1, and mitf) as well as several differentially expressed genes involved in purine synthesis and iridophore development (e.g., arfgap1, arfgap2, airc, and gart). Our results provide evidence that several gene networks known to affect color and pattern in vertebrates play a role in color and pattern variation in this species of poison frog.}, journal={BMC EVOLUTIONARY BIOLOGY}, author={Stuckert, Adam M. M. and Moore, Emily and Coyle, Kaitlin P. and Davison, Ian and MacManes, Matthew D. and Roberts, Reade and Summers, Kyle}, year={2019}, month={Apr} }
 @article{peterson_cline_moore_roberts_roberts_2017, title={Genetic sex determination in Astatotilapia calliptera, a prototype species for the Lake Malawi cichlid radiation}, volume={104}, ISSN={["1432-1904"]}, DOI={10.1007/s00114-017-1462-8}, abstractNote={East African cichlids display extensive variation in sex determination systems. The species Astatotilapia calliptera is one of the few cichlids that reside both in Lake Malawi and in surrounding waterways. A. calliptera is of interest in evolutionary studies as a putative immediate outgroup species for the Lake Malawi species flock and possibly as a prototype ancestor-like species for the radiation. Here, we use linkage mapping to test association of sex in A. calliptera with loci that have been previously associated with genetic sex determination in East African cichlid species. We identify a male heterogametic XY system segregating at linkage group (LG) 7 in an A. calliptera line that originated from Lake Malawi, at a locus previously shown to act as an XY sex determination system in multiple species of Lake Malawi cichlids. Significant association of genetic markers and sex produce a broad genetic interval of approximately 26 megabases (Mb) using the Nile tilapia genome to orient markers; however, we note that the marker with the strongest association with sex is near a gene that acts as a master sex determiner in other fish species. We demonstrate that alleles of the marker are perfectly associated with sex in Metriaclima mbenjii, a species from the rock-dwelling clade of Lake Malawi. While we do not rule out the possibility of other sex determination loci in A. calliptera, this study provides a foundation for fine mapping of the cichlid sex determination gene on LG7 and evolutionary context regarding the origin and persistence of the LG7 XY across diverse, rapidly evolving lineages.}, number={5-6}, journal={SCIENCE OF NATURE}, author={Peterson, Erin N. and Cline, Maggie E. and Moore, Emily C. and Roberts, Natalie B. and Roberts, Reade B.}, year={2017}, month={Jun} }
 @article{roberts_moore_kocher_2017, title={An allelic series at pax7a is associated with colour polymorphism diversity in Lake Malawi cichlid fish}, volume={26}, ISSN={["1365-294X"]}, DOI={10.1111/mec.13975}, abstractNote={AbstractDespite long‐standing interest in the evolution and maintenance of discrete phenotypic polymorphisms, the molecular genetic basis of such polymorphism in the wild is largely unknown. Female sex‐associated blotched colour polymorphisms found in cichlids of Lake Malawi, East Africa, represent a highly successful polymorphic phenotype, found and maintained in four genera across the geographic expanse of the lake. Previously, we identified an association with an allelic variant of the paired‐box transcription factor gene pax7a and blotched colour morphs in Lake Malawi cichlid fishes. Although a diverse range of blotched phenotypes are present in Lake Malawi cichlid species, they all appeared to result from an allele of pax7a that produces increased levels of transcript. Here, we examine the developmental and genetic basis of variation among blotched morphs. First, we confirm that pax7a‐associated blotch morphs result primarily from modulation of melanophore development and survival. From laboratory crosses and natural population studies, we identify at least three alleles of pax7a associated with discrete subtypes of blotched morphs, in addition to the ancestral pax7a allele. Genotypes at pax7a support initial evolution of a novel pax7a allele to produce the blotched class of morphs, followed by subsequent evolution of that pax7a blotched allele to produce additional alleles associated with discrete colour morphs. Variant alleles of pax7a produce different levels of pax7a transcript, correlating with pigmentation phenotype at the cellular level. This naturally selected allelic series should serve as a case study for understanding the molecular genetic control of pax7a expression and the evolution of sex‐associated alleles.}, number={10}, journal={MOLECULAR ECOLOGY}, author={Roberts, Reade B. and Moore, Emily C. and Kocher, Thomas D.}, year={2017}, month={May}, pages={2625–2639} }
 @article{moore_roberts_2016, title={Genital morphology and allometry differ by species and sex in Malawi cichlid fishes}, volume={791}, ISSN={0018-8158 1573-5117}, url={http://dx.doi.org/10.1007/s10750-016-2912-6}, DOI={10.1007/s10750-016-2912-6}, abstractNote={The African cichlid fishes show great diversity in mating displays and reproductive strategies, yet species differences in genital morphology have been little studied. Observational notes have described broad sex differences in external genital shape between males and females, but these differences have not been quantified. We examined three aspects of genital morphology (relative anogenital distance, relative vent length, and relative external genital area) in two riverine and eleven Lake Malawi African cichlid species from eight genera. We find the most sexually distinct morphology in the Lake Malawi rock cichlids and the least sexual dimorphism in the riverine outgroup; additionally, diversity in metrics within genus indicates that these traits are recently evolving. Sexual dimorphism in morphology is present in most species, and, in the Lake Malawi species, multivariate discriminant analysis allows for accurate assignment of gonadal sex based on genital morphology and body size. This will serve as a useful method for sexing fish in a nonlethal fashion and provides a starting point for further examination of the evolution of genital morphology in this diverse group of fishes.}, number={1}, journal={Hydrobiologia}, publisher={Springer Nature}, author={Moore, Emily C. and Roberts, Reade B.}, year={2016}, month={Jul}, pages={127–143} }
 @article{moore_roberts_2013, title={Polygenic sex determination}, volume={23}, ISSN={["0960-9822"]}, DOI={10.1016/j.cub.2013.04.004}, abstractNote={What is sex determination? Sex determination is the mechanism by which sexual organisms direct gonad development towards distinct but reproductively compatible outcomes. Molecular signaling cascades in the developing gonad provide instructions to the tissue to develop as male or female (or in some cases hermaphrodite), and these signals can be initiated in different ways. Sex can be determined by environmental cues (such as temperature), or genetically. Genetic sex determination occurs when an inherited difference in genes or chromosomes initiates the sex determination signal, acting as a ‘master switch’ for male or female development. Perhaps the most widely known genetic sex determination system is the male heterogametic XX/XY system found in most mammals, where the Sry gene on the Y chromosome determines male sex. Thus, XY individuals develop as males, and XX individuals develop as females. Many other organisms, including birds, have a ZZ/ZW chromosomal system, where heterogametic ZW individuals develop as female, and homogametic ZZ individuals develop as male (Figure 1). How is polygenic sex determination different? In the XY and ZW systems described above, a single genetic locus, often on a morphologically distinct chromosome, acts as the master switch for sex determination. In polygenic sex determination (PSD), multiple, independently segregating sex ‘switch’ loci or alleles determine sex within a species. Polygenic systems can arise through modifications of existing sex chromosomes that create a third functional sex chromosome at the same locus, or through modifications of autosomal loci elsewhere in the genome that create new inputs for regulation of gonad development. The term ‘polygenic sex determination’ appears to have been coined by Kosswig around 1964, shortly after PSD was described in platyfish (Xiphophorus spp.). In the case of platyfish, some populations have both a Y male determination allele and a W female determination allele segregating at the same chromosome pair. Despite the discovery and description of PSD nearly fifty years ago, the phenomenon remains relatively unknown, and only recently have we begun realizing the potential extent of PSD systems across taxa. What species have PSD? Polygenic sex determination is known to occur naturally in various species of insects, mammals, fish, and plants. Some housefly (Musca domestica) populations have male and female sex determination loci on autosomes in addition to a male sex determiner on a morphologically distinct Y chromosome. Among vertebrates, birds and mammals generally have evolutionarily conserved monogenic sex determination systems; however, African pygmy mice (Mus minutoides), some species of South American field mice (Akodon spp.) and two species of lemmings (Myopus schisticolor and Dicrostonyx torquatus) have independently evolved an additional, independently assorting female sex determination locus. Fish have been the most well studied vertebrate lineage with regard to variety of sex determination mechanisms, and it is within this group that PSD was initially discovered. Additional examples of PSD have recently been found in fish, including in African cichlid fish (Metriaclima spp.) and the developmental model zebrafish (Danio rerio). Outside of the animal kingdom, some gynodioecious plants (such as Thymus vulgaris and Plantago coronopus) appear to determine hermaphroditic versus female sex through interactions of multiple cytoplasmic and nuclear loci. Do all species with multiple sex chromosomes have PSD? Not necessarily. For example, the platypus (Orinthorhynchus anatinus) has five sex chromosome pairs — males have five X and five Y chromosomes. However, these chromosomes form chains and segregate together during meiosis, so that they effectively behave as a single X and a single Y chromosome when distributed to gametes, rather than five independently segregating pairs of chromosomes. Similar scenarios occur in sticklebacks and other fishes, where multiple sex chromosomes are present, but pair in such a way as to consistently segregate as if they were a single chromosome pair. Since there do not appear to be multiple genetic sex switch loci, and the sex chromosomes are not segregating independently, these cases do not meet the requirements of the PSD definition above. In PSD, which sex determination locus ‘wins’ to determine sex? The locus that wins and ultimately determines the fate of the gonad depends on the system being examined (Figure 1). In platyfish, pygmy mice, and lemmings, the ancestral state was an XY system. In these cases, one of the X chromosomes gained a female sex-determination allele that is dominant to the Y, directing ovary development in WY (also referred to as X∗Y) individuals. Some species of cichlid fish from Lake Malawi have an XY locus and a WZ locus on distinct chromosome pairs, and when these occur in the same individual, the W female determiner wins, and the individual develops as female. The end result of PSD is not always skewed towards females; in some housefly populations, a sex determination locus on an autosome causes XX flies to develop as male. In other cases, including zebrafish and cichlids, sex determination likely results from a combination of additive and epistatic effects at many loci. Thus, an allele that wins in one combination of sex determination loci genotypes may lose in another. Indeed, in some gynodioecious plants, the outcome of a genetic contest between ‘anti-male’ mitochondrial loci and nuclear ‘pro-male’ restorer loci ultimately determines female versus hermaphrodite development. Truly, there is striking diversity in the different ways PSD has independently evolved across these taxa. Why haven’t I heard of PSD before? Simply put, historical and technical bias. Genetic sex determination was first identified in insects, where it was found in the form simplest to detect and easiest to understand: a single, highly differentiated sex chromosome was found in one sex but not the other. This precedent was confirmed in mammals, birds, and important model systems like Drosophila melanogaster. Later, additional types of chromosome-level sex determination were identified, including XO systems (found in the nematode Caenorhabditis elegans) and haploid–diploid systems (found in Hymenopteran insects, including ants and bees). The ease of studying chromosomal sex, where sex chromosomes could be readily identified under a microscope, surely biased the study of sex determination against autosomal sex determination loci systems for the greater part of the last century. Since this historical bias had a large conceptual impact on the study of biology from evolutionary theory to developmental research, PSD systems may have remained largely undiscovered, or, when they were identified, dismissed as odd exceptions to the rule. Early studies of sex ratios in some species suggested PSD, but until relatively recently, the technology was not available to readily identify multiple, interacting sex determination loci in many species. With the advent of less expensive genome sequencing, and more sophisticated strategies for genetic mapping, we expect that instances of PSD will become easier to find, and the catalog of examples will grow. In fact, some species traditionally thought to have a monogenic sex determination system may demonstrably have PSD upon further study, including those species for which sex determination has not been examined or has only been examined in a small number of families or populations. For example, when mapping sex determination in some African cichlids, PSD could be missed by chance sampling of families whose parents carry only one sex determiner (e.g., a cross between a ZZ/XY male and a ZZ/XX female would allow mapping of the XY locus, but not the ZW locus). Ultimately, discovery of PSD systems requires truly representative mapping strategies as well as openness to the possibility that multiple sex determination loci may be segregating in a population. Why does PSD exist? One hypothesis to explain the evolution of PSD is that a novel sex determination locus will be maintained if it provides a benefit to individuals carrying it. For example, in both houseflies and South American field mice, individuals with the more recently evolved sex determination alleles have higher reproductive fitness. It is unclear whether the gene that acts as the overriding primary sex switch has pleiotropic effects modulating fitness, or if the novel sex determination locus is linked to another gene that provides enhanced fitness. Novel sex determination loci may also arise and be maintained if they resolve a sexual conflict involving an allele that provides an adaptive benefit to one sex to the detriment of the other. Such a scenario appears in African cichlid fish, where a pigmentation allele provides camouflage to females, but disrupts sexually selected male nuptial color and thus reduces male mating success. The pigmentation allele is tightly linked to a recently evolved female sex determination locus, ensuring that the color trait will only be expressed in females, the benefiting sex. Similar sexual conflicts could be evolutionarily intertwined with each sex determination locus in PSD systems. Is PSD evolutionarily stable? The answer is not entirely clear. One argument against stable PSD is that one sex determination allele would provide a reproductive fitness benefit over another, and selection would fix it as the sole sex determiner. Another concern is that PSD could produce highly skewed sex ratios, depending on the number of loci and how they interact. However, depending on how different sex switches are integrated during sexual development, and the frequencies of sex determination alleles in populations, these arguments may not be valid in all circumstances. In a simple sense, PSD systems may be inherently unstable if they can easily revert to single factor systems by loss of sex determination loci via drift or selection. In some species with PSD (such as houseflies and cichlids), sex determination occurs normally if only a single genetic factor is present, and different populations appear to have monogenic versus polygenic sex determination. Thus, it appears that only a single genetic switch is required for proper sexual reproduction in these species, even though multiple sex determination loci can be present. However, we suggest that the widespread presence of PSD across taxa suggests that it represents an evolutionarily stable strategy in some scenarios. The alternative would require that the examples cataloged thus far all represent temporary destabilization of a fundamental fitness trait in species, or evolutionary transitions between sex determination systems. One hypothesis for the stability of PSD is that it could readily produce multiple phenotypic or reproductive classes within a sex, or more than two sex types. If these class or type differences result in alternative fitness benefits, selection may maintain them in the population, contributing to PSD being an evolutionarily stable scenario. How many sexes are there? The traditional view of primary, gonadal sex is of a binary trait — each individual is either male or female. With multiple interacting loci determining primary sex, there are as many genetic sexes for a given group as there are possible combinations of sex determination loci. In known cases of PSD in animals, primary sex remains binary, but evidence suggests that genotypically different individuals of the same primary sex can have differential reproductive success, as mentioned above. Thus, even though primary sex may be binary in these cases, PSD may produce different classes within a single sex, or individuals of the same primary sex with strikingly different secondary sexual characteristics. In some plants, PSD systems may produce what could be considered more than two sexes. For example, in the domesticated cantaloupe, Cucumis melo, multiple loci interact to produce four sexes, with andromonoecious, monoecious, gynoecious, and hermaphrodite individuals in some cultivars (though it is not clear if such a system occurs naturally). In light of the variability in the genetic controls of sex determination and development, it may be beneficial to re-evaluate our view of sex as a binary trait. Why study PSD? Organisms with PSD provide us with models of multiple genetic switches that interact in different combinations to produce a fundamental fitness phenotype and resounding effects throughout an organism. These models can be used to study the evolution of gene networks and epistasis, and allow us to ask questions about the developmental regulation of genes that are traditionally thought of as members of core sex signaling networks. Species with PSD also provide snapshots of possible transitions from one mode of sex determination to another, providing insight into the evolution of sex determination. Identification of additional sex determination genes and interactions should also provide insight into sexual development and disease. Ultimately, studying intrasex differences in PSD models may provide insight into the continuum of sex differences in humans, and challenge long held notions of the evolution and development of sex and sexual dimorphism.}, number={12}, journal={CURRENT BIOLOGY}, author={Moore, Emily C. and Roberts, Reade B.}, year={2013}, month={Jun}, pages={R510–R512} }