@article{carrino-kyker_coyle_kluber_burke_2020, title={Fungal and Bacterial Communities Exhibit Consistent Responses to Reversal of Soil Acidification and Phosphorus Limitation over Time}, volume={8}, ISSN={["2076-2607"]}, DOI={10.3390/microorganisms8010001}, abstractNote={Chronic acid deposition affects many temperate hardwood forests of the northeastern United States, reduces soil pH and phosphorus (P) availability, and can alter the structure and function of soil microbial communities. The strategies that microorganisms possess for survival in acidic, low P soil come at a carbon (C) cost. Thus, how microbial communities respond to soil acidification in forests may be influenced by plant phenological stage as C allocation belowground varies; however, this remains largely unexplored. In this study, we examined microbial communities in an ecosystem level manipulative experiment where pH and/or P availability were elevated in three separate forests in Northeastern Ohio. Tag-encoded pyrosequencing was used to examine bacterial and fungal community structure at five time points across one year corresponding to plant phenological stages. We found significant effects of pH treatment and time on fungal and bacterial communities in soil. However, we found no interaction between pH treatment and time of sampling for fungal communities and only a weak interaction between pH elevation and time for bacterial communities, suggesting that microbial community responses to soil pH are largely independent of plant phenological stage. In addition, fungal communities were structured largely by site, suggesting that fungi were responding to differences between the forests, such as plant community differences.}, number={1}, journal={MICROORGANISMS}, author={Carrino-Kyker, Sarah R. and Coyle, Kaitlin P. and Kluber, Laurel A. and Burke, David J.}, year={2020}, month={Jan} }
 @article{faber-hammond_coyle_bacheller_roberts_mellies_roberts_renn_2019, title={The intestinal environment as an evolutionary adaptation to mouthbrooding in the Astatotilapia burtoni cichlid}, volume={95}, ISSN={["1574-6941"]}, DOI={10.1093/femsec/fiz016}, abstractNote={ABSTRACT Many of the various parental care strategies displayed by animals are accompanied by a significant reduction in food intake that imposes a substantial energy trade-off. Mouthbrooding, as seen in several species of fish in which the parent holds the developing eggs and fry in the buccal cavity, represents an extreme example of reduced food intake during parental investment and is accompanied by a range of physiological adaptations. In this study we use 16S sequencing to characterize the gut microbiota of female Astatotilapia burtoni cichlid fish throughout the obligatory phase of self-induced starvation during the brooding cycle in comparison to stage-matched females that have been denied food for the same duration. In addition to a reduction of gut epithelial turnover, we find a dramatic reduction in species diversity in brooding stages that recovers upon release of fry and refeeding that is not seen in females that are simply starved. Based on overall species diversity as well as differential abundance of specific bacterial taxa, we suggest that rather than reflecting a simple deprivation of caloric intake, the gut microbiota is more strongly influenced by physiological changes specific to mouthbrooding including the reduced epithelial turnover and possible production of antimicrobial agents.}, number={3}, journal={FEMS MICROBIOLOGY ECOLOGY}, author={Faber-Hammond, Josh J. and Coyle, Kaitlin P. and Bacheller, Shannon K. and Roberts, Cameron G. and Mellies, Jay L. and Roberts, Reade B. and Renn, Suzy C. P.}, year={2019}, month={Mar} }
 @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{thoemmes_stewart_hernandez-aguilar_bertone_baltzegar_borski_cohen_coyle_piel_dunn_2018, title={Ecology of sleeping: the microbial and arthropod associates of chimpanzee beds}, volume={5}, ISSN={["2054-5703"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85047125198&partnerID=MN8TOARS}, DOI={10.1098/rsos.180382}, abstractNote={The indoor environment created by the construction of homes and other buildings is often considered to be uniquely different from other environments. It is composed of organisms that are less diverse than those of the outdoors and strongly sourced by, or dependent upon, human bodies. Yet, no one has ever compared the composition of species found in contemporary human homes to that of other structures built by mammals, including those of non-human primates. Here we consider the microbes and arthropods found in chimpanzee beds, relative to the surrounding environment ( n = 41 and 15 beds, respectively). Based on the study of human homes, we hypothesized that the microbes found in chimpanzee beds would be less diverse than those on nearby branches and leaves and that their beds would be primarily composed of body-associated organisms. However, we found that differences between wet and dry seasons and elevation above sea level explained nearly all of the observed variation in microbial diversity and community structure. While we can identify the presence of a chimpanzee based on the assemblage of bacteria, the dominant signal is that of environmental microbes. We found just four ectoparasitic arthropod specimens, none of which appears to be specialized on chimpanzees or their structures. These results suggest that the life to which chimpanzees are exposed while in their beds is predominately the same as that of the surrounding environment.}, number={5}, journal={ROYAL SOCIETY OPEN SCIENCE}, author={Thoemmes, Megan S. and Stewart, Fiona A. and Hernandez-Aguilar, R. Adriana and Bertone, Matthew A. and Baltzegar, David A. and Borski, Russell J. and Cohen, Naomi and Coyle, Kaitlin P. and Piel, Alexander K. and Dunn, Robert R.}, year={2018}, month={May} }
 @article{carrino-kyker_kluber_coyle_burke_2017, title={Detection of phosphate transporter genes from arbuscular mycorrhizal fungi in mature tree roots under experimental soil pH manipulation}, volume={72}, number={2}, journal={Symbiosis}, author={Carrino-Kyker, S. R. and Kluber, L. A. and Coyle, K. P. and Burke, D. J.}, year={2017}, pages={123–133} }
 @article{burford reiskind_coyle_daniels_labadie_reiskind_roberts_roberts_schaff_vargo_2016, title={Development of a universal double-digest RAD sequencing approach for a group of nonmodel, ecologically and economically important insect and fish taxa}, volume={16}, ISSN={1755-098X}, url={http://dx.doi.org/10.1111/1755-0998.12527}, DOI={10.1111/1755-0998.12527}, abstractNote={The generation of genome-scale data is critical for a wide range of questions in basic biology using model organisms, but also in questions of applied biology in nonmodel organisms (agriculture, natural resources, conservation and public health biology). Using a genome-scale approach on a diverse group of nonmodel organisms and with the goal of lowering costs of the method, we modified a multiplexed, high-throughput genomic scan technique utilizing two restriction enzymes. We analysed several pairs of restriction enzymes and completed double-digestion RAD sequencing libraries for nine different species and five genera of insects and fish. We found one particular enzyme pair produced consistently higher number of sequence-able fragments across all nine species. Building libraries off this enzyme pair, we found a range of usable SNPs between 4000 and 37 000 SNPS per species and we found a greater number of usable SNPs using reference genomes than de novo pipelines in STACKS. We also found fewer reads in the Read 2 fragments from the paired-end Illumina Hiseq run. Overall, the results of this study provide empirical evidence of the utility of this method for producing consistent data for diverse nonmodel species and suggest specific considerations for sequencing analysis strategies.}, number={6}, journal={Molecular Ecology Resources}, publisher={Wiley}, author={Burford Reiskind, M. O. and Coyle, K. and Daniels, H. V. and Labadie, P. and Reiskind, M. H. and Roberts, N. B. and Roberts, R. B. and Schaff, J. and Vargo, E. L.}, year={2016}, month={May}, pages={1303–1314} }
 @article{roberts_juntti_coyle_dumont_stanley_ryan_fernald_roberts_2016, title={Polygenic sex determination in the cichlid fish Astatotilapia burtoni}, volume={17}, ISSN={["1471-2164"]}, DOI={10.1186/s12864-016-3177-1}, abstractNote={The East African riverine cichlid species Astatotilapia burtoni serves as an important laboratory model for sexually dimorphic physiology and behavior, and also serves as an outgroup species for the explosive adaptive radiations of cichlid species in Lake Malawi and Lake Victoria. An astounding diversity of genetic sex determination systems have been revealed within the adaptive radiation of East African cichlids thus far, including polygenic sex determination systems involving the epistatic interaction of multiple, independently segregating sex determination alleles. However, sex determination has remained unmapped in A. burtoni. Here we present mapping results supporting the presence of multiple, novel sex determination alleles, and thus the presence of polygenic sex determination in A. burtoni.Using mapping in small families in conjunction with restriction-site associated DNA sequencing strategies, we identify associations with sex at loci on linkage group 13 and linkage group 5-14. Inheritance patterns support an XY sex determination system on linkage group 5-14 (a chromosome fusion relative to other cichlids studied), and an XYW system on linkage group 13, and these associations are replicated in multiple families. Additionally, combining our genetic data with comparative genomic analysis identifies another fusion that is unassociated with sex, with linkage group 8-24 and linkage group 16-21 fused in A. burtoni relative to other East African cichlid species.We identify genetic signals supporting the presence of three previously unidentified sex determination alleles at two loci in the species A. burtoni, strongly supporting the presence of polygenic sex determination system in the species. These results provide a foundation for future mapping of multiple sex determination genes and their interactions. A better understanding of sex determination in A. burtoni provides important context for their use in behavioral studies, as well as studies of the evolution of genetic sex determination and sexual conflicts in East African cichlids.}, journal={BMC GENOMICS}, author={Roberts, Natalie B. and Juntti, Scott A. and Coyle, Kaitlin P. and Dumont, Bethany L. and Stanley, M. Kaitlyn and Ryan, Allyson Q. and Fernald, Russell D. and Roberts, Reade B.}, year={2016}, month={Oct} }
 @article{albertson_powder_hu_coyle_roberts_parsons_2014, title={Genetic basis of continuous variation in the levels and modular inheritance of pigmentation in cichlid fishes}, volume={23}, ISSN={["1365-294X"]}, DOI={10.1111/mec.12900}, abstractNote={Variation in pigmentation type and levels is a hallmark of myriad evolutionary radiations, and biologists have long been fascinated by the factors that promote and maintain variation in coloration across populations. Here, we provide insights into the genetic basis of complex and continuous patterns of colour variation in cichlid fishes, which offer a vast diversity of pigmentation patterns that have evolved in response to both natural and sexual selection. Specifically, we crossed two divergent cichlid species to generate an F2 mapping population that exhibited extensive variation in pigmentation levels and patterns. Our experimental design is robust in that it combines traditional quantitative trait locus (QTL) analysis with population genomics, which has allowed us to move efficiently from QTL interval to candidate gene. In total, we detected 41 QTL and 13 epistatic interactions that underlie melanocyte- and xanthophore-based coloration across the fins and flanks of these fishes. We also identified 2 QTL and 1 interaction for variation in the magnitude of integration among these colour traits. This finding in particular is notable as there are marked differences both within and between species with respect to the complexity of pigmentation patterns. While certain individuals are characterized by more uniform ‘integrated’ colour patterns, others exhibit many more degrees of freedom with respect to the distribution of colour ‘modules’ across the fins and flank. Our data reveal, for the first time, a genetic basis for this difference. Finally, we implicate pax3a as a mediator of continuous variation in the levels of xanthophore-based colour along the cichlid flank.}, number={21}, journal={MOLECULAR ECOLOGY}, author={Albertson, R. Craig and Powder, Kara E. and Hu, Yinan and Coyle, Kaitlin P. and Roberts, Reade B. and Parsons, Kevin J.}, year={2014}, month={Nov}, pages={5135–5150} }