Skip to main content

The Genomic Substrate for Adaptive Radiation: Copy Number Variation across 12 Tribes of African Cichlid Species (2019)
Journal Article
Faber-Hammond, J. J., Bezault, E., Lunt, D. H., Joyce, D. A., & Renn, S. C. P. (2019). The Genomic Substrate for Adaptive Radiation: Copy Number Variation across 12 Tribes of African Cichlid Species. Genome Biology and Evolution, 11(10), 2856-2874. https://doi.org/10.1093/gbe/evz185

The initial sequencing of five cichlid genomes revealed an accumulation of genetic variation, including extensive copy number variation in cichlid lineages particularly those that have undergone dramatic evolutionary radiation. Gene duplication has t... Read More about The Genomic Substrate for Adaptive Radiation: Copy Number Variation across 12 Tribes of African Cichlid Species.

The genomic basis of cichlid fish adaptation within the deepwater “twilight zone” of Lake Malawi (2017)
Journal Article
Hahn, C., Genner, M. J., Turner, G. F., & Joyce, D. A. (2017). The genomic basis of cichlid fish adaptation within the deepwater “twilight zone” of Lake Malawi. Evolution Letters, 1(4), 184-198. https://doi.org/10.1002/evl3.20

Deepwater environments are characterized by low levels of available light at narrow spectra, great hydrostatic pressure, and low levels of dissolved oxygen—conditions predicted to exert highly specific selection pressures. In Lake Malawi over 800 cic... Read More about The genomic basis of cichlid fish adaptation within the deepwater “twilight zone” of Lake Malawi.

Quantifying mating success of territorial males and sneakers in a bower-building cichlid fish (2017)
Journal Article
Magalhaes, I. S., Smith, A. M., & Joyce, D. A. (2017). Quantifying mating success of territorial males and sneakers in a bower-building cichlid fish. Scientific reports, 7(1), doi:10.1038/srep41128

The strategies and traits males evolve to mate with females are incredible in their diversity. Theory on the evolution of secondary sexual characters suggests that evolving any costly trait or strategy will pay off and stabilise in the population if... Read More about Quantifying mating success of territorial males and sneakers in a bower-building cichlid fish.

Interactive lectures: Clickers or personal devices? (2015)
Journal Article
Morrell, L. J., & Joyce, D. A. (2015). Interactive lectures: Clickers or personal devices?. F1000Research, 4, 64. https://doi.org/10.12688/f1000research.6207.1

Audience response systems (‘clickers’) are frequently used to promote participation in large lecture classes, and evidence suggests that they convey a number of benefits to students, including improved academic performance and student satisfaction. T... Read More about Interactive lectures: Clickers or personal devices?.

Secondary contact seeds phenotypic novelty in cichlid fishes (2015)
Journal Article
Nichols, P., Genner, M. J., van Oosterhout, C., Smith, A., Parsons, P., Sungani, H., …Joyce, D. A. (2015). Secondary contact seeds phenotypic novelty in cichlid fishes. Proceedings of the Royal Society B: Biological Sciences, 282(1798), https://doi.org/10.1098/rspb.2014.2272

Theory proposes that genomic admixture between formerly reproductively isolated populations can generate phenotypic novelty for selection to act upon. Secondary contact may therefore be a significant promoter of phenotypic novelty that allows species... Read More about Secondary contact seeds phenotypic novelty in cichlid fishes.

Gene duplication in an African cichlid adaptive radiation (2014)
Journal Article
Machado, H. E., Jui, G., Joyce, D. A., Reilly, C. R. L., Lunt, D. H., & Renn, S. C. (2014). Gene duplication in an African cichlid adaptive radiation. BMC Genomics, 15(1), 161. https://doi.org/10.1186/1471-2164-15-161

Background Gene duplication is a source of evolutionary innovation and can contribute to the divergence of lineages; however, the relative importance of this process remains to be determined. The explosive divergence of the African cichlid adaptive r... Read More about Gene duplication in an African cichlid adaptive radiation.

Altering an extended phenotype reduces intraspecific male aggression and can maintain diversity in cichlid fish (2013)
Journal Article
Joyce, D. A., Croft, G. E., & Magalhaes, I. S. (2013). Altering an extended phenotype reduces intraspecific male aggression and can maintain diversity in cichlid fish. PeerJ, 1(1), (e209). doi:10.7717/peerj.209. ISSN 2167-8359

Reduced male aggression towards different phenotypes generating negative frequency-dependent intrasexual selection has been suggested as a mechanism to facilitate the invasion and maintenance of novel phenotypes in a population. To date, the best emp... Read More about Altering an extended phenotype reduces intraspecific male aggression and can maintain diversity in cichlid fish.

Comparative analysis of teleost genome sequences reveals an ancient intron size expansion in the zebrafish lineage (2011)
Journal Article
Moss, S. P., Joyce, D. A., Humphries, S., Tindall, K. J., & Lunt, D. H. (2011). Comparative analysis of teleost genome sequences reveals an ancient intron size expansion in the zebrafish lineage. Genome Biology and Evolution, 3(1), 1187-1196. doi:10.1093/gbe/evr090

We have developed a bioinformatics pipeline for the comparative evolutionary analysis of Ensembl genomes and have used it to analyze the introns of the five available teleost fish genomes. We show our pipeline to be a powerful tool for revealing vari... Read More about Comparative analysis of teleost genome sequences reveals an ancient intron size expansion in the zebrafish lineage.

Repeated colonization and hybridization in Lake Malawi cichlids (2011)
Journal Article
Joyce, D., Lunt, D. H., Genner, M. J., Turner, G. F., Bills, R., & Seehausen, O. (2011). Repeated colonization and hybridization in Lake Malawi cichlids. Current biology : CB, 21(3), (R108-R109). doi:10.1016/j.cub.2010.11.029. ISSN 0960-9822

Through adaptive radiation, ancestral species rapidly diversify into multiple species with different ecological adaptations. The haplochromine cichlid fishes of the East African Great Lakes are considered classic examples of adaptive radiation, but o... Read More about Repeated colonization and hybridization in Lake Malawi cichlids.

Development of a real-world direct interface for integrated DNA extraction and amplification in a microfluidic device (2010)
Journal Article
Shaw, K. J., Joyce, D., Docker, P. T., Dyer, C. E., Greenway, G. M., Greenman, J., & Haswell, S. J. (2011). Development of a real-world direct interface for integrated DNA extraction and amplification in a microfluidic device. Lab on a chip, 11(3), 443-448. https://doi.org/10.1039/c0lc00346h

Integrated DNA extraction and amplification have been carried out in a microfluidic device using electro-osmotic pumping (EOP) for fluidic control. All the necessary reagents for performing both DNA extraction and polymerase chain reaction (PCR) ampl... Read More about Development of a real-world direct interface for integrated DNA extraction and amplification in a microfluidic device.

Sequential female assessment drives complex sexual selection on bower shape in a cichlid fish (2010)
Journal Article
Young, K. A., Genner, M. J., Haesler, M. P., & Joyce, D. A. (2010). Sequential female assessment drives complex sexual selection on bower shape in a cichlid fish. Evolution, 64(8), 2246-2253. doi:10.1111/j.1558-5646.2010.00984.x

In many animals, sexual selection on male traits results from female mate choice decisions made during a sequence of courtship behaviors. We use a bower-building cichlid fish, Nyassachromis cf. microcephalus, to show how applying standard selection a... Read More about Sequential female assessment drives complex sexual selection on bower shape in a cichlid fish.

Do taxonomic divisions reflect genetic differentiation? A comparison of morphological and genetic data in Coenonympha tullia (Müller), Satyrinae (2009)
Journal Article
Joyce, D. A., Dennis, R. L. H., Bryant, S. R., Shreeve, T. G., Pullin, A. S., & Ready, J. S. (2009). Do taxonomic divisions reflect genetic differentiation? A comparison of morphological and genetic data in Coenonympha tullia (Müller), Satyrinae. Biological journal of the Linnean Society, 97(2), 314-327. doi:10.1111/j.1095-8312.2009.01213.x

Historically, morphological variation has been used to classify many species (and subspecies) of Lepidop tera. However, some of this variation may be unsuitable for inferring the recent evolutionary history of populations. Genetic data provide an alt... Read More about Do taxonomic divisions reflect genetic differentiation? A comparison of morphological and genetic data in Coenonympha tullia (Müller), Satyrinae.

Solutions for PCR, cloning and sequencing errors in population genetic analysis (2009)
Journal Article
Cummings, S. M., McMullan, M., Joyce, D. A., & van Oosterhout, C. (2010). Solutions for PCR, cloning and sequencing errors in population genetic analysis. Conservation genetics, 11(3), (1095-1097). doi:10.1007/s10592-009-9864-6. ISSN 1566-0621

PCR and sequencing artefacts can seriously bias population genetic analyses, particularly of populations with low genetic variation such as endangered vertebrate populations. Here, we estimate the error rates, discuss their population genetics implic... Read More about Solutions for PCR, cloning and sequencing errors in population genetic analysis.

Simple practical approach for sample loading prior to DNA extraction using a silica monolith in a microfluidic device (2009)
Journal Article
Shaw, K. J., Docker, P. T., Haswell, S. J., Joyce, D. A., Dyer, C. E., Greenman, J., & Greenway, G. M. (2009). Simple practical approach for sample loading prior to DNA extraction using a silica monolith in a microfluidic device. Lab on a chip, 9(23), 3430-3432. https://doi.org/10.1039/b913309g

A novel DNA loading methodology is presented for performing DNA extraction on a microfluidic system. DNA in a chaotropic salt solution was manually loaded onto a silica monolith orthogonal to the subsequent flow of wash and elution solutions. DNA was... Read More about Simple practical approach for sample loading prior to DNA extraction using a silica monolith in a microfluidic device.

Disruptive sexual selection on male nuptial coloration in an experimental hybrid population of cichlid fish (2008)
Journal Article
Seehausen, O., van der Sluijs, I., Pierotti, M. E. R., Stelkens, R. B., Smith, A. M., & Joyce, D. A. (2008). Disruptive sexual selection on male nuptial coloration in an experimental hybrid population of cichlid fish. Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 363(1505), 2861-2870. doi:10.1098/rstb.2008.0049

Theory suggests that genetic polymorphisms in female mating preferences may cause disruptive selection on male traits, facilitating phenotypic differentiation despite gene flow, as in reinforcement or other models of speciation with gene flow. Very l... Read More about Disruptive sexual selection on male nuptial coloration in an experimental hybrid population of cichlid fish.

Indirect mate choice, direct mate choice and species recognition in a bower-building cichlid fish lek (2008)
Journal Article
Genner, M. J., Young, K. A., Haesler, M. P., & Joyce, D. A. (2008). Indirect mate choice, direct mate choice and species recognition in a bower-building cichlid fish lek. Journal of evolutionary biology, 21(5), 1387-1396. doi:10.1111/j.1420-9101.2008.01558.x

Sexual selection arising through female mate choice typically favours males with larger, brighter and louder signals. A critical challenge in sexual selection research is to determine the degree to which this pattern results from direct mate choice,... Read More about Indirect mate choice, direct mate choice and species recognition in a bower-building cichlid fish lek.

Age of cichlids: New dates for ancient lake fish radiations (2007)
Journal Article
Genner, M. J., Seehausen, O., Lunt, D. H., Joyce, D. A., Shaw, P. W., Carvalho, G. R., & Turner, G. F. (2007). Age of cichlids: New dates for ancient lake fish radiations. Molecular biology and evolution, 24(5), 1269-1282. doi:10.1093/molbev/msm050

Timing divergence events allow us to infer the conditions under which biodiversity has evolved and gain important insights into the mechanisms driving evolution. Cichlid fishes are a model system for studying speciation and adaptive radiation, yet, w... Read More about Age of cichlids: New dates for ancient lake fish radiations.

An extant cichlid fish radiation emerged in an extinct Pleistocene lake (2005)
Journal Article
Joyce, D. A., Lunt, D. H., Bills, R., Turner, G. F., Katongo, C., Duftner, N., …Seehausen, O. (2005). An extant cichlid fish radiation emerged in an extinct Pleistocene lake. Nature, 435(7038), 90-95. doi:10.1038/nature03489

The haplochromine cichlid fish of the East African Great Lakes represent some of the fastest and most species-rich adaptive radiations known(1), but rivers in most of Africa accommodate only a few morphologically similar species of haplochromine cich... Read More about An extant cichlid fish radiation emerged in an extinct Pleistocene lake.