My work combines the collection of genetic data with the development of new analytical methods. A recent example is a collaboration with SMD virologist Judy Breuer on the DNA sequences of chicken pox virus, which has led us to reevaluate the orthodoxy about its mode of spread, and has led to a two new projects on the way the virus spreads in the human body. I am also developing similar methods to study the movement of DNA sequences around the genome. We have detected spectacular movement of ribosomal DNA within a grasshopper genome, with populations separated by a few hundred metres having no ribosomal loci in common. These populations are part of the same species, but the offspring must be severely affected where the populations cross. Studying the processes leading to this unexpected and dramatic rearrangement of the genome may explain the origins of incompatibilities between isolated populations.
Publications
Simon Renny-Byfield, Ales Kova??k, Michael Chester, Richard A Nichols, Jiri Macas, Petr Nov?k, Andrew R Leitch (2012). Independent, Rapid and Targeted Loss of Highly Repetitive DNA in Natural and Synthetic Allopolyploids of Nicotiana tabacum. PloS one 7:e36963 Google Scholar
Simon Renny-Byfield, Michael Chester, Ales Kova??k, Steven C Le Comber, Marie-Ang?le Grandbastien, Marc Deloger, Richard A Nichols, Jiri Macas, Petr Nov?k, Mark W Chase, Andrew R Leitch (2011). Next generation sequencing reveals genome downsizing in allotetraploid Nicotiana tabacum, predominantly through the elimination of paternally derived repetitive DNAs. Molecular biology and evolution 28:2843-2854 Google Scholar | Reprint
RODERICK C DEWAR, WILLIAM B SHERWIN, EMMA THOMAS, CLARE E HOLLELEY, RICHARD A NICHOLS (2011). Predictions of single?nucleotide polymorphism differentiation between two populations in terms of mutual information. Molecular Ecology : Google Scholar | doi:10.1111/j.1365-294X.2011.05171.x
Louise J Johnson, James A Cotton, Conrad P Lichtenstein, Greg S Elgar, Richard A Nichols (2011). Stops making sense: translational trade-offs and stop codon reassignment. BMC evolutionary biology 11:227 Google Scholar
Dilrini De Silva, Richard Nichols, Greg Elgar (2011). Department of Bioengineering and Bioinformatics of MV Lomonosov Moscow State University 3:86 Google Scholar
Ruth M Brown, William C Jordan, Chris G Faulkes, Carl G Jones, Leandro Bugoni, Vikash Tatayah, Ricardo L Palma, Richard A Nichols (2011). Phylogenetic relationships in Pterodroma petrels are obscured by recent secondary contact and hybridization. PloS one 6:e20350 Google Scholar
RK Kanda, ML Quinlivan, AA Gershon, RA Nichols, J Breuer (2011). Population diversity in batches of the varicella Oka vaccine. Vaccine : Google Scholar | Reprint
Clare E Holleley, Richard A Nichols, Michael R Whitehead, Melissa R Gunn, Jyoutsna Gupta, William B Sherwin (2011). Induced dispersal in wildlife management: experimental evaluation of the risk of hybrid breakdown and the benefit of hybrid vigor in the F1 generation. Conservation Genetics 12:31-40 Google Scholar | Reprint
RUTH M BROWN, RICHARD A NICHOLS, CHRIS G FAULKES, CARL G JONES, LEANDRO BUGONI, VIKASH TATAYAH, DADA GOTTELLI, WILLIAM C JORDAN (2010). Range expansion and hybridization in Round Island petrels (Pterodroma spp.): evidence from microsatellite genotypes. Molecular ecology 19:3157-3170 Google Scholar | Reprint
AMBER GF TEACHER, TRENTON WJ GARNER, RICHARD A NICHOLS (2009). Population genetic patterns suggest a behavioural change in wild common frogs (Rana temporaria) following disease outbreaks (Ranavirus). Molecular Ecology 18:3163-3172 Google Scholar | Reprint
P Veltsos, I Keller, RA Nichols (2009). Geographically localised bursts of ribosomal DNA mobility in the grasshopper Podisma pedestris. Heredity 103:54-61 Google Scholar | Reprint
Amber GF Teacher, Trenton WJ Garner, Richard A Nichols (2009). Evidence for directional selection at a novel major histocompatibility class I marker in wild common frogs (Rana temporaria) exposed to a viral pathogen (Ranavirus). PLoS One 4:e4616 Google Scholar | Reprint
AGF Teacher, TWJ Garner, RA Nichols (2009). European phylogeography of the common frog (Rana temporaria): routes of postglacial colonization into the British Isles, and evidence for an Irish glacial refugium. Heredity 102:490-496 Google Scholar | Reprint
Paris Veltsos, Irene Keller, Richard A Nichols (2008). The inexorable spread of a newly arisen neo-Y chromosome. PLoS genetics 4:e1000082 Google Scholar | Reprint
Irene Keller, Paris Veltsos, Richard A Nichols (2008). The frequency of rDNA variants within individuals provides evidence of population history and gene flow across a grasshopper hybrid zone. Evolution 62:833-844 Google Scholar | Reprint | See more...
OS Paulo, J Pinheiro, A Miraldo, MW Bruford, WC Jordan, RA Nichols (2008). The role of vicariance vs. dispersal in shaping genetic patterns in ocellated lizard species in the western Mediterranean. Molecular Ecology 17:1535-1551 Google Scholar | Reprint | See more...
HELEN R WILCOCK, MICHAEL W BRUFORD, RICHARD A NICHOLS, ALAN G HILDREW (2007). Landscape, habitat characteristics and the genetic population structure of two caddisflies. Freshwater Biology 52:1907-1929 Google Scholar | Reprint | See more...
Judith Breuer, Mark Quinlivan, Mahmoud Al Bassam, Susannah Macdonald, Richard A Nichols, Sharon P Steinberg, Philip La Russa, Anne A Gershon (2007). DNA sequence variability in Oka vaccine isolates. Journal of Infectious Diseases 196:801 Google Scholar | Reprint | See more...
Mario JF Pulquerio, Richard A Nichols (2007). Dates from the molecular clock: how wrong can we be?. Trends in Ecology & Evolution 22:180-184 Google Scholar | Reprint | See more...
Irene Keller, Douda Bensasson, Richard A Nichols (2007). Transition-transversion bias is not universal: a counter example from grasshopper pseudogenes. PLoS genetics 3:e22 Google Scholar | Reprint | See more...
Mark L Quinlivan, Anne A Gershon, Mahmoud M Al Bassam, Sharon P Steinberg, Philip LaRussa, Richard A Nichols, Judith Breuer (2007). Natural selection for rash-forming genotypes of the varicella-zoster vaccine virus detected within immunized human hosts. Proceedings of the National Academy of Sciences 104:208 Google Scholar | Reprint | See more...
Irene Keller, Ioana C Chintauan-Marquier, Paris Veltsos, Richard A Nichols (2006). Ribosomal DNA in the grasshopper Podisma pedestris: escape from concerted evolution. Genetics 174:863 Google Scholar | Reprint | See more...
Ilik J Saccheri, Richard A Nichols, Paul M Brakefield (2006). Morphological differentiation following experimental bottlenecks in the butterfly Bicyclus anynana (Nymphalidae). Biological Journal of the Linnean Society 89:107-115 Google Scholar | Reprint | See more...
C Szmaragd, GR Foster, A Manica, A Bartholomeusz, RA Nichols, F Balloux (2006). Genome-wide characterisation of hepatitis B mutations involved in clinical outcome. Heredity 97:389-397 Google Scholar | Reprint | See more...
Mark A Quinlivan, Anne A Gershon, Richard A Nichols, Philip La Russa, Sharon P Steinberg, Judy Breuer (2006). Vaccine Oka varicella-zoster virus genotypes are monomorphic in single vesicles and polymorphic in respiratory tract secretions. Journal of Infectious Diseases 193:927 Google Scholar | Reprint | See more...
Camille Szmaragd, Richard A Nichols, Fran?ois Balloux (2006). A novel approach to characterise pathogen candidate genetic polymorphisms involved in clinical outcome. Infection, Genetics and Evolution 6:38-45 Google Scholar | Reprint | See more...
Helen R Wilcock, Michael W Bruford, Alan G Hildrew, Richard A Nichols (2005). Recruitment, kin and the spatial genetic structure of a caddisfly Plectrocnemia conspersa in a southern English stream. Freshwater Biology 50:1499-1514 Google Scholar | Reprint | See more...
RA Nichols (2005). Quantitative genetics focus issue. Heredity 94:273-274 Google Scholar | See more...
Jim J Groombridge, Carl G Jones, Richard A Nichols, Mark Carlton, Michael W Bruford (2004). Molecular phylogeny and morphological change in the Psittacula parakeets. Molecular phylogenetics and evolution 31:96-108 Google Scholar | Reprint | See more...
RA Nichols, KLM Freeman (2004). Using molecular markers with high mutation rates to obtain estimates of relative population size and to distinguish the effects of gene flow and mutation: a demonstration using data from endemic Mauritian skinks. Molecular Ecology 13:775-787 Google Scholar | Reprint | See more...
L Murad, JP Bielawski, R Matyasek, A Kovarik, RA Nichols, AR Leitch, CP Lichtenstein (2004). The origin and evolution of geminivirus-related DNA sequences in Nicotiana. Heredity 92:352-358 Google Scholar | Reprint | See more...
ADJ Overall, M Ahmad, MG Thomas, RA Nichols (2003). An analysis of consanguinity and social structure within the UK Asian population using microsatellite data. Annals of human genetics 67:525-537 Google Scholar | Reprint | See more...
Helen R Wilcock, Richard A Nichols, Alan G Hildrew (2003). Genetic population structure and neighbourhood population size estimates of the caddisfly Plectrocnemia conspersa. Freshwater Biology 48:1813-1824 Google Scholar | Reprint | See more...
Stewart J Hinchliffe, Karen E Isherwood, Richard A Stabler, Michael B Prentice, Alexander Rakin, Richard A Nichols, Petra CF Oyston, Jason Hinds, Richard W Titball, Brendan W Wren (2003). Application of DNA microarrays to study the evolutionary genomics of Yersinia pestis and Yersinia pseudotuberculosis. Genome research 13:2018-2029 Google Scholar | Reprint | See more...
Jim J Groombridge, Carl G Jones, Michelle K Bayes, Anthony J van Zyl, Jos? Carrillo, Richard A Nichols, Michael W Bruford (2002). A molecular phylogeny of African kestrels with reference to divergence across the Indian Ocean. Molecular phylogenetics and evolution 25:267-277 Google Scholar | Reprint | See more...
Loun?s Chikhi, Richard A Nichols, Guido Barbujani, Mark A Beaumont (2002). Y genetic data support the Neolithic demic diffusion model. Proceedings of the National Academy of Sciences 99:11008 Google Scholar | Reprint | See more...
ADJ Overall, M Ahmad, RA Nichols (2002). The effect of reproductive compensation on recessive disorders within consanguineous human populations. Heredity 88:474-479 Google Scholar | Reprint | See more...
Oct?vio S Paulo, William C Jordan, Michael W Bruford, Richard A Nichols (2002). Using nested clade analysis to assess the history of colonization and the persistence of populations of an Iberian lizard. Molecular Ecology 11:809-819 Google Scholar | Reprint | See more...
Oscar E Gaggiotti, Felicity Jones, William M Lee, William Amos, John Harwood, Richard A Nichols (2002). Patterns of colonization in a metapopulation of grey seals. Nature 416:424-427 Google Scholar | Reprint | See more...
Winsome Barrett Muir, Richard Nichols, Judith Breuer (2002). Phylogenetic analysis of varicella-zoster virus: evidence of intercontinental spread of genotypes and recombination. Journal of virology 76:1971-1979 Google Scholar | Reprint | See more...
OCT?VIO S PAULO, ISABEL PINTO, MICHAEL W BRUFORD, WILLIAM C JORDAN, RICHARD A NICHOLS (2002). The double origin of Iberian peninsular chameleons. Biological Journal of the Linnean Society 75:1-7 Google Scholar | Reprint | See more...
HR Wilcock, AG Hildrew, RA Nichols, MW Bruford (2001). Microsatellites for the net?spinning caddisfly Plectrocnemia conspersa (Polycentropodidae). Molecular Ecology Notes 1:318-319 Google Scholar | Reprint | See more...
ADJ Overall, RA Nichols (2001). A method for distinguishing consanguinity and population substructure using multilocus genotype data. Molecular biology and evolution 18:2048-2056 Google Scholar | Reprint | See more...
OS Paulo, C Dias, MW Bruford, WC Jordan, RA Nichols (2001). The persistence of Pliocene populations through the Pleistocene climatic cycles: evidence from the phylogeography of an Iberian lizard. Proceedings of the Royal Society of London. Series B: Biological Sciences 268:1625 Google Scholar | Reprint | See more...
Helen R Wilcock, Alan G Hildrew, Richard A Nichols (2001). Genetic differentiation of a European caddisfly: past and present gene flow among fragmented larval habitats. Molecular Ecology 10:1821-1834 Google Scholar | Reprint | See more...
Richard Nichols (2001). Gene trees and species trees are not the same. Trends in Ecology & Evolution 16:358-364 Google Scholar | Reprint | See more...
Jim J Groombridge, Michael W Bruford, Carl G Jones, Richard A Nichols (2001). Evaluating the severity of the population bottleneck in the Mauritius kestrel Falco punctatus from ringing records using MCMC estimation. Journal of animal ecology 70:401-409 Google Scholar | Reprint | See more...
TM Burland, EM Barratt, RA Nichols, PA Racey (2001). Mating patterns, relatedness and the basis of natal philopatry in the brown long?eared bat, Plecotus auritus. Molecular Ecology 10:1309-1321 Google Scholar | Reprint | See more...
Ilik J Saccheri, Richard A Nichols, Paul M Brakefield (2001). Effects of bottlenecks on quantitative genetic variation in the butterfly Bicyclus anynana. Genetical research 77:167-181 Google Scholar | Reprint | See more...
Richard A Nichols, Michael W Bruford, Jim J Groombridge (2001). Sustaining genetic variation in a small population: evidence from the Mauritius kestrel. Molecular Ecology 10:593-602 Google Scholar | Reprint | See more...
Jim J Groombridge, Carl G Jones, Michael W Bruford, Richard A Nichols (2000). Ghost\" alleles of the Mauritius kestrel. Nature 403:616 Google Scholar | Reprint | See more...
J Flint, J Bond, DC Rees, AJ Boyce, JM Roberts-Thomson, L Excoffier, JB Clegg, MA Beaumont, RA Nichols, RM Harding (1999). Minisatellite mutational processes reduce F ST estimates. Human genetics 105:567-576 Google Scholar | Reprint | See more...
Richard A Nichols (1999). Interpreting DNA Evidence: Statistical Genetics for Forensic Scientists. Heredity 82:585-586 Google Scholar | See more...
Ilik J Saccheri, Ian J Wilson, Richard A Nichols, Michael W Bruford, Paul M Brakefield (1999). Inbreeding of bottlenecked butterfly populations: estimation using the likelihood of changes in marker allele frequencies. Genetics 151:1053-1063 Google Scholar | Reprint | See more...
Katharine Byrne, Richard A Nichols (1999). Culex pipiens in London underground tunnels: differentiation between surface and subterranean populations. Heredity 82:7-15 Google Scholar | Reprint | See more...
RJ Brown, CA Malcolm, PL Mason, RA Nichols (1997). Genetic differentiation between and within strains of the saw?toothed grain beetle, Oryzaephilus surinamensis (Coleoptera: Silvanidae) at RAPD loci. Insect molecular biology 6:285-289 Google Scholar | Reprint | doi:10.1046/j.1365-2583.1997.00184.x | See more...
Mark A Beaumont, Richard A Nichols (1996). Evaluating loci for use in the genetic analysis of population structure. Proceedings of the Royal Society of London. Series B: Biological Sciences 263:1619-1626 Google Scholar | Reprint | See more...
Ilik J Saccheri, Paul M Brakefield, Richard A Nichols (1996). Severe inbreeding depression and rapid fitness rebound in the butterfly Bicyclus anynana (Satyridae). Evolution :2000-2013 Google Scholar | Reprint | See more...
David J Balding, Matthew Greenhalgh, Richard A Nichols (1996). Population genetics of STR loci in Caucasians. International journal of legal medicine 108:300-305 Google Scholar | See more...
David J Balding, Richard A Nichols (1995). A method for quantifying differentiation between populations at multi-allelic loci and its implications for investigating identity and paternity. Genetica 96:3-12 Google Scholar | See more...
PL Mason, RA Nichols, GM Hewitt (1995). Philopatry in the alpine grasshopper, Podisma pedestris: a novel experimental and analytical method. Ecological entomology 20:137-145 Google Scholar | See more...
David J Balding, Peter Donnelly, Richard A Nichols (1994). [DNA Fingerprinting: A Review of the Controversy]: Comment: Some Causes for Concern about DNA Profiles. Statistical Science 9:248-251 Google Scholar | Reprint | See more...
David J Balding, Richard A Nichols (1994). DNA profile match probability calculation: how to allow for population stratification, relatedness, database selection and single bands. Forensic Science International 64:125-140 Google Scholar | See more...
David J Balding, Richard A Nichols, David M Hunt (1992). Detecting gene conversion: primate visual pigment genes. Proceedings of the Royal Society of London. Series B: Biological Sciences 249:275 Google Scholar | Reprint | See more...
Richard A Nichols (1989). The fragmentation of tension zones in sparsely populated areas. The American Naturalist 134:969-977 Google Scholar | Reprint | See more...
Richard A Nichols (1989). Trends in Ecology & Evolution 4:192-193 Google Scholar | See more...
Richard A Nichols, Roger K Butlin (1989). Does runaway sexual selection work in finite populations?. Journal of Evolutionary Biology 2:299-313 Google Scholar | Reprint | See more...
Godfrey M Hewitt, Richard A Nichols, Michael G Ritchie (1988). 1868 and all that for Magicicada. 336:206-207 Google Scholar | See more...
Richard A Nichols (1988). Trends in Ecology & Evolution 3:94-95 Google Scholar | See more...
RICHARD A NICHOLS, GODFREY M HEWITT (1988). Genetical and ecological differentiation across a hybrid zone. Ecological Entomology 13:39-49 Google Scholar | Reprint | See more...
RA Nichols, GM Hewitt (1986). Population structure and the shape of a chromosomal cline between two races of Podisma pedestris (Orthoptera: Acrididae). Biological Journal of the Linnean Society 29:301-316 Google Scholar | Reprint | See more...