Publications: PROF Richard Nichols
(
2025
)
.
European ash pangenome reveals widespread structural variation and a diverse genetic basis for low ash dieback susceptibility
.
(
2025
)
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Can genomic analysis actually estimate past population size?
.
Trends in Genetics
vol.
41
,
(
7
)
559
-
567
.
(
2025
)
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Rapid polygenic adaptation in a wild population of ash trees under a novel fungal epidemic
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Science
vol.
388
,
(
6754
)
1422
-
1425
.
(
2025
)
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Quantitative measurement of phenotype dynamics during cancer drug resistance evolution using genetic barcoding
.
Nature Communications
vol.
16
,
(
1
)
Article
5282
,
(
2025
)
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Quantitative measurement of phenotype dynamics during cancer drug resistance evolution using genetic barcoding
.
(
2025
)
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Recurrent evolution of cryptic triploids in cultivated enset increases yield
.
(
2024
)
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Combined phylogenetic and geographic data can predict plant-pest interactions with high accuracy
.
(
2024
)
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Nitrogen and phosphorus interactions at a 21 nitrogen:1 phosphorus Redfield‐like ratio impact growth and seed yield in wheat (<i>Triticum aestivum</i> L.)
.
Food and Energy Security
vol.
13
,
(
4
)
Article
e564
,
(
2024
)
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Identification of Novel Endogenous Retroviruses in Anura
.
(
2023
)
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Maintenance and expansion of genetic and trait variation following domestication in a clonal crop
.
Molecular Ecology
vol.
32
,
(
15
)
4165
-
4180
.
(
2023
)
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Assembly‐free quantification of vagrant <scp>DNA</scp> inserts
.
Molecular Ecology Resources
vol.
23
,
(
5
)
1002
-
1013
.
(
2023
)
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Assembly-free quantification of vagrant DNA inserts
.
(
2022
)
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Non-Lethal Detection of Frog Virus 3-Like (RUK13) and Common Midwife Toad Virus-Like (PDE18) Ranaviruses in Two UK-Native Amphibian Species
.
Viruses
vol.
14
,
(
12
)
2635
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2635
.
(
2022
)
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Cyto-nuclear incompatibilities across a bluebell hybrid zone in northern Spain do not prevent genome-wide introgression of neutral markers
.
Evolutionary Journal of the Linnean Society
vol.
1
,
(
1
)
Article
kzac003
,
(
2022
)
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Rapid polygenic adaptation in a wild population of ash trees under a novel fungal epidemic
.
(
2022
)
.
Whi3 mnemon association with endoplasmic reticulum membranes confines the memory of deceptive courtship to the yeast mother cell
.
Current Biology
vol.
32
,
(
5
)
963
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974.e7
.
(
2021
)
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Evidence for the Widespread Occurrence of Bacteria Implicated in Acute Oak Decline from Incidental Genetic Sampling
.
Forests
vol.
12
,
(
12
)
1683
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1683
.
(
2021
)
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Evidence for the Widespread Occurrence of Bacteria Implicated in Acute Oak Decline from Incidental Genetic Sampling
.
(
2021
)
.
Spatially clustered count data provide more efficient search strategies in invasion biology and disease control
.
Ecological Applications
vol.
31
,
(
5
)
Article
e02329
,
(
2020
)
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Correction: Genomic architecture and evolutionary antagonism drive allelic expression bias in the social supergene of red fire ants
.
eLife
vol.
9
,
Article
e64678
,
(
2020
)
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Genomic architecture and evolutionary antagonism drive allelic expression bias in the social supergene of red fire ants
.
eLife
vol.
9
,
Article
e55862
,
(
2020
)
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A mechanism to prevent transformation of the Whi3 mnemon into a prion
.
(
2020
)
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Genomic architecture and evolutionary conflict drive allele-specific expression in the social supergene of the red fire ant
.
(
2019
)
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Genomic assessment of local adaptation in dwarf birch to inform assisted gene flow
.
Evolutionary Applications
vol.
13
,
(
1
)
161
-
175
.
(
2019
)
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Genomic basis of European ash tree resistance to ash dieback fungus
.
Nature Ecology & Evolution
vol.
3
,
(
12
)
1686
-
1696
.
(
2019
)
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Mitochondrial sequences or Numts – By-catch differs between sequencing methods
.
(
2019
)
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Genomic assessment of local adaptation in dwarf birch to inform assisted gene flow
.
(
2019
)
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Modelling Ranavirus Transmission in Populations of Common Frogs (Rana temporaria) in the United Kingdom
.
Viruses
vol.
11
,
(
6
)
556
-
556
.
(
2019
)
.
Genome-wide haplotype analysis improves trait predictions in Brassica napus hybrids
.
Plant Science
vol.
283
,
157
-
164
.
(
2019
)
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Effects of historic and projected climate change on the range and impacts of an emerging wildlife disease
.
Global Change Biology
vol.
25
,
(
8
)
2648
-
2660
.
(
2019
)
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Genomic basis of European ash tree resistance to ash dieback fungus
.
(
2019
)
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Interactions between plant genome size, nutrients and herbivory by rabbits, molluscs and insects on a temperate grassland
.
Proceedings of the Royal Society B: Biological Sciences
vol.
286
,
(
1899
)
20182619
-
20182619
.
(
2018
)
.
Genetic diversity maintained among fragmented populations of a tree undergoing range contraction
.
Heredity
vol.
121
,
(
4
)
304
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318
.
(
2018
)
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Temperature is a key driver of a wildlife epidemic and future warming will increase impacts
.
(
2017
)
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The fire ant social chromosome supergene variant Sb shows low diversity but high divergence from SB
.
Molecular Ecology
vol.
26
,
(
11
)
2864
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2879
.
(
2017
)
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Genetic linkage to explain genetic variation
.
Proceedings 22nd International Congress on Modelling and Simulation Modsim 2017
.
127
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133
.
(
2016
)
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Reconstructing the emergence of a lethal infectious disease of wildlife supports a key role for spread through translocations by humans
.
Proceedings of the Royal Society B: Biological Sciences
vol.
283
,
(
1839
)
20160952
-
20160952
.
(
2016
)
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Documentation for MAVERICK software: Version 1.0
.
Genetics
vol.
203
,
(
4
)
(
2016
)
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Estimating the Number of Subpopulations (<i>K</i>) in Structured Populations
.
Genetics
vol.
203
,
(
4
)
1827
-
1839
.
(
2016
)
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File s1: Derivation of evidence estimators and model comparison statistics
.
Genetics
vol.
203
,
(
4
)
(
2016
)
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Unidirectional diploid–tetraploid introgression among British birch trees with shifting ranges shown by restriction site‐associated markers
.
Molecular Ecology
vol.
25
,
(
11
)
2413
-
2426
.
(
2016
)
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Genome size and ploidy influence angiosperm species' biomass under nitrogen and phosphorus limitation
.
New Phytologist
vol.
210
,
(
4
)
1195
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1206
.
(
2016
)
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Genomic Prediction of Testcross Performance in Canola (Brassica napus)
.
PLOS ONE
vol.
11
,
(
1
)
e0147769
-
e0147769
.
(
2015
)
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Estimating<i>K</i>in Genetic Mixture Models
.
(
2015
)
.
Analysis of the giant genomes of <i><scp>F</scp>ritillaria</i> (<scp>L</scp>iliaceae) indicates that a lack of <scp>DNA</scp> removal characterizes extreme expansions in genome size
.
New Phytologist
vol.
208
,
(
2
)
596
-
607
.
(
2015
)
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Rates of Vaccine Evolution Show Strong Effects of Latency: Implications for Varicella Zoster Virus Epidemiology
.
Molecular Biology and Evolution
vol.
32
,
(
4
)
1020
-
1028
.
(
2014
)
.
Detection of a frog virus 3-like ranavirus in native and introduced amphibians in the United Kingdom in 2007 and 2008
.
Herpetological Review
vol.
45
,
(
4
)
608
-
610
.
(
2014
)
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Experimental evidence in support of single host maintenance of a multihost pathogen
.
Ecosphere
vol.
5
,
(
11
)
1
-
11
.
(
2014
)
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Collapse of Amphibian Communities Due to an Introduced Ranavirus
.
Current Biology
vol.
24
,
(
21
)
2586
-
2591
.
(
2014
)
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What is genetic differentiation, and how should we measure it—<scp><i>G</i><sub>ST</sub></scp>,<i> D</i>, neither or both?
.
Molecular Ecology
vol.
23
,
(
17
)
4216
-
4225
.
(
2014
)
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Purifying Selection in Deeply Conserved Human Enhancers Is More Consistent than in Coding Sequences
.
PLoS ONE
vol.
9
,
(
7
)
e103357
-
e103357
.
(
2014
)
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Molecular footprints of the <scp>H</scp>olocene retreat of dwarf birch in <scp>B</scp>ritain
.
Molecular Ecology
vol.
23
,
(
11
)
2771
-
2782
.
(
2014
)
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Spatial targeting of infectious disease control: identifying multiple, unknown sources
.
Methods in Ecology and Evolution
vol.
5
,
(
7
)
647
-
655
.
(
2014
)
.
Inside the Melanoplinae: New molecular evidence for the evolutionary history of the Eurasian Podismini (Orthoptera: Acrididae)
.
Molecular Phylogenetics and Evolution
vol.
71
,
224
-
233
.
(
2014
)
.
Molecular footprints of the Holocene retreat of dwarf birch in Britain
.
Molecular Ecology
(
2013
)
.
Conservation Genetic Resources for Effective Species Survival (ConGRESS): Bridging the divide between conservation research and practice
.
Journal for Nature Conservation
vol.
21
,
(
6
)
433
-
437
.
(
2013
)
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Investigations into the life history stages of the common frog (Rana temporaria) affected by an amphibian ranavirus in the United Kingdom
.
Herpetological Review
vol.
44
,
(
2
)
260
-
263
.
(
2013
)
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Deep Sequencing of Viral Genomes Provides Insight into the Evolution and Pathogenesis of Varicella Zoster Virus and Its Vaccine in Humans
.
Molecular Biology and Evolution
vol.
31
,
(
2
)
397
-
409
.
(
2013
)
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Testing single-sample estimators of effective population size in genetically structured populations
.
Conservation Genetics
vol.
15
,
(
1
)
23
-
35
.
(
2013
)
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Diploidization and genome size change in allopolyploids is associated with differential dynamics of low- and high-copy sequences
.
Plant Journal
vol.
74
,
(
5
)
829
-
839
.
(
2013
)
.
Godfrey M Hewitt (1940–2013): highlights in Heredity from a career in evolutionary genetics
.
Heredity
vol.
110
,
(
5
)
405
-
406
.
(
2013
)
.
Diploidization and genome size change in allopolyploids is associated with differential dynamics of low‐ and high‐copy sequences
.
The Plant Journal
vol.
74
,
(
5
)
829
-
839
.
(
2013
)
.
Sample Planning Optimization Tool for conservation and population Genetics (<scp>SPOTG</scp>): a software for choosing the appropriate number of markers and samples
.
Methods in Ecology and Evolution
vol.
4
,
(
3
)
299
-
303
.
(
2013
)
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Hybridization and speciation
.
Journal of Evolutionary Biology
vol.
26
,
(
2
)
229
-
246
.
(
2013
)
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Bringing genetic diversity to the forefront of conservation policy and management
.
Conservation Genetics Resources
vol.
5
,
(
2
)
593
-
598
.
(
2012
)
.
Next generation sequencing analysis reveals a relationship between rDNA unit diversity and locus number in Nicotiana diploids
.
BMC Genomics
vol.
13
,
(
1
)
Article
722
,
(
2012
)
.
Independent, Rapid and Targeted Loss of Highly Repetitive DNA in Natural and Synthetic Allopolyploids of Nicotiana tabacum
.
PLoS ONE
vol.
7
,
(
5
)
e36963
-
e36963
.
(
2011
)
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Next Generation Sequencing Reveals Genome Downsizing in Allotetraploid Nicotiana tabacum, Predominantly through the Elimination of Paternally Derived Repetitive DNAs
.
MOL BIOL EVOL
vol.
28
,
(
10
)
2843
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2854
.
(
2011
)
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Predictions of single-nucleotide polymorphism differentiation between two populations in terms of mutual information
.
MOL ECOL
vol.
20
,
(
15
)
3156
-
3166
.
(
2011
)
.
Stops making sense: translational trade-offs and stop codon reassignment
.
BMC EVOL BIOL
vol.
11
,
Article
227
,
(
2011
)
.
Phylogenetic Relationships in Pterodroma Petrels Are Obscured by Recent Secondary Contact and Hybridization
.
PLOS ONE
vol.
6
,
(
5
)
Article
e20350
,
(
2011
)
.
Population diversity in batches of the varicella Oka vaccine
.
Vaccine
vol.
29
,
(
17
)
3293
-
3298
.
(
2011
)
.
Household size is critical to varicella-zoster virus transmission in the tropics despite lower viral infectivity
.
Epidemics
vol.
3
,
(
1
)
12
-
18
.
(
2010
)
.
Range expansion and hybridization in Round Island petrels (Pterodroma spp.): evidence from microsatellite genotypes
.
MOL ECOL
vol.
19
,
(
15
)
3157
-
3170
.
(
2009
)
.
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
vol.
12
,
(
1
)
31
-
40
.
(
2009
)
.
Population genetic patterns suggest a behavioural change in wild common frogs (<i>Rana temporaria</i>) following disease outbreaks (<i>Ranavirus</i>)
.
Molecular Ecology
vol.
18
,
(
15
)
3163
-
3172
.
(
2009
)
.
Geographically localised bursts of ribosomal DNA mobility in the grasshopper Podisma pedestris
.
HEREDITY
vol.
103
,
(
1
)
54
-
61
.
(
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
vol.
4
,
(
2
)
e4616
-
e4616
.
(
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
vol.
102
,
(
5
)
490
-
496
.
(
2008
)
.
Sustaining genetic variation in a small population: evidence from the Mauritius kestrel
.
Molecular Ecology
vol.
10
,
(
3
)
593
-
602
.
(
2008
)
.
The inexorable spread of a newly arisen neo-Y chromosome
.
PLOS GENET
vol.
4
,
(
5
)
Article
e1000082
,
(
2008
)
.
Philopatry in the alpine grasshopper, <i>Podisma pedestris:</i> a novel experimental and analytical method
.
Ecological Entomology
vol.
20
,
(
2
)
137
-
145
.
(
2008
)
.
The role of vicariance vs. dispersal in shaping genetic patterns in ocellated lizard species in the western Mediterranean
.
Molecular Ecology
vol.
17
,
(
6
)
1535
-
1551
.
(
2008
)
.
THE FREQUENCY OF rDNA VARIANTS WITHIN INDIVIDUALS PROVIDES EVIDENCE OF POPULATION HISTORY AND GENE FLOW ACROSS A GRASSHOPPER HYBRID ZONE
.
Evolution
vol.
62
,
(
4
)
833
-
844
.
(
2008
)
.
Population structure and the shape of a chromosomal cline between two races of Podisma pedestris (Orthoptera: Acrididae)
.
Biological Journal of the Linnean Society
vol.
29
,
(
4
)
301
-
316
.
(
2007
)
.
DNA Sequence Variability in Oka Vaccine Isolates
.
The Journal of Infectious Diseases
vol.
196
,
(
5
)
801
-
802
.
(
2007
)
.
A method for quantifying differentiation between populations at multi-allelic loci and its implications for investigating identity and paternity
.
Genetica
vol.
133
,
(
1
)
107
-
107
.
(
2007
)
.
Landscape, habitat characteristics and the genetic population structure of two caddisflies
.
Freshwater Biology
vol.
52
,
(
10
)
1907
-
1929
.
(
2007
)
.
Dates from the molecular clock: how wrong can we be?
.
TRENDS ECOL EVOL
vol.
22
,
(
4
)
180
-
184
.
(
2007
)
.
Transition-transversion bias is not universal: a counter example from grasshopper pseudogenes
.
PLoS genetics
vol.
3
,
(
2
)
(
2007
)
.
Transition-transversion bias is not universal: A counter example from grasshopper pseudogenes
.
PLOS GENET
vol.
3
,
(
2
)
Article
e22
,
185
-
191
.
(
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
vol.
104
,
(
1
)
208
-
212
.
(
2006
)
.
Ribosomal DNA in the grasshopper Podisma pedestris: Escape from concerted evolution
.
GENETICS
vol.
174
,
(
2
)
863
-
874
.
(
2006
)
.
Genome-wide characterisation of Hepatitis B mutations involved in clinical outcome
.
Heredity
vol.
97
,
(
6
)
389
-
397
.
(
2006
)
.
400 Hepatitis B virus mutations involved in clinical outcome
.
Journal of Hepatology
.
vol.
44
,
S151
-
S151
.
(
2006
)
.
A novel approach to characterise pathogen candidate genetic polymorphisms involved in clinical outcome
.
Infection, Genetics and Evolution
vol.
6
,
(
1
)
38
-
45
.
(
2006
)
.
Hepatitis B virus mutations involved in clinical outcome
.
JOURNAL OF HEPATOLOGY
vol.
44
,
Article
Suppl. 2
,
400
-
400
.
(
2006
)
.
Morphological differentiation following experimental bottlenecks in the butterfly <i>Bicyclus anynana</i> (Nymphalidae)
.
BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY
vol.
89
,
(
1
)
107
-
115
.
(
2006
)
.
Natural selection of rash-forming genotypes of the varicella vaccine virus within humans
.
Journal of Clinical Virology
.
vol.
36
,
S23
-
S23
.
(
2006
)
.
Vaccine Oka varicella-zoster virus genotypes are monomorphic in single vesicles and polymorphic in respiratory tract secretions
.
JOURNAL OF INFECTIOUS DISEASES
vol.
193
,
(
7
)
927
-
930
.
(
2005
)
.
Recruitment, kin and the spatial genetic structure of a caddisfly <i>Plectrocnemia conspersa</i> in a southern English stream
.
Freshwater Biology
vol.
50
,
(
9
)
1499
-
1514
.
(
2005
)
.
Microsatellites for the net‐spinning caddisfly <i>Plectrocnemia conspersa</i> (Polycentropodidae)
.
Molecular Ecology Notes
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1
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(
4
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318
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319
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(
2005
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Quantitative genetics focus issue
.
Heredity
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94
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(
3
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273
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274
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(
2005
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Genetic and Evolutionary Impacts of Climate Change
.
Climate Change and Biodiversity
,
Yale University Press
(
New Haven
),
(
2004
)
.
Molecular phylogeny and morphological change in the Psittacula parakeets
.
MOL PHYLOGENET EVOL
vol.
31
,
(
1
)
96
-
108
.
(
2004
)
.
The origin and evolution of geminivirus-related DNA sequences in Nicotiana
.
HEREDITY
vol.
92
,
(
4
)
352
-
358
.
(
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
.
MOL ECOL
vol.
13
,
(
4
)
775
-
787
.
(
2003
)
.
An analysis of consanguinity and social structure within the UK Asian population using microsatellite data
.
ANN HUM GENET
vol.
67
,
525
-
537
.
(
2003
)
.
Genetic population structure and neighbourhood population size estimates of the caddisfly <i>Plectrocnemia conspersa</i>
.
Freshwater Biology
vol.
48
,
(
10
)
1813
-
1824
.
(
2003
)
.
Application of DNA mcroarrays to study the evolutionary genomics of Yersinia pestis and Yersinia pseudotuberculosis
.
GENOME RES
vol.
13
,
(
9
)
2018
-
2029
.
(
2002
)
.
Does runaway sexual selection work in finite populations?
.
Journal of Evolutionary Biology
vol.
2
,
(
4
)
299
-
313
.
(
2002
)
.
A molecular phylogeny of African kestrels with reference to divergence across the Indian Ocean
.
Molecular Phylogenetics and Evolution
vol.
25
,
(
2
)
267
-
277
.
(
2002
)
.
Y genetic data support the Neolithic demic diffusion model
.
Proceedings of the National Academy of Sciences
vol.
99
,
(
17
)
11008
-
11013
.
(
2002
)
.
The effect of reproductive compensation on recessive disorders within consanguineous human populations
.
HEREDITY
vol.
88
,
474
-
479
.
(
2002
)
.
Using nested clade analysis to assess the history of colonization and the persistence of populations of an Iberian Lizard
.
Molecular Ecology
vol.
11
,
(
4
)
809
-
819
.
(
2002
)
.
Patterns of colonization in a metapopulation of grey seals
.
Nature
vol.
416
,
(
6879
)
424
-
427
.
(
2002
)
.
Phylogenetic Analysis of Varicella-Zoster Virus: Evidence of Intercontinental Spread of Genotypes and Recombination
.
Journal of Virology
vol.
76
,
(
4
)
1971
-
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