Richard Nichols - Academia.edu (original) (raw)

Papers by Richard Nichols

Molecular Phylogenetics and Evolution, Apr 1, 2004

We reconstruct a phylogeny of the African and Asian Psittacula parakeets using approximately 800 ... more We reconstruct a phylogeny of the African and Asian Psittacula parakeets using approximately 800 bp of mitochondrial cytochrome b sequence to examine their evolutionary relationships in reference to their head plumage and major morphological tail innovations. Our phylogeny identifies three groups, whose distinctiveness is also apparent from their possession of three different head plumage characters: a neck ring, a distinctive colouration of the head, and a ÔmoustacheÕ-shaped pattern that extends from the chin to the cheek. We examine the extent of sexual dimorphism in tail length across the phylogeny and reveal large differences between closely related forms. We apply a range of published avian cytochrome b substitution rates to our data, as an alternative to internal calibration of a molecular clock arising from incomplete paleontological information. An ancestral Psittacula form appears to have evolved during the late Miocene-early Pliocene (3.4-9.7 MYA), a time when regional geological processes on the Asian continent may have promoted subsequent diversity at the species level, and many forms diverged relatively early on in the evolutionary history of Psittacula (between 2.5 and 7.7 MYA). However, others, such as the derbyan and moustached parakeets, diverged as recently as 0.2 MYA. Our phylogeny also suggests that the echo parakeet from Mauritius diverged from the Indian ringneck parakeet as opposed to the African ringneck, and may have done so relatively recently. The molecular results indicate support for a southwards radiation from India across the Indian Ocean to Mauritius, where the arrival-date of the echo parakeet appears consistent with the islandÕs volcanic formation.

Journal for Nature Conservation, 2013

Policy makers and managers are increasingly called upon to assess the state of biodiversity, and ... more Policy makers and managers are increasingly called upon to assess the state of biodiversity, and make decisions regarding potential interventions. Genetic tools are well-recognized in the research community as a powerful approach to evaluate species and population status, reveal ecological and demographic processes, and inform nature conservation decisions. The wealth of genetic data and power of genetic methods are rapidly growing, but the consideration of genetic information and concerns in policy and management is limited by currently low capacity of decision-makers to access and apply genetic resources. Here we describe a freely-available, user-friendly online resource for decision-makers at local and national levels (http://congressgenetics.eu), which increases access to current knowledge, facilitates implementation of studies and interpretation of available data, and fosters collaboration between researchers and practitioners. This resource was created in partnership with conservation practitioners across the European Union, and includes a spectrum of taxa, ecosystems and conservation issues. Our goals here are to (1) introduce the rationale and context, (2) describe the specific tools (knowledge summaries, publications database, decision making tool, project planning tool, forum, community directory), and the challenges they help solve, and (3) summarize lessons learned. This articles provides an outlook and model for similar efforts to build policy and management capacity.

Forests, 2021

Acute Oak Decline (AOD) is complex syndrome affecting Britain’s keystone native oak species, (Que... more Acute Oak Decline (AOD) is complex syndrome affecting Britain’s keystone native oak species, (Quercus robur L. and Q. petraea L. (Matt.) Liebl.), in some cases causing mortality within five years of symptom development. The most distinguishable symptom is weeping stem lesions, from which four species of bacteria have been isolated: Brenneria goodwinii, Gibbsiella quercinecans, Lonsdalea britannica and Rahnella victoriana. We do not yet know where else these bacteria exist, and little is known about the relationship of the wider oak leaf microbiome (phyllosphere) to acute oak decline. Here we investigate whether incidental evidence from a large oak genome re-sequencing dataset could be used to detect these bacteria in oak foliage, and whether bacterial incidence co-varied with AOD status or location. Oak leaves and buds were sampled from 421 trees at five sites in England. Whole genomic DNA from these samples was shot-gun sequenced with short reads. Non-oak reads were extracted from ...

When populations of a rare species are small, isolated and declining under climate change, some p... more When populations of a rare species are small, isolated and declining under climate change, some populations may become locally maladapted. Detecting this maladaptation may allow effective rapid conservation interventions, even if based on incomplete knowledge. Population maladaptation may be estimated by finding genome-environment associations (GEA) between allele frequencies and environmental variables across a local species range, and identifying populations whose allele frequencies do not fit with these trends. We can then design assisted gene flow strategies for maladapted populations, to adjust their allele frequencies, entailing lower levels of intervention than with undirected conservation action. Here, we investigate this strategy in Scottish populations of the montane plant dwarf birch (Betula nana). In genome-wide single nucleotide polymorphism (SNP) data we found 267 significant associations between SNP loci and environmental variables. We ranked populations by maladaptat...

Molecular Ecology, 2016

Hybridisation may lead to introgression of genes among species. Introgression may be bidirectiona... more Hybridisation may lead to introgression of genes among species. Introgression may be bidirectional or unidirectional, depending on factors such as the demography of the hybridising species, or the nature of reproductive barriers between them. Previous microsatellite studies suggested bidirectional introgression between diploid Betula nana (dwarf birch) and tetraploid B. pubescens (downy birch) and also between B. pubescens and diploid B. pendula (silver birch) in Britain. Here we analyse introgression among these species using 51,237 variants in restriction-site associated (RAD) markers in 194 individuals, called with allele dosages in the tetraploids. In contrast to the microsatellite study, we found unidirectional introgression into B. pubescens from both of the diploid species. This pattern fits better with the expected nature of the reproductive barrier between diploids and tetraploids. As in the microsatellite study, introgression into B. pubescens showed clear clines with increasing introgression from B. nana in the north and from B. pendula in the south. Unlike B. pendula alleles, introgression of B. nana alleles was found far from the current area of sympatry or allopatry between B. nana and B. pubescens. This pattern fits a shifting zone of hybridisation due to Holocene reduction in the range of B. nana, and expansion in the range of B. pubescens.

PloS one, 2016

Genomic selection (GS) is a modern breeding approach where genome-wide single-nucleotide polymorp... more Genomic selection (GS) is a modern breeding approach where genome-wide single-nucleotide polymorphism (SNP) marker profiles are simultaneously used to estimate performance of untested genotypes. In this study, the potential of genomic selection methods to predict testcross performance for hybrid canola breeding was applied for various agronomic traits based on genome-wide marker profiles. A total of 475 genetically diverse spring-type canola pollinator lines were genotyped at 24,403 single-copy, genome-wide SNP loci. In parallel, the 950 F1 testcross combinations between the pollinators and two representative testers were evaluated for a number of important agronomic traits including seedling emergence, days to flowering, lodging, oil yield and seed yield along with essential seed quality characters including seed oil content and seed glucosinolate content. A ridge-regression best linear unbiased prediction (RR-BLUP) model was applied in combination with 500 cross-validations for ea...

PloS one, 2011

The classification of petrels (Pterodroma spp.) from Round Island, near Mauritius in the Indian O... more The classification of petrels (Pterodroma spp.) from Round Island, near Mauritius in the Indian Ocean, has confounded researchers since their discovery in 1948. In this study we investigate the relationships between Round Island petrels and their closest relatives using evidence from mitochondrial DNA sequence data and ectoparasites. Far from providing clear delimitation of species boundaries, our results reveal that hybridization among species on Round Island has led to genetic leakage between populations from different ocean basins. The most common species on the island, Pterodroma arminjoniana, appears to be hybridizing with two rarer species (P. heraldica and P. neglecta), subverting the reproductive isolation of all three and allowing gene flow. P. heraldica and P. neglecta breed sympatrically in the Pacific Ocean, where P. arminjoniana is absent, but no record of hybridization between these two exists and they remain phenotypically distinct. The breakdown of species boundaries...

Trends in Ecology & Evolution, 2001

Trends in Ecology & Evolution, 2007

Nature, 2002

from the slab hydration source that permits refractory mantle to flow) that may have promoted the... more from the slab hydration source that permits refractory mantle to flow) that may have promoted the propagation of the CLSC to replace this system. Spreading in the Lau back-arc basin is at present well-organized, as at mid-ocean ridges 5,12 , but, as we have shown, the supply of magma is modulated by mantle wedge compositional controls and arc melt additions. Similar controls are indicated in the Mariana trough, even though the slab there is steeper, and rates of spreading and subduction are slower 30. In the northern Mariana trough 16 , the spreading centre varies from magmatically robust, to magma starved, to normal as it separates from the volcanic front, and in the southern trough the spreading centre changes from an axial valley to an axial high as it approaches the volcanic front 30. These variations in relative magma supply with proximity to the volcanic front are similar to those we report here for the Lau basin, and support the generality of our model of mantle wedge control on back-arc crustal accretion.

Molecular Ecology, 2010

Historical records suggest that the petrels of Round Island (near Mauritius, Indian Ocean) repres... more Historical records suggest that the petrels of Round Island (near Mauritius, Indian Ocean) represent a recent, long-distance colonization by species originating from the Atlantic and Pacific Oceans. The majority of petrels on Round Island appear most similar to Pterodroma arminjoniana, a species whose only other breeding locality is Trindade Island in the South Atlantic. Using nine microsatellite loci, patterns of genetic differentiation in petrels from Round and Trindade Islands were analysed. The two populations exhibit low but significant levels of differentiation in allele frequencies and estimates of migration rate between islands using genetic data are also low, supporting the hypothesis that these populations have recently separated but are now isolated from one another. A second population of petrels, most similar in appearance to the Pacific species P. neglecta, is also present on Round Island and observations suggest that the two petrel species are hybridizing. Vocalizations recorded on the island also suggest that hybrid birds may be present within the population. Data from microsatellite genotypes support this hypothesis and indicate that there may have been many generations of hybridization and back-crossing between P. arminjoniana and P. neglecta on Round Island. Our results provide an insight into the processes of dispersal and the consequences of secondary contact in Procellariiformes.

Journal of Evolutionary Biology, 2013

Heredity, 1989

Individual virgin females of two races of Podisma pedestris were mated sequentially with a male o... more Individual virgin females of two races of Podisma pedestris were mated sequentially with a male of each race in one or other reciprocal orders, giving four types of double matings. The embryos were karyotyped to determine the extent of each male's paternity. This gave an excess of racial homozygotes as well as showing a predominance of the first male's sperm in fertilization. This confirms the previous indication of assortative fertilization producing homogamy, and reveals first sperm precedence, which is rare in insects. There was some infertility and a biased sex ratio. The implications for the evolution of assortment, reproductive isolation, sperm competition, male-female conflict and mating strategies are discussed.

Heredity, 1994

Rare long distance dispersal may have little impact on gene frequencies in established population... more Rare long distance dispersal may have little impact on gene frequencies in established populations but it can dramatically increase gene flow during episodes of range expansion. We model the invasion of new territory by genetically distinct populations of the same species to investigate the dynamics of such episodes. If long distance dispersal is sufficiently frequent, the populations do not spread as a wave of advance but instead found intermingled isolates. We argue that this process can explain many otherwise puzzling patterns in the geographical distribution of alleles.

Heredity, 1999

Genetic variation was quantified between surface-dwelling populations of Culex pipiens and the so... more Genetic variation was quantified between surface-dwelling populations of Culex pipiens and the so-called molestus form found in the London Underground (the Underground) railway system. The molestus form is a commercially important biting nuisance and in the southern part of its range is also a disease vector. The surface and subterranean populations were genetically distinct, with no evidence of gene flow between closely adjacent populations of the different forms, whereas there was little differentiation between the different populations of each form. The substantially reduced heterozygosity in the Underground populations and the allelic composition suggest that colonization of the Underground has occurred once or very few times. Breeding experiments show compatibility between the Underground populations but not with those breeding above ground. There is evidence of greater gene flow and a mixing of molestus and pipiens traits in the south of the species range. This paper considers the processes that may allow establishment of reproductive isolation in the north of the species range but not in the south.

Heredity, 1987

Females of the grasshopper Podisima pedestris were collected from the middle of a hybrid zone bet... more Females of the grasshopper Podisima pedestris were collected from the middle of a hybrid zone between two chromosomal races in the Alpes Maritimes. They had already mated in the field, and could therefore lay fertilised eggs in the laboratory. The embryos were karyotyped, and found to contain an excess of chromosomal homozygotes. No evidence of assortative mating was found from copulating pairs taken in the field. The excess appears to have been caused by a combination of multiple insemination and assortative fertilisation. The genetics of the assortment, and the implications for the evolution of reproductive isolation are discussed.

American Journal of Human Biology, 2000

Heredity, 1996

We examined the impact of three forms of dispersal, stepping-stone, normal and leptokurtic, on sp... more We examined the impact of three forms of dispersal, stepping-stone, normal and leptokurtic, on spatial genetic structure of expanding populations using computer simulations. When dispersal beyond neighbouring demes is allowed, rare long-distance migration leads to the establishment of pocket populations in advance of the main invasion front and results in spatial clustering of genotypes which persists for hundreds of generations. Patchiness is more pronounced when dispersal is leptokurtic as is the case in many animal and plant species. These results are of particular interest because population genetic parameters such as gene flow and effective population size are commonly estimated using gene frequency divergence information assuming equilibrium conditions and island models. We show how the three forms of dispersal during colonization bring about contrasting population genetic structures and how this affects estimates of gene flow. The implications for experimental studies of the spatial dimension of population genetic structure are discussed.

Viruses, 2019

Ranaviruses began emerging in common frogs (Rana temporaria) in the United Kingdom in the late 19... more Ranaviruses began emerging in common frogs (Rana temporaria) in the United Kingdom in the late 1980s and early 1990s, causing severe disease and declines in the populations of these animals. Herein, we explored the transmission dynamics of the ranavirus(es) present in common frog populations, in the context of a simple susceptible-infected (SI) model, using parameters derived from the literature. We explored the effects of disease-induced population decline on the dynamics of the ranavirus. We then extended the model to consider the infection dynamics in populations exposed to both ulcerative and hemorrhagic forms of the ranaviral disease. The preliminary investigation indicated the important interactions between the forms. When the ulcerative form was present in a population and the hemorrhagic form was later introduced, the hemorrhagic form of the disease needed to be highly contagious, to persist. We highlighted the areas where further research and experimental evidence is needed...