ORCID Profile
0000-0003-4736-0954
Current Organisation
University of Sheffield
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Publisher: Wiley
Date: 30-10-2007
Publisher: Wiley
Date: 05-2021
DOI: 10.1111/EVO.14235
Publisher: Oxford University Press (OUP)
Date: 12-2021
DOI: 10.1002/EVL3.260
Abstract: Inversions often underlie complex adaptive traits, but the genic targets inside them are largely unknown. Gene expression profiling provides a powerful way to link inversions with their phenotypic consequences. We examined the effects of the Cf-Inv(1) inversion in the seaweed fly Coelopa frigida on gene expression variation across sexes and life stages. Our analyses revealed that Cf-Inv(1) shapes global expression patterns, most likely via linked variation, but the extent of this effect is variable, with much stronger effects in adults than larvae. Furthermore, within adults, both common as well as sex-specific patterns were found. The vast majority of these differentially expressed genes mapped to Cf-Inv(1). However, genes that were differentially expressed in a single context (i.e., in males, females, or larvae) were more likely to be located outside of Cf-Inv(1). By combining our findings with genomic scans for environmentally associated SNPs, we were able to pinpoint candidate variants in the inversion that may underlie mechanistic pathways that determine phenotypes. Together the results of this study, combined with previous findings, support the notion that the polymorphic Cf-Inv(1) inversion in this species is a major factor shaping both coding and regulatory variation resulting in highly complex adaptive effects.
Publisher: The Royal Society
Date: 25-02-2009
Abstract: Range margins are spatially complex, with environmental, genetic and phenotypic variations occurring across a range of spatial scales. We examine variation in temperature, genes and metabolomic profiles within and between populations of the subalpine perennial plant Arabidopsis lyrata ssp. petraea from across its northwest European range. Our surveys cover a gradient of fragmentation from largely continuous populations in Iceland, through more fragmented Scandinavian populations, to increasingly widely scattered populations at the range margin in Scotland, Wales and Ireland. Temperature regimes vary substantially within some populations, but within-population variation represents a larger fraction of genetic and especially metabolomic variances. Both physical distance and temperature differences between sites are found to be associated with genetic profiles, but not metabolomic profiles, and no relationship was found between genetic and metabolomic population structures in any region. Genetic similarity between plants within populations is the highest in the fragmented populations at the range margin, but differentiation across space is the highest there as well, suggesting that regional patterns of genetic ersity may be scale dependent.
Publisher: Elsevier BV
Date: 07-2001
DOI: 10.1016/S0169-5347(01)02160-7
Abstract: The power of sexual selection to drive changes in mate recognition traits gives it the potential to be a potent force in speciation. Much of the evidence to support this possibility comes from comparative studies that examine differences in the number of species between clades that apparently differ in the intensity of sexual selection. We argue that more detailed studies are needed, examining extinction rates and other sources of variation in species richness. Typically, investigations of extant natural populations have been too indirect to convincingly conclude speciation by sexual selection. Recent empirical work, however, is beginning to take a more direct approach and rule out confounding variables.
Publisher: Wiley
Date: 17-10-2007
Publisher: Springer Science and Business Media LLC
Date: 06-1997
DOI: 10.1038/42355
Publisher: Wiley
Date: 25-08-2005
Publisher: Wiley
Date: 25-02-2019
DOI: 10.1111/MEC.14972
Publisher: Authorea, Inc.
Date: 05-12-2022
DOI: 10.22541/AU.167023671.11036754/V1
Abstract: Next-generation sequencing of pooled s les (Pool-seq) is a popular method to assess genome-wide ersity patterns in natural and experimental populations. However, Pool-seq is associated with specific sources of noise, such as unequal in idual contributions. Consequently, using Pool-seq for the reconstruction of evolutionary history has remained underexplored. Here we describe a method to simulate Pool-seq data, implemented in an Approximate Bayesian Computation (ABC) framework to infer demographic history under models with two and four populations. By jointly modeling Pool-seq data, demographic history and the effects of selection due to barrier loci, we obtain estimates of demographic history parameters accounting for technical errors associated with Pool-seq. Rather than simulating genome-wide data, we perform ABC on subsets of loci, using relative summary statistics and parameter estimates. Our simulation study results indicate Pool-seq data allows distinction between general scenarios of ecotype formation (single versus parallel origin), and to infer relevant demographic parameters (e.g., effective sizes, split times). We exemplify the application of our method to Pool-seq data from the rocky-shore gastropod \\textit{Littorina saxatilis}, s led on a narrow geographical scale at two Swedish locations where two ecotypes (wave and crab) are found. Our model choice and parameter estimates show that ecotypes formed before colonization of the two locations (i.e., single origin) and are maintained despite gene flow. These results indicate that demographic modeling and inference can be successful based on pool-sequencing using ABC, contributing to the development of suitable null models that allow for a better understanding of the genetic basis of ergent adaptation.
Publisher: Wiley
Date: 2009
DOI: 10.1111/J.1558-5646.2008.00526.X
Abstract: Whether chromosomal rearrangements promote speciation by providing barriers to gene exchange between populations is one of the long-standing debates in evolutionary biology. This question can be addressed by studying patterns of gene flow and selection in hybrid zones between chromosomally erse taxa. Here we present results of the first study of the genetic structure of a hybrid zone between chromosomal races of morabine grasshoppers Vandiemenella viatica, P24(XY) and viatica17, on Kangaroo Island, Australia. Chromosomal and 11 nuclear markers revealed a narrow hybrid zone with strong linkage disequilibrium and heterozygote deficits, most likely maintained by a balance between dispersal and selection. Widths and positions of clines for these markers are concordant and coincident, suggesting that selection is unlikely to be concentrated on a few chromosomes. In contrast, a mitochondrial marker showed a significantly wider cline with centre offset toward the P24(XY) side. We argue that the discordance between the mitochondrial and nuclear/chromosomal clines and overall asymmetry of the clines suggest a secondary origin of the contact zone and potential movement of the zone after contact. Genome-wide scans using many genetic markers and chromosomal mapping of these markers are needed to investigate whether chromosomal differences directly reduce gene flow after secondary contact.
Publisher: Springer Science and Business Media LLC
Date: 11-2007
DOI: 10.1038/NATURE06341
Publisher: Springer Science and Business Media LLC
Date: 2000
Publisher: Cold Spring Harbor Laboratory
Date: 13-02-2023
DOI: 10.1101/2023.02.13.528213
Abstract: Key innovations are fundamental to biological ersification, but their genetic architecture is poorly understood. A recent transition from egg-laying to live-bearing in Littorina snails provides the opportunity to study the architecture of an innovation that has evolved repeatedly in animals. S les do not cluster by reproductive mode in a genome-wide phylogeny, but local genealogical analysis revealed numerous genomic regions where all live-bearers carry the same core haplotype. Associated regions show evidence for live-bearer-specific positive selection, and are enriched for genes that are differentially expressed between egg-laying and live-bearing reproductive systems. Ages of selective sweeps suggest live-bearing alleles accumulated gradually, involving selection at different times in the past. Our results suggest that innovation can have a polygenic basis, and that novel functions can evolve gradually, rather than in a single step.
Publisher: Wiley
Date: 20-07-2023
Abstract: Next‐generation sequencing of pooled s les (Pool‐seq) is a popular method to assess genome‐wide ersity patterns in natural and experimental populations. However, Pool‐seq is associated with specific sources of noise, such as unequal in idual contributions. Consequently, using Pool‐seq for the reconstruction of evolutionary history has remained underexplored. Here we describe a novel Approximate Bayesian Computation (ABC) method to infer demographic history, explicitly modelling Pool‐seq sources of error. By jointly modelling Pool‐seq data, demographic history and the effects of selection due to barrier loci, we obtain estimates of demographic history parameters accounting for technical errors associated with Pool‐seq. Our ABC approach is computationally efficient as it relies on simulating subsets of loci (rather than the whole‐genome) and on using relative summary statistics and relative model parameters. Our simulation study results indicate Pool‐seq data allows distinction between general scenarios of ecotype formation (single versus parallel origin) and to infer relevant demographic parameters (e.g. effective sizes and split times). We exemplify the application of our method to Pool‐seq data from the rocky‐shore gastropod Littorina saxatilis , s led on a narrow geographical scale at two Swedish locations where two ecotypes (Wave and Crab) are found. Our model choice and parameter estimates show that ecotypes formed before colonization of the two locations (i.e. single origin) and are maintained despite gene flow. These results indicate that demographic modelling and inference can be successful based on pool‐sequencing using ABC, contributing to the development of suitable null models that allow for a better understanding of the genetic basis of ergent adaptation.
Publisher: Wiley
Date: 04-06-2009
DOI: 10.1111/J.1365-2656.2009.01545.X
Abstract: 1. In most social animals, the prevalence of directly transmitted pathogens increases in larger groups and at higher population densities. Such patterns are predicted by models of Mycobacterium bovis infection in European badgers (Meles meles). 2. We investigated the relationship between badger abundance and M. bovis prevalence, using data on 2696 adult badgers in 10 populations s led at the start of the Randomized Badger Culling Trial. 3. M. bovis prevalence was consistently higher at low badger densities and in small social groups. M. bovis prevalence was also higher among badgers whose genetic profiles suggested that they had immigrated into their assigned social groups. 4. The association between high M. bovis prevalence and small badger group size appeared not to have been caused by previous small-scale culling in study areas, which had been suspended, on average, 5 years before the start of the current study. 5. The observed pattern of prevalence might occur through badgers in smaller groups interacting more frequently with members of neighbouring groups detailed behavioural data are needed to test this hypothesis. Likewise, longitudinal data are needed to determine whether the size of infected groups might be suppressed by disease-related mortality. 6. Although M. bovis prevalence was lower at high population densities, the absolute number of infected badgers was higher. However, this does not necessarily mean that the risk of M. bovis transmission to cattle is highest at high badger densities, since transmission risk depends on badger behaviour as well as on badger density.
Publisher: Springer Science and Business Media LLC
Date: 22-07-1999
DOI: 10.1038/22419
Publisher: MDPI AG
Date: 18-03-2011
Publisher: Wiley
Date: 21-02-2018
DOI: 10.1111/GEB.12722
Publisher: Springer Science and Business Media LLC
Date: 07-02-2009
Publisher: The Royal Society
Date: 13-07-2020
Abstract: The evolution of strong reproductive isolation (RI) is fundamental to the origins and maintenance of biological ersity, especially in situations where geographical distributions of taxa broadly overlap. But what is the history behind strong barriers currently acting in sympatry? Using whole-genome sequencing and single nucleotide polymorphism genotyping, we inferred (i) the evolutionary relationships, (ii) the strength of RI, and (iii) the demographic history of ergence between two broadly sympatric taxa of intertidal snail. Despite being cryptic, based on external morphology, Littorina arcana and Littorina saxatilis differ in their mode of female reproduction (egg-laying versus brooding), which may generate a strong post-zygotic barrier. We show that egg-laying and brooding snails are closely related, but genetically distinct. Genotyping of 3092 snails from three locations failed to recover any recent hybrid or backcrossed in iduals, confirming that RI is strong. There was, however, evidence for a very low level of asymmetrical introgression, suggesting that isolation remains incomplete. The presence of strong, asymmetrical RI was further supported by demographic analysis of these populations. Although the taxa are currently broadly sympatric, demographic modelling suggests that they initially erged during a short period of geographical separation involving very low gene flow. Our study suggests that some geographical separation may kick-start the evolution of strong RI, facilitating subsequent coexistence of taxa in sympatry. The strength of RI needed to achieve sympatry and the subsequent effect of sympatry on RI remain open questions. This article is part of the theme issue ‘Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers'.
Publisher: Wiley
Date: 11-05-2007
Publisher: Cold Spring Harbor Laboratory
Date: 03-06-2021
DOI: 10.1101/2021.06.03.446913
Abstract: Inversions often underlie complex adaptive traits, but the genic targets inside them are largely unknown. Gene expression profiling provides a powerful way to link inversions with their phenotypic consequences. We examined the effects of the Cf-Inv(1) inversion in the seaweed fly Coelopa frigida on gene expression variation across sexes and life stages. Our analyses revealed that Cf-Inv(1) shapes global expression patterns but the extent of this effect is variable with much stronger effects in adults than larvae. Furthermore, within adults, both common as well as sex specific patterns were found. The vast majority of these differentially expressed genes mapped to Cf-Inv(1) . However, genes that were differentially expressed in a single context (i.e. in males, females or larvae) were more likely to be located outside of Cf-Inv(1). By combining our findings with genomic scans for environmentally associated SNPs, we were able to pinpoint candidate variants in the inversion that may underlie mechanistic pathways that determine phenotypes. Together the results in this study, combined with previous findings, support the notion that the polymorphic Cf-Inv(1) inversion in this species is a major factor shaping both coding and regulatory variation resulting in highly complex adaptive effects.
Publisher: American Association for the Advancement of Science (AAAS)
Date: 06-12-2019
Abstract: A common genomic architecture allowed a marine snail to rapidly adapt to heterogeneous environments in a replicated way.
Publisher: Wiley
Date: 08-2009
Publisher: Oxford University Press (OUP)
Date: 2023
DOI: 10.1093/EVOLINNEAN/KZAD002
Abstract: Understanding the factors that have shaped the current distributions and ersity of species is a central and longstanding aim of evolutionary biology. The recent inclusion of genomic data into phylogeographic studies has dramatically improved our understanding in organisms where evolutionary relationships have been challenging to infer. We used whole-genome sequences to study the phylogeography of the intertidal snail Littorina saxatilis, which has successfully colonized and ersified across a broad range of coastal environments in the northern hemisphere amid repeated cycles of glaciation. Building on past studies based on short DNA sequences, we used genome-wide data to provide a clearer picture of the relationships among s les spanning most of the species natural range. Our results confirm the trans-Atlantic colonization of North America from Europe, and have allowed us to identify rough locations of glacial refugia and to infer likely routes of colonization within Europe. We also investigated the signals in different datasets to account for the effects of genomic architecture and non-neutral evolution, which provides new insights about ersification of four ecotypes of L. saxatilis (the crab, wave, barnacle and brackish ecotypes) at different spatial scales. Overall, we provide a much clearer picture of the biogeography of L. saxatilis, providing a foundation for more detailed phylogenomic and demographic studies.
Publisher: Cold Spring Harbor Laboratory
Date: 11-2021
DOI: 10.1101/2021.11.01.466799
Abstract: Sandy beaches are biogeochemical hotspots that bridge marine and terrestrial ecosystems via the transfer of marine organic matter, such as seaweed (termed wrack). A keystone of this unique ecosystem is the microbial community, which helps to degrade wrack and re-mineralize nutrients. However, little is known about the wrackbed microbiome, its composition, trophic ecology, or how it varies over time and space. Here we characterize the wrackbed microbiome as well as the microbiome of a primary consumer, the seaweed fly Coelopa frigida , and examine how they change along one of the most studied ecological gradients in the world, the transition from the marine North Sea to the brackish Baltic Sea. We found that polysaccharide degraders dominated both the wrackbed and seaweed fly microbiomes but there were still consistent differences between wrackbed and fly s les. Furthermore, we observed a shift in both microbial communities and functionality between the North and Baltic Sea. These shifts were mostly due to changes in the frequency of different groups of known polysaccharide degraders (Proteobacteria and Bacteroidota). We hypothesize that microbes were selected for their abilities to degrade different polysaccharides corresponding to a shift in polysaccharide content in the seaweed communities of the North vs. Baltic Sea. Our results reveal the complexities of both the wracked microbial community, with different groups specialized to different roles, and the cascading trophic consequences of shifts in the near shore algal community.
Publisher: Oxford University Press (OUP)
Date: 06-2021
DOI: 10.1002/EVL3.227
Abstract: Chromosomal inversions have long been recognized for their role in local adaptation. By suppressing recombination in heterozygous in iduals, they can maintain coadapted gene complexes and protect them from homogenizing effects of gene flow. However, to fully understand their importance for local adaptation we need to know their influence on phenotypes under ergent selection. For this, the marine snail Littorina saxatilis provides an ideal study system. Divergent ecotypes adapted to wave action and crab predation occur in close proximity on intertidal shores with gene flow between them. Here, we used F2 in iduals obtained from crosses between the ecotypes to test for associations between genomic regions and traits distinguishing the Crab-/Wave-adapted ecotypes including size, shape, shell thickness, and behavior. We show that most of these traits are influenced by two previously detected inversion regions that are ergent between ecotypes. We thus gain a better understanding of one important underlying mechanism responsible for the rapid and repeated formation of ecotypes: ergent selection acting on inversions. We also found that some inversions contributed to more than one trait suggesting that they may contain several loci involved in adaptation, consistent with the hypothesis that suppression of recombination within inversions facilitates differentiation in the presence of gene flow.
Publisher: Wiley
Date: 11-2008
DOI: 10.1111/J.1755-0998.2008.02190.X
Abstract: We describe a convenient, cost-effective and flexible medium-throughput single nucleotide polymorphism (SNP) genotyping method, Multiplex SNP-SCALE, which enables the simultaneous lification by polymerase chain reaction (PCR) of up to 25 (or potentially more) loci followed by electrophoresis in an automated DNA sequencer. We extended the original SNP-SCALE method to include (i) use of a commercial multiplex PCR kit, (ii) a four-dye system, (iii) much-reduced (2-µL) reaction volumes, (iv) drying down of template DNA before PCR, (v) use of pig-tailed primers, (vi) a PCR product weighting system, (vii) a standard optimized touchdown PCR thermocycling programme, and (viii) software (SNP-SCALE Primer Designer) that automatically designs suitable SNP-SCALE primers for a batch of loci. This new protocol was validated for different types of SNPs. The method is cost- and time-effective for medium-scale evolutionary and ecological projects involving 10s to 100s of loci.
Publisher: Public Library of Science (PLoS)
Date: 10-10-2012
Publisher: Oxford University Press (OUP)
Date: 31-01-2003
Publisher: Cold Spring Harbor Laboratory
Date: 29-09-2023
Publisher: Proceedings of the National Academy of Sciences
Date: 05-07-2011
Abstract: Understanding the processes underlying the origin of species is a fundamental goal of biology. It is widely accepted that speciation requires an interruption of gene flow between populations: ongoing gene exchange is considered a major hindrance to population ergence and, ultimately, to the evolution of new species. Where a geographic barrier to reproductive isolation is lacking, a biological mechanism for speciation is required to counterbalance the homogenizing effect of gene flow. Speciation with initially strong gene flow is thought to be extremely rare, and few convincing empirical ex les have been published. However, using phylogenetic, karyological, and ecological data for the flora of a minute oceanic island (Lord Howe Island, LHI), we demonstrate that speciation with gene flow may, in fact, be frequent in some instances and could account for one in five of the endemic plant species of LHI. We present 11 potential instances of species ergence with gene flow, including an in situ radiation of five species of Coprosma (Rubiaceae, the coffee family). These results, together with the speciation of Howea palms on LHI, challenge current views on the origin of species ersity.
Publisher: Wiley
Date: 12-2002
Publisher: Cold Spring Harbor Laboratory
Date: 20-09-2023
Publisher: Authorea, Inc.
Date: 05-12-2022
Publisher: Wiley
Date: 11-2020
DOI: 10.1111/EVO.14111
Location: United Kingdom of Great Britain and Northern Ireland
Location: Mexico
No related grants have been discovered for Roger Butlin.