| 1. |
- Bensch, Staffan, et al.
(author)
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Conflicting patterns of mitochondrial and nuclear DNA diversity in Phylloscopus warblers
- 2006
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In: Molecular Ecology. - 0962-1083. ; 15:1, s. 161-171
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Journal article (peer-reviewed)abstract
- Molecular variation is often used to infer the demographic history of species, but sometimes the complexity of species history can make such inference difficult. The willow warbler, Phylloscopus trochilus, shows substantially less geographical variation than the chiffchaff, Phylloscopus collybita, both in morphology and in mitochondrial DNA (mtDNA) divergence. We therefore predicted that the willow warbler should harbour less nuclear DNA diversity than the chiffchaff. We analysed sequence data obtained from multiple samples of willow warblers and chiffchaffs for the mtDNA cytochrome b gene and four nuclear genes. We confirmed that the mtDNA diversity among willow warblers is low (π = 0.0021). Sequence data from three nuclear genes (CHD-Z, AFLP-WW1 and MC1R) not linked to the mitochondria demonstrated unexpectedly high nucleotide diversity (π values of 0.0172, 0.0141 and 0.0038) in the willow warbler, on average higher than the nucleotide diversity for the chiffchaff (π values of 0.0025, 0.0017 and 0.0139). In willow warblers, Tajima's D analyses showed that the mtDNA diversity, but not the nuclear DNA diversity, has been reduced relative to the neutral expectation of molecular evolution, suggesting the action of a selective sweep affecting the maternally inherited genes. The large nuclear diversity seen within willow warblers is not compatible with processes of neutral evolution occurring in a population with a constant population size, unless the long-term effective population size has been very large (Ne > 106). We suggest that the contrasting patterns of genetic diversity in the willow warbler may reflect a more complex evolutionary history, possibly including historical demographic fluctuations or historical male-biased introgression of nuclear genes from a differentiated population of Phylloscopus warblers.
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| 2. |
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| 3. |
- Irwin, Darren, et al.
(author)
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Speciation by distance in a ring species.
- 2005
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In: Science. - : American Association for the Advancement of Science (AAAS). - 1095-9203 .- 0036-8075. ; 307:5708, s. 414-416
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Journal article (other academic/artistic)abstract
- Ring species, which consist of two reproductively isolated forms connected by a chain of intergrading populations, have often been described as examples of speciation despite gene flow between populations, but this has never been demonstrated. We used amplified fragment length polymorphism (AFLP) markers to study gene flow in greenish warblers (Phylloscopus trochiloides). These genetic markers show distinct differences between two reproductively isolated forms but gradual change through the ring connecting these forms. These findings provide the strongest evidence yet for "speciation by force of distance" in the face of ongoing gene flow.
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| 4. |
- Bensch, Staffan, et al.
(author)
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The use of AFLP to find an informative SNP: genetic differences across a migratory divide in willow warblers
- 2002
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In: Molecular Ecology. - 0962-1083. ; 11:11, s. 2359-2366
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Journal article (peer-reviewed)abstract
- We used the amplified fragment length polymorphism (AFLP) method to obtain genetic markers distinguishing two subspecies of willow warblers Phylloscopus trochilus that have different migratory behaviours but are not differentiated in mitochondrial DNA or at several microsatellite loci. With the inverse-polymerase chain reaction (PCR) approach we converted a dominant AFLP-marker to a codominant single nucleotide polymorphism (SNP). Across Scandinavia we typed 621 birds at the SNP locus AFLP-WW1 and we found a sigmoid change in allele frequencies centred around 62 degrees latitude. North of the latitudinal cline was a west-east cline. Both clines are narrower than one would expect from dispersal distances in willow warblers, which suggests that these are maintained by selection. The latitudinal cline at the locus AFLP-WW1 is paralleled by changes in several other traits, all of which might be maintained by a single selective force. The most plausible selection factor that we have identified is selection against hybrids because of inferior migratory behaviour. The selective force maintaining the east-west cline is less obvious. We discuss alternatives to the selection scenario, involving colonization history and asymmetric gene flow.
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| 5. |
- Delmore, Kira E, et al.
(author)
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Comparative analysis examining patterns of genomic differentiation across multiple episodes of population divergence in birds
- 2018
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In: Evolution letters. - : Oxford University Press (OUP). - 2056-3744. ; 2:2, s. 76-87
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Journal article (peer-reviewed)abstract
- Heterogeneous patterns of genomic differentiation are commonly documented between closely related populations and there is considerable interest in identifying factors that contribute to their formation. These factors could include genomic features (e.g., areas of low recombination) that promote processes like linked selection (positive or purifying selection that affects linked neutral sites) at specific genomic regions. Examinations of repeatable patterns of differentiation across population pairs can provide insight into the role of these factors. Birds are well suited for this work, as genome structure is conserved across this group. Accordingly, we reestimated relative (FST ) and absolute (dXY ) differentiation between eight sister pairs of birds that span a broad taxonomic range using a common pipeline. Across pairs, there were modest but significant correlations in window-based estimates of differentiation (up to 3% of variation explained for FST and 26% for dXY ), supporting a role for processes at conserved genomic features in generating heterogeneous patterns of differentiation; processes specific to each episode of population divergence likely explain the remaining variation. The role genomic features play was reinforced by linear models identifying several genomic variables (e.g., gene densities) as significant predictors of FST and dXY repeatability. FST repeatability was higher among pairs that were further along the speciation continuum (i.e., more reproductively isolated) providing further insight into how genomic differentiation changes with population divergence; early stages of speciation may be dominated by positive selection that is different between pairs but becomes integrated with processes acting according to shared genomic features as speciation proceeds.
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| 6. |
- English, Andrew, et al.
(author)
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Genomic, Proteomic, and Phenotypic Biomarkers of COVID-19 Severity: Protocol for a Retrospective Observational Study
- 2024
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In: JMIR Research Protocols. - : JMIR PUBLICATIONS, INC. - 1929-0748. ; 13
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Journal article (peer-reviewed)abstract
- Background: Health organizations and countries around the world have found it difficult to control the spread of COVID-19. To minimize the future impact on the UK National Health Service and improve patient care, there is a pressing need to identify individuals who are at a higher risk of being hospitalized because of severe COVID-19. Early targeted work was successful in identifying angiotensin-converting enzyme -2 receptors and type II transmembrane serine protease dependency as drivers of severe infection. Although a targeted approach highlights key pathways, a multiomics approach will provide a clearer and more comprehensive picture of severe COVID-19 etiology and progression. Objective: The COVID-19 Response Study aims to carry out an integrated multiomics analysis to identify biomarkers in blood and saliva that could contribute to host susceptibility to SARS-CoV-2 and the development of severe COVID-19. Methods: The COVID-19 Response Study aims to recruit 1000 people who recovered from SARS-CoV-2 infection in both community and hospital settings on the island of Ireland. This protocol describes the retrospective observational study component carried out in Northern Ireland (NI; Cohort A); the Republic of Ireland cohort will be described separately. For all NI participants (n=519), SARS-CoV-2 infection has been confirmed by reverse transcription -quantitative polymerase chain reaction. A prospective Cohort B of 40 patients is also being followed up at 1, 3, 6, and 12 months postinfection to assess longitudinal symptom frequency and immune response. Data will be sourced from whole blood, saliva samples, and clinical data from the electronic care records, the general health questionnaire, and a 12 -item general health questionnaire mental health survey. Saliva and blood samples were processed to extract DNA and RNA before whole-genome sequencing, RNA sequencing, DNA methylation analysis, microbiome analysis, 16S ribosomal RNA gene sequencing, and proteomic analysis were performed on the plasma. Multiomics data will be combined with clinical data to produce sensitive and specific prognostic models for severity risk. Results: An initial demographic and clinical profile of the NI Cohort A has been completed. A total of 249 hospitalized patients and 270 nonhospitalized patients were recruited, of whom 184 (64.3%) were female, and the mean age was 45.4 (SD 13) years. High levels of comorbidity were evident in the hospitalized cohort, with cardiovascular disease and metabolic and respiratory disorders being the most significant (P<.001), grouped according to the International Classification of Diseases 10 codes. Conclusions: This study will provide a comprehensive opportunity to study the mechanisms of COVID-19 severity in recontactable participants.
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| 7. |
- Irwin, Darren
(author)
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Phylogeographic breaks without geographic barriers to gene flow
- 2002
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In: Evolution. - 1558-5646. ; 56:12, s. 2383-2394
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Journal article (peer-reviewed)abstract
- The spatial distribution of genetic markers can be useful both in estimating patterns of gene flow and in reconstructing biogeographic history, particularly when gene genealogies can be estimated. Genealogies based on nonrecombining genetic units such as mitochondrial and chloroplast DNA often consist of geographically separated clades that come into contact in narrow regions. Such phylogeographic breaks are usually assumed to be the result of long-term barriers to gene flow. Here I show that deep phylogeographic breaks can form within a continuously distributed species even when there are no barriers to gene flow. The likelihood of observing phylogeographic breaks increases as the average individual dispersal distance and population size decrease. Those molecular markers that are most likely to show evidence of real geographic barriers are also most likely to show phylogeographic breaks that formed without any barrier to gene flow. These results might provide an explanation as to why some species, such as the greenish warblers (Phylloscopus trochiloides), have phylogeographic breaks in mitochondrial or chloroplast DNA that do not coincide with sudden changes in other traits.
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| 8. |
- Irwin, Darren, et al.
(author)
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Speciation in a ring
- 2001
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 409:6818, s. 333-337
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Journal article (peer-reviewed)abstract
- The evolutionary divergence of a single species into two has never been directly observed in nature, primarily because speciation can take a long time to occur. A ring species, in which a chain of intergrading populations encircles a barrier and the terminal forms coexist without interbreeding, provides a situation in which variation in space can be used to infer variation in time(1-3). Here we reconstruct the pathway to speciation between two reproductively isolated forms of greenish warbler (Phylloscopus trochiloides). These two taxa do not interbreed in central Siberia but are connected by a long chain of intergrading populations encircling the Tibetan Plateau to the south(4). Molecular data and climatic history imply that the reproductively isolated taxa came into contact following expansions northward around the western and eastern sides of the plateau. Parallel selection pressures for increased song complexity during the northward expansions have been accompanied by divergence in song structure. Playback experiments show that the two Siberian forms do not recognize each other's songs. Our results show how gradual divergence in a trait involved in mate choice leads to the formation of new species.
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| 9. |
- Åkesson, Susanne, et al.
(author)
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Blowfly Trypocalliphora braueri (Diptera: Calliphoridae) larvae infestation in willow warblers Phylloscopus trochilus breeding in a hybrid zone.
- 2002
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In: Ornis Svecica. - 1102-6812. ; 12:1-2, s. 83-88
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Journal article (other academic/artistic)abstract
- We examined the occurrence of blowfly larvae Trypocalliphora brauneri in Swedish willow warbler Phylloscopus trochilus nestlings at three nearby breeding sites in Central Sweden. The occurrence of parasites was examined in nestlings by visual inspection during ringing. Larvae were encapsulated in the wings, head, neck, or the sides of the body of the nestlings and caused large swellings. Some of the larvae had already left the site of burrowing by an opening in the skin that was visible as a dark crater surrounded by dry skin. Tissue near the encapsulated larvae was swollen and showed clear symptoms of inflammation, in some cases causing deformation of wings. We observed parasites at two of the three sites in 5 out of a total of 36 nests ( 14%) in two years, corresponding to 20 (9.6%) out of 208 nestlings inspected. In nests with parasites 74.1% of the chicks were infested, each containing one to five parasites. No nestlings were found dead in the nests at the date of inspection.
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