Eleanor F. Miller

Eleanor F. Miller
Imperial College London | Imperial · National Heart and Lung Institute

Doctor of Philosophy

About

36
Publications
1,059
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
44
Citations
Introduction
We live in an era of significant environmental and climatic change. Concerningly, this rapid rate of change stresses species across the globe, forcing them to adapt to new biotic and abiotic dynamics. To understand how species and ecosystems might cope under different climate scenarios we can explore how they have responded to rapid environmental change in the past. To that end, I’m interested in how populations have changed through evolutionary time.

Publications

Publications (36)
Preprint
Full-text available
Extensive sequencing of modern and ancient human genomes has revealed that contemporary populations can be explained as the result of recent mixing of a few distinct ancestral genetic lineages ¹ . But the small number of aDNA samples that predate the Last Glacial Maximum means that the origins of these lineages are not well understood. Here, we cir...
Article
Full-text available
During the Quaternary, large climate oscillations impacted the distribution and demography of species globally. Two approaches have played a major role in reconstructing changes through time: Bayesian Skyline Plots (BSP), which reconstruct population fluctuations based on genetic data, and Species Distribution Models, which allow us to back‐cast th...
Preprint
Full-text available
During the glacial periods of the Pleistocene, swathes of the Northern Hemisphere were covered by ice sheets, tundra and permafrost leaving large areas uninhabitable for temperate and boreal species. The glacial refugia paradigm proposes that, during glaciations, species living in the Northern Hemisphere were forced southwards, forming isolated, in...
Article
Full-text available
Background Today an unprecedented amount of genetic sequence data is stored in publicly available repositories. For decades now, mitochondrial DNA (mtDNA) has been the workhorse of genetic studies, and as a result, there is a large volume of mtDNA data available in these repositories for a wide range of species. Indeed, whilst whole genome sequenci...
Preprint
Full-text available
Today an unprecedented amount of genetic sequence data is stored in publicly available repositories. For decades now, mitochondrial DNA (mtDNA) has been the workhorse of genetic studies, and as a result, there is a large volume of mtDNA data available in these repositories for a wide range of species. Indeed, whilst whole genome sequencing is an ex...
Preprint
Full-text available
During the Quaternary, large climate oscillations had profound impacts on the distribution, demography and diversity of species globally. Birds offer a special opportunity for studying these impacts because surveys of geographical distributions, publicly-available genetic sequence data, and the existence of species with adaptations to life in struc...
Data
Supplementary Figure 3. Neighbour-joining tree based on the similarity of EBSP profiles.
Data
Supplementary Figure 4. Global position of sampling sites with all profiles from each major region overlaid.
Data
Supplementary Figure 1. EBSPs of populations with the largest sample sizes from each of the four major regions.
Article
Full-text available
The Neolithic transition has led to marked increases in census population sizes across the world, as recorded by a rich archaeological record. However, previous attempts to detect such changes using genetic markers, especially mitochondrial DNA (mtDNA), have mostly been unsuccessful. We use complete mtDNA genomes from over 1700 individuals, from th...
Article
Full-text available
Species diversity varies greatly across the different taxonomic groups that comprise the Tree of Life (ToL). This imbalance is particularly conspicuous within angiosperms, but is largely unexplained. Seed mass is one trait that may help clarify why some lineages diversify more than others because it confers adaptation to different environments, whi...
Data
Angiosperm phylogenetic tree collapsed to monophyletic clades of ≤6000 species. The name of one representative species per clade is shown, and the numbers in parentheses indicate the number of species included in each clade. The BAMM analyses were carried out for six monophyletic clades (shown in red, yellow, green, blue, dark blue and pink) and on...
Data
Phylogenetic tree of 13,577 angiosperm species with branch colours indicating the rate of seed mass evolution estimated with BAMM. Branches were scaled by speciation rate as determined by a BAMM analysis on a larger 19,703 tree. (TIF)
Data
Prior and posterior distribution of the number of rate shifts in BAMM. a) the speciation/extinction and b) phenotypic evolution analyses for expectedNumberOfShifts = 25, 50 and 100 and 250. The analyses in the main text were carried out with expectedNumberOfShifts = 50 for both speciation/extinction and phenotypic evolution analyses. (TIF)
Data
Comparison of the speciation rates at the tip of the tree obtained with the complete Zanne tree (29,703 species) and the seed size filtered tree (13,577 species). The dotted line represents the 1:1 reference line. (TIF)
Data
Correlation of speciation with seed mass and seed mass rate of evolution in the clade-based analysis only considering congeneric species. (a) PGLS slope of the relationship of speciation rate—estimated with the method-of-moments estimator—with mean clade seed mass across 10 time slices. The size of the circles represents the number of clades in eac...
Data
Correlation between speciation rate and rate of seed size evolution in a random sample of the BAMM posterior. The dotted line represents the Spearman correlation (ρ = 0.47, p-value < 0.001). (TIF)
Data
Type I error analysis. We estimated the type I error rate of our analysis by simulating neutral traits on the angiosperm phylogenetic tree. We performed 1,000 simulations and then ran 1,000 STRAPP tests with each simulated dataset. We estimated the corresponding p-values for the association between traits and diversification and calculated the type...
Data
Correlations between mean clade seed mass and speciation rate (estimated with RPANDA) across time slices. (a) 0 to 2 million years (myr); (b) 2 to 4 myr; (c) 4 to 6 myr; (d) 6 to 8 myr; (e) 8 to 10 myr; (f) 10 to 12 myr; (g) 12 to 14 myr; (h) 14 to 16 myr; (i) 16 to 18 myr; and (j) 18 to 20 myr. The degrees of freedom (df) are equivalent to the num...
Data
Seed mass and its rate of evolution are associated with speciation in the clade-based analyses. (a) PGLS slope of the relationship between speciation rate (λ) from the method-of-moments estimator and the rate of seed mass evolution across 10 time slices. Circles are scaled to the number of clades in each time slice while colour indicates the signif...
Data
Proposed effects of seed mass and other life history traits on diversification. (Solid lines). Dashed lines indicate correlations between life history traits. Numbers indicate reference where the link is proposed. (TIF)
Data
Correlations between clade rate of seed size evolution and speciation rate (estimated with RPANDA) across time slices. (a) 0 to 2 million years (myr); (b) 2 to 4 myr; (c) 4 to 6 myr; (d) 6 to 8 myr; (e) 8 to 10 myr; (f) 10 to 12 myr; (g) 12 to 14 myr; (h) 14 to 16 myr; (i) 16 to 18 myr; and (j) 18 to 20 myr. The degrees of freedom (df) are equivale...
Data
Correlation of (a) rate of seed mass evolution and (b) seed mass with net diversification rate (r) estimated using RPANDA in the clade-based analysis. The strength of correlations is shown as PGLS slopes and was calculated using mean clade-level seed mass across 10 time slices. The size of the circles represents the number of clades in each time sl...
Data
Mean genus seed mass of strict annual (n = 214) and perennial (n = 793) genera. No significant difference between the means of the two groups was found when accounting for phylogeny (phylANOVA: p-value = 0.308, significance assessed with 1,000 random simulations). (TIF)
Data
RPANDA diversification models for the clade-based analyses. For each 2-million year (myr) time slice, we counted the number of clades where the best-fitting model was either i) birth-death model with constant λ (speciation) and μ (extinction) (lambda.cst.mu.cst); pure birth model with constant λ (lambda.cst.mu0); pure birth model with exponential λ...
Data
STRAPP correlations (rho) for 1,007 species of angiosperms with seed size, genome size (i.e., C-value), life cycle, height, woodiness data and rates of seed size, C-value and height evolution. Significant correlation are shown in bold and p-values are shown in parentheses. (DOCX)
Data
STRAPP correlations of diversification and phenotypic traits for 1,007 angiosperm species. The distribution of the absolute difference in the observed correlation minus the null correlation is plotted for each trait. The coloured dotted lines indicate the mean of that distribution, and the black dotted line indicates 0; a distribution with mean = 0...
Data
Phylogenetic tree of 353 angiosperm families with representatives in our analyses. The red bars indicate the levels of sampling for each family. (TIF)
Data
Correlation of mean speciation and mean phenotypic rates across all the branches of the angiosperm phylogenetic tree. The dotted line is the ordinary least squares regression (R2 = 0.31, p-value < 0.001). (TIF)
Data
Correlations between mean clade seed mass and speciation rate (estimated with the method-of-moments estimator) across time slices. (a) 0 to 2 million years (myr); (b) 2 to 4 myr; (c) 4 to 6 myr; (d) 6 to 8 myr; (e) 8 to 10 myr; (f) 10 to 12 myr; (g) 12 to 14 myr; (h) 14 to 16 myr; (i) 16 to 18 myr; and (j) 18 to 20 myr. (TIF)
Data
Correlations between clade rate of seed size evolution and speciation rate (estimated with the method-of-moments estimator) across time slices. (a) 0 to 2 million years (myr); (b) 2 to 4 myr; (c) 4 to 6 myr; (d) 6 to 8 myr; (e) 8 to 10 myr; (f) 10 to 12 myr; (g) 12 to 14 myr; (h) 14 to 16 myr; (i) 16 to 18 myr; and (j) 18 to 20 myr. (TIF)
Data
Correlations of seed size and other phenotypic traits. Trait values were obtained from a 1,007 species tree where all species had data for seed size, C-value and plant height. The values are the slopes of the PGLS regressions and asterisks denote statistically significant correlations (p-value < 0.05). (DOCX)
Data
Correlations of seed size rate of evolution and other phenotypic rates of evolution. Rate values were obtained from a 1,007 species tree where all species had data for seed size, C-value and plant height. The values are the slopes of the PGLS regressions and asterisks denote statistically significant correlations (p-value < 0.05). (DOCX)

Network

Cited By