Bernard E Pfeil

Bernard E Pfeil
University of Gothenburg | GU · Department of Biological & Environmental Sciences

Docent

About

129
Publications
28,579
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Introduction
Bernard E Pfeil currently works at the Department of Biological & Environmental Sciences, University of Gothenburg. Bernard does research in Systematics (Taxonomy) and Evolutionary Biology.

Publications

Publications (129)
Article
Full-text available
Background The great diversity in plant genome size and chromosome number is partly due to polyploidization (i.e. genome doubling events). The differences in genome size and chromosome number among diploid plant species can be a window into the intriguing phenomenon of past genome doubling that may be obscured through time by the process of diploid...
Article
Full-text available
Human induced environmental change may require rapid adaptation of plant populations and crops, but the genomic basis of environmental adaptation remain poorly understood. We analyzed polymorphic loci from the perennial crop Medicago sativa (alfalfa or lucerne) and the annual legume model species M. truncatula to search for a common set of candidat...
Preprint
Full-text available
Background: The great diversity in plant genome size and chromosome number is partly due to polyploidization (i.e., genome doubling events). The differences in genome size and chromosome number among diploid plant species can be a window into the intriguing phenomenon of past genome doubling that may be obscured through time by the process of diplo...
Preprint
Full-text available
Background: The great diversity in plant genome size and chromosome number is partly due to polyploidization (i.e., genome doubling events). The differences in genome size and chromosome number among diploid plant species can be a window into the intriguing phenomenon of past genome doubling that may be obscured through time by the process of diplo...
Preprint
Full-text available
Background: The great diversity in plant genome size and chromosome number is partly due to polyploidization (i.e. genome doubling events). The differences in genome size and chromosome number among diploid plant species can be a window into the intriguing phenomenon of past genome doubling that may be obscured through time by the process of diploi...
Preprint
Full-text available
Background: The great diversity in plant genome size and chromosome number is partly due to polyploidization (i.e. genome doubling events). The differences in genome size and chromosome number among diploid plant species can be a window into the intriguing phenomenon of past genome doubling that may be obscured through time by the process of diploi...
Article
Full-text available
Premise: Although hybridization has played an important role in the evolution of many plant species, phylogenetic reconstructions that include hybridizing lineages have been historically constrained by the available models and data. Restriction-site-associated DNA sequencing (RADseq) has been a popular sequencing technique for the reconstruction o...
Article
Full-text available
Building the Tree of Life (ToL) is a major challenge of modern biology, requiring advances in cyberinfrastructure, data collection, theory, and more. Here, we argue that phylogenomics stands to benefit by embracing the many heterogeneous genomic signals emerging from the first decade of large-scale phylogenetic analysis spawned by high-throughput s...
Article
Full-text available
Background: Whole genome duplication plays a central role in plant evolution. There are two main classes of polyploid formation: autopolyploids which arise within one species by doubling of similar homologous genomes; in contrast, allopolyploidy (hybrid polyploidy) arise via hybridization and subsequent doubling of nonhomologous (homoeologous) gen...
Preprint
Although hybridization has played an important role in the evolution of many species, phylogenetic reconstructions that include hybridizing lineages have been historically constrained by the available models and data. Recently, the combined development of high-throughput sequencing and evolutionary network models offer new opportunities for phyloge...
Article
Full-text available
Background Current evidence suggests that for more robust estimates of species tree and divergence times, several unlinked genes are required. However, most phylogenetic trees for non-model organisms are based on single sequences or just a few regions, using traditional sequencing methods. Techniques for massive parallel sequencing or next generati...
Data
DNA sequence alignment with loops down-weighted. The file contains the chloroplast sequence alignment and a Mr Bayes analysis block that excludes poorly aligned sites, as well as down-weighting the inverted loop regions by excluding all but one character in each inverted loop.
Data
DNA sequence alignment with loops. The file contains the chloroplast sequence alignment and a Mr Bayes analysis block that excludes poorly aligned sites, but includes the entire inverted loop regions.
Article
Full-text available
Advances in high-throughput sequencing techniques now allow relatively easy and affordable sequencing of large portions of the genome, even for non-model organisms. Many phylogenetic studies reduce costs by focusing their sequencing efforts on a selected set of targeted loci, commonly enriched using sequence capture. The advantage of this approach...
Preprint
Full-text available
Advances in high-throughput sequencing techniques now allow relatively easy and affordable sequencing of large portions of the genome, even for non-model organisms. Many phylogenetic studies reduce costs by focusing their sequencing efforts on a selected set of targeted loci, commonly enriched using sequence capture. The advantage of this approach...
Article
Full-text available
Several studies have demonstrated the contribution of northern immigrants to the flora of the tropical Andes-the world's richest and most diverse biodiversity hotspot. However, much less is known about the biogeographic history and diversification of Andean groups with southern origins, although it has been suggested that northern and southern grou...
Data
Matrices of dispersal and areas allowed used in BioGeoBEARS for each slice of time (0–30, 30–40 and 40–90 Mya)
Data
Traitgram of ancestral states of Gunnera climatic niche Black lines correspond to a projection of the phylogenetic tree in a space defined by the bioclimatic variable mean annual temperature and annual precipitation.
Data
Results from model comparison of climatic niche evolution
Data
DNA sequences associated with this manuscript that are deposited in GenBank
Data
Morphological diversity of Gunnera. (A) G. manicata (subgenus Panke), (B) G. insignis (subgenus Panke), (C) G. perpensa (subgenus Gunnera), (D) G. magellanica (subgenus Misandra), (E) G. dentata (subgenus Milligania), (F) G. herteri (subgenus Ostenigunnera). Photos: A. Antonelli.
Preprint
Full-text available
Background. Current evidence suggests that for more robust estimates of species tree and divergence times, several unlinked genes are required. However, most phylogenetic trees for non-model organisms are based on single sequences or just a few regions, using traditional sequencing methods. Techniques for massive parallel sequencing or Next Generat...
Preprint
Full-text available
Background. Current evidence suggests that for more robust estimates of species tree and divergence times, several unlinked genes are required. However, most phylogenetic trees for non-model organisms are based on single sequences or just a few regions, using traditional sequencing methods. Techniques for massive parallel sequencing or Next Generat...
Preprint
Full-text available
Building the Tree of Life (ToL) is a major challenge of modern biology, requiring major advances in cyberinfrastructure, data collection, theory, and more. Here, we argue that phylogenomics stands to benefit by embracing the many heterogeneous genomic signals emerging from the first decade of large-scale phylogenetic analysis spawned by High-throug...
Preprint
Full-text available
Building the Tree of Life (ToL) is a major challenge of modern biology, requiring major advances in cyberinfrastructure, data collection, theory, and more. Here, we argue that phylogenomics stands to benefit by embracing the many heterogeneous genomic signals emerging from the first decade of large-scale phylogenetic analysis spawned by High-throug...
Preprint
Full-text available
Building the Tree of Life (ToL) is a major challenge of modern biology, requiring major advances in cyberinfrastructure, data collection, theory, and more. Here, we argue that phylogenomics stands to benefit by embracing the many heterogeneous genomic signals emerging from the first decade of large-scale phylogenetic analysis spawned by High-throug...
Preprint
Full-text available
Building the Tree of Life (ToL) is a major challenge of modern biology, requiring major advances in cyberinfrastructure, data collection, theory, and more. Here, we argue that phylogenomics stands to benefit by embracing the many heterogeneous genomic signals emerging from the first decade of large-scale phylogenetic analysis spawned by next-genera...
Article
Full-text available
We give an overview of recently developed methods to reconstruct phylog-enies of taxa that include allopolyploids that have originated in relatively recent times-in other words, taxa for which at least some of the parental lineages of lower ploidy levels are not extinct and for which ploidy information is clearly shown by variation in chromosome co...
Preprint
Full-text available
Several studies have demonstrated the contribution of northern immigrants to the flora of the tropical Andes – the world’s “hottest” biodiversity hotspot. However, much less is known about the biogeographic history and diversification of Andean groups with southern origins, although it has been suggested that northern and southern groups have contr...
Preprint
Full-text available
Several studies have demonstrated the contribution of northern immigrants to the flora of the tropical Andes – the world’s “hottest” biodiversity hotspot. However, much less is known about the biogeographic history and diversification of Andean groups with southern origins, although it has been suggested that northern and southern groups have contr...
Article
Full-text available
Recombination events among distinct alleles complicate phylogenetic estimation. Various in vivo and in vitro processes can bring distinct alleles into the same genome to then undergo recombination, which may subsequently mislead phylogenetic inference if not assessed properly. Among the processes bringing divergent alleles together, hybridisation i...
Article
Two new species of Pavonia subgenus Goetheoides are described (Pavonia gerleniae and Pavonia macrobracteolata) from the wet coastal forests of eastern Brazil. This increases the number of species in the subgenus to 30, which is considered a high level of diversity for arborescent species in this geographically and ecologically limited area. We pres...
Article
Several well-documented evolutionary processes are known to cause conflict between species level phylogenies and gene level phylogenies. Three of the most challenging processes for species tree inference are incomplete lineage sorting, hybridisation and gene duplication, which may result in unwarranted comparisons of paralogous genes. Several exist...
Article
Although hybridisation through genome duplication is well known, hybridisation without genome duplication (homoploid hybrid speciation, HHS) is not. Few well-documented cases have been reported. A possible instance of HHS in Medicago prostrata Jacq. was suggested previously, based on only two genes and one individual. We tested whether this species...
Article
Full-text available
In natural habitats, plants frequently experience rapid changes in the intensity of sunlight. To cope with these changes and maximize growth, plants adjust photosynthetic light utilization in electron transport and photoprotective mechanisms. This involves a proton motive force (PMF) across the thylakoid membrane, postulated to be affected by unkno...
Data
Supplementary Figures 1 - 22, Supplementary Tables 1 - 3 and Supplementary References
Data
Expanded version of Supplementary Figure 2 and MAFTT alignment.
Article
Full-text available
The species phylogeny of Medicago L. (Leguminosae) remains unresolved, as there is significant incongruence between the published gene phylogenies. Here, we compare six of these gene phylogenies of Medicago, inferred from unlinked loci from the nuclear, chloroplast and mitochondrial genomes. Data from all loci were re-analysed, including gap-coding...
Article
Full-text available
The phylogeny of Rutaceae subfamily Aurantioideae has previously been estimated only using plastid and repetitive nuclear sequences. We added sequences of two low copy nuclear loci to allow further diagnosis of phenomena that may mislead phylogenetic inference. After testing for patterns expected under recombination, positive selection, and hybridi...
Article
Full-text available
There is a rising awareness that species trees are best inferred from multiple loci while taking into account processes affecting individual gene trees, such as substitution model error (failure of the model to account for the complexity of the data) and coalescent stochasticity (presence of incomplete lineage sorting). Although most studies have b...
Article
Full-text available
Next-generation sequencing technology has increased the capacity to generate molecular data for plant biological research, including phylogenetics, and can potentially contribute to resolving complex phylogenetic problems. The evolutionary history of Medicago L. (Leguminosae: Trifoliae) remains unresolved due to incongruence between published phylo...
Article
One new order, one new family, and one new combination are presented, as the result of molecular phylogenetic analyses. The new order Stereopsidales and the new family Stereopsidaceae are described incorporating Stereopsis radicans and S. globosa, formerly Clavulicium globosum. We show that not only do these species represent an old overlooked line...
Article
Full-text available
Erysimum includes 150–350 species distributed in the Northern Hemisphere, with Eurasia being the centre of greatest diversity. It is well known for its taxonomic complexity as a result of overlapping morphological characters. We present the first densely sampled phylogenetic analysis of Erysimum using internal transcribed spacer (ITS) DNA sequences...
Article
Full-text available
Despite being one of the larger genera of Caryophyllaceae with about 60 cushion-forming subshrubby species, Acanthophyllum is represented poorly in previous molecular phylogenetic studies. The genus is an important component of the subalpine steppe flora in Central to Southwest Asia. Although the placement of Acanthophyllum in the tribe Caryophylle...
Article
Full-text available
One new order, one new family, and one new combination are presented, as the result of molecular phylogenetic analyses. The new order Stereopsidales and the new family Stereopsidaceae are described incorporating Stereopsis radicans and S. globosa, formerly Clavulicium globosum. We show that not only do these species represent an old overlooked line...