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Publications (148)
We have studied the inheritance of mitochondria in Pelargonium section Ciconium using 36 interspecific crosses generated. We designed KASP markers targeting four mitochondrial loci, belonging to the mitomes of four main crossing parents, enabling tracking the transmission of each mitome in the crosses. These markers discriminate between an individu...
We have studied the inheritance of mitochondria in Pelargonium section Ciconium using interspecific crosses. We generated 36 different interspecific crosses. We designed KAPS markers targeting four individual mitochondrial markers, belonging to the four main crossing parents, that discriminate between an individual species and the other section Cic...
Cyto-Nuclear Incompatibility (CNI), in which there is a mismatch in the interaction between organelles and nucleus, impacts plant species evolution as it has a direct effect on the fitness of plants. It can reduce fertility and/or result in bleached plants devoid of functional chloroplasts. Understanding the processes leading to CNI could help to i...
Background and aims:
The Lythraceae are a mainly subtropical to tropical family of the order Myrtales with 28 currently accepted genera and approximately 600 species. There is currently no well-supported phylogenetic and biogeographical hypothesis of the Lythraceae incorporating all currently accepted genera, which we sought to provide.
Methods:...
Jongkindia, a small tree species endemic to a local area in southeast Liberia, is described as a new monotypic genus of Passifloraceae sens. lat. Its only species Jong-kindia mulbahii combines floral characteristics of the Turneraceae and fruit characteristics of the Passifloraceae s.s. (or subfamily Passifloroideae in APG) and can therefore be reg...
This study generated and analyzed complete plastome and internal transcribed spacer (ITS) data of 46 Lactuca species, 13 African endemic (AE) Lactuca species, and 15 species from eight related genera in Lactucinae. The new plastome and nuclear ITS sequences were then used to reconstruct the phylogenetic relationships of Lactuca species. The whole-p...
Brassica oleracea displays enormous phenotypic variation, including vegetables like cabbage, broccoli, cauliflower, kohlrabi, kales etc. Its domestication has not been clarified, despite several genetic studies and investigations of ancient literature. We used 14 152 high-quality SNP markers for population genetic studies and species-tree estimatio...
The repetitive part of the genome (the 'repeatome') contains a wealth of often overlooked information that can be used to resolve phylogenetic relationships and test evolutionary hypotheses for clades of related plant species such as Pelargonium. We have generated genome skimming data for 18 accessions of Pelargonium section Ciconium and one outgro...
The genetics underlying Cyto-Nuclear Incompatibility (CNI) was studied in Pelargonium interspecific hybrids. We created hybrids of 12 closely related crop wild relatives (CWR) with the ornamental P. × hortorum. Ten of the resulting 12 (F1) interspecific hybrids segregate for chlorosis suggesting biparental plastid inheritance. The segregation ratio...
The consequences of the Cretaceous-Paleogene (K-Pg) boundary (KPB) mass extinction for the evolution of plant diversity remain poorly understood, even though evolutionary turnover of plant lineages at the KPB is central to understanding assembly of the Cenozoic biota. The apparent concentration of whole genome duplication (WGD) events around the KP...
Background
Variation in floral shapes has long fascinated biologists and its modelling enables testing of evolutionary hypotheses. Recent comparative studies that explore floral shape have largely ignored 3D floral shape. We propose quantifying floral shape by using geometric morphometrics on a virtual3D model reconstructed from 2D photographical d...
Environmental DNA (eDNA) is used for monitoring the occurrence of freshwater organisms. Various studies show a relation between the amount of eDNA detected and target organism abundance, thus providing a potential proxy for reconstructing population densities. However, environmental factors such as water temperature and microbial activity are known...
Receptor like kinases represent the largest group of cell surface receptors in plants, of which monophyletic LRR‐RLK subfamily II is considered to contain the somatic embryogenesis receptor kinases (SERK), NSP interacting kinase (NIK) known to be involved in both developmental processes as well as cellular immunity in plants. In terms of phylogenet...
Natural history museums are unique spaces for interdisciplinary research and educational innovation. Through extensive exhibits and public programming and by hosting rich communities of amateurs, students, and researchers at all stages of their careers, they can provide a place-based window to focus on integration of science and discovery, as well...
Phylogenomics is increasingly used to infer deep‐branching relationships while revealing the complexity of evolutionary processes such as incomplete lineage sorting, hybridization/introgression and polyploidization. We investigate the deep‐branching relationships among subfamilies of the Leguminosae (or Fabaceae), the third largest angiosperm famil...
Background. Variation in floral shapes has long fascinated biologists and its modelling enables testing of evolutionary hypotheses. Recent comparative studies that explore floral shape have largely ignored 3D floral shape. We propose quantifying floral shape by using geometric morphometrics on a 3D model based on 2D photographical data and demonstr...
Background. Variation in floral shapes has long fascinated biologists and its modelling enables testing of evolutionary hypotheses. Recent comparative studies that explore floral shape have largely ignored 3D floral shape. We propose quantifying floral shape by using geometric morphometrics on a 3D model based on 2D photographical data and demonstr...
Mitochondria retain their own genome, a hallmark of their bacterial ancestry. Mitochondrial genomes (mtDNA) are highly diverse in size, shape and structure, despite their conserved function across most eukaryotes. Exploring extreme cases of mtDNA architecture can yield important information on fundamental aspects of genome biology. We discovered th...
Natural history museums are unique spaces for interdisciplinary research and for educational innovation. Through extensive exhibits and public programming and by hosting rich communities of amateurs, students, and researchers at all stages of their careers, they provide a place-based window to focus on integration of science and discovery, as well...
Natural history museums are unique spaces for interdisciplinary research and for educational innovation. Through extensive exhibits and public programming and by hosting rich communities of amateurs, students, and researchers at all stages of their careers, they provide a place-based window to focus on integration of science and discovery, as well...
The consequences of the Cretaceous-Paleogene (K-Pg) boundary (KPB) mass extinction for the evolution of plant diversity are poorly understood, even although evolutionary turnover of plant lineages at the KPB is central to understanding the assembly of the Cenozoic biota. One aspect that has received considerable attention is the apparent concentrat...
The predominantly South-African plant genus Pelargonium L'Hér. (Geraniaceae) displays remarkable morphological diversity, several basic chromosome numbers as well as high levels of organelle genomic rearrangements, and represents the 7th largest Cape Floristic Region clade. In this study, we reconstructed a phylogenetic tree based on 74 plastome ex...
Herbarium genomics, allowing testing of historic biological hypotheses in plant science, is a promising field mainly driven by recent advances in next-generation sequencing (NGS) technology. Herbarium collections represent an enormous botanical repository of both specimens and of phenotypic observations and locality data, of sometimes long-extinct...
Using massive parallel sequencing, which has become known as second-generation sequencing, some of the classic roadblocks to using herbarium DNA have been overcome. For instance, no longer is the degraded nature of most herbarium DNA preventing sequencing (because of blocking effective amplification). Instead, several kilobases of genomic sequence...
Lettuce (Lactuca sativa L.) belongs to the genus Lactuca L. and is an important vegetable worldwide. Over the past decades, there have been many controversies about the phylogeny of Lactuca species due to their complex and diverse morphological characters and insufficient molecular sampling. In this study we provide the most extensive molecular phy...
The phylogenetic relationships within Specklinia (Pleurothallidinae; Orchidaceae) and related genera are re-evaluated using Bayesian analyses of nrITS and chloroplast matK sequence data of a wide sampling of species. Specklinia is found paraphyletic in the DNA based trees, with species alternatively assigned to Muscarella proven distinct, monophyle...
Background – Botanical exploration of the Sapo National Park in Liberia resulted in the discovery of a new species, which, after DNA investigation, was identified as belonging to Soyauxia of the small family Peridiscaceae.
Methods – Normal practices of herbarium taxonomy and DNA sequence analysis have been applied. All the relevant herbarium mater...
Herbarium genomics is proving promising as next-generation sequencing approaches are well suited to deal with the usually fragmented nature of archival DNA. We show that routine assembly of partial plastome sequences from herbarium specimens is feasible, from total DNA extracts and with specimens up to 146 years old. We use genome skimming and an a...
Abstract—
Rinorea is a pantropical genus of shrubs and small trees within the family Violaceae. The genus is particularly diverse in Africa where species are ecologically important as they are often abundant or even dominant in particular forest types and act as larval
host plants for highly specialized Cymothoe butterflies. Despite their importanc...
Next Generation Sequencing (NGS) may enable estimating relationships among genotypes using allelic variation of multiple nuclear genes simultaneously. We explored the potential and caveats of this strategy in four genetically distant Lilium cultivars to estimate their genetic divergence from transcriptome sequences using three approaches: POFAD (Ph...
We explored genetic variation by sequencing a selection of 84 tomato accessions and related wild species representative for the Lycopersicon, Arcanum, Eriopersicon, and Neolycopersicon groups which has yielded a huge amount of precious data on sequence diversity in the tomato clade. Three new reference genomes were reconstructed to support our comp...
The Annonaceae includes cultivated species of economic interest and represents an important source of information for better understanding the evolution of tropical rainforests. In phylogenetic analyses of DNA sequence data that are used to address evolutionary questions, it is imperative to use appropriate statistical models. Annonaceae are cases...
Stelis, one of the largest genera within Pleuro- thallidinae, was recently recircumscribed to include a few hundred more species, most of which had previously been assigned to Pleurothallis. Here, a new phylogenetic anal- ysis of Stelis and closely related genera based on DNA sequences from nuclear ITS and chloroplast matK, based on a much larger s...
Unlocking the vast genomic diversity stored in natural history collections would create unprecedented opportunities for genome-scale evolutionary, phylogenetic, domestication and population genomic studies. Many researchers have been discouraged from using historical specimens in molecular studies because of both generally limited success of DNA ex...
Percentage, mean and maximum read coverage over all nucleotide positions for chromosomes, scaffolds or linkage groups (LG).
(DOCX)
Average nucleotide mis-incorporation rates (substitutions per base) observed in fresh and collection DNA.
(DOCX)
Integrity of herbarium DNA. Top, DNA extracts from L. anagyroides fresh (A) and herbarium (B), A. thaliana herbarium (C) and fresh (D), L. tulipifera herbarium (E) and fresh (F), and 1 kb Plus DNA Ladder (Invitrogen), after electrophoresis on 0.8% agarose gels. Bottom, herbarium DNA extracts of A. bisporus (G), P. ostreatus (H) and L. bicolor (I),...
ANOVA on nucleotide mis-incorporation rates for each of the six nucleotide substitution types.
(DOCX)
Best BLASTx hits of CDS regions with high number of SNPs or indels.
(DOCX)
Specimen information.
(DOCX)
Genotyping and total number of SNPs and indels in coding sequences (CDS).
(DOCX)
Cannabaceae includes ten genera that are widely distributed in tropical to temperate regions of the world. Because of limited taxon and character sampling in previous studies, intergeneric phylogenetic relationships within this family have been poorly resolved. We conducted a molecular phylogenetic study based on four plastid loci (atpB-rbcL, rbcL,...
Extant clades may differ greatly in their species richness, suggesting differential rates of species diversification.
Based on phylogenetic trees, it is possible to identify potential correlates of such differences. Here, we examine
species diversification in a clade of 82 tropical African forest butterfly species (Cymothoe), together with its
mono...
1. Plant organ biomass partitioning has been hypothesized to be driven by resources, such that species from drier environments allocate more biomass to roots than species from wetter environments to access water at greater soil depths. In savanna systems, fire may select for greater allocation to root biomass, especially in humid environments where...
Herbarium collections are potentially an enormous resource for DNA studies, but the use of herbarium specimens in molecular studies has thus far been slowed down by difficulty in obtaining amplifiable DNA. Here we compare a set of commercially available DNA extraction protocols and their performance in terms of DNA purity and yield, and PCR amplifi...
Details of the experimentally dried herbarium samples.
(DOC)
Details of DNA extraction protocols used.
(DOC)
Details of the herbarium samples used in the study.
(DOC)
Most fungal plant pathogens secrete effector proteins during pathogenesis to manipulate their host's defense and promote disease. These are so highly diverse in sequence and distribution, they are essentially considered as species-specific. However, we have recently shown the presence of homologous effectors in fungal species of the Dothideomycetes...
Recently diverged species are challenging for identification, yet they are frequently of special interest scientifically as well as from a regulatory perspective. DNA barcoding has proven instrumental in species identification, especially in insects and vertebrates, but for the identification of recently diverged species it has been reported to be...
Relative method performance based on simulated data for all species. Boxplots of query identification success (N = 300) of six methods that were applied to ‘recently diverged’ species in simulated query data sets. NJ = neighbor joining, PAR = parsimony, NN = nearest neighbor. Success scores not significantly different in post-hoc pairwise Wilcoxon...
Influence of divergence time on species identification success per method compared.
(PDF)
Simulated ultrametric species tree. Tree with 50 species simulated under the Yule model and with a total tree depth of 1 million generations. Terminal branches subtending species considered as ‘recently diverged’ are in red, those subtending species considered as ‘old’ are in blue.
(TIF)
Method performance based on simulated data for all species.
(PDF)
Results for all 112 species represented by 5 or more sequences in the Cypraeidae empirical data set.
(PDF)
Influence of effective population size (
Ne
) on species identification success per method compared.
(PDF)
Results for all 15 species represented by 5 or more sequences in the
Drosophila
empirical data set.
(PDF)
Results for all 35 species represented by 5 or more sequences in the
Inga
empirical data set.
(PDF)
Most fungal plant pathogens secrete effector proteins during pathogenesis to manipulate their host’s defense and promote disease. These are so highly diverse in sequence and distribution, they are essentially considered as species-specific. However, we have recently shown the presence of homologous effectors in fungal species of the Dothideomycetes...
1. Plant organ biomass partitioning has been hypothesized to be driven by resources, such that species from drier environments allocate more biomass to roots than species from wetter environ-ments to access water at greater soil depths. In savanna systems, fire may select for greater alloca-tion to root biomass, especially in humid environments whe...
Plant specimens, specimen information and mean DNA yield.
(DOCX)
Real-time PCR primers and performance of standard curves.
(DOCX)
Titanium fusion primers used for 454-sequencing.
(DOCX)
Mean DNA yield and mean gene copy numbers for plastid, mitochondrial and nuclear DNA regions.
(DOCX)
PCR primers and corresponding amplification targets.
(DOCX)
Copy numbers of chloroplast, mitochondrial and nuclear gene amplicons in fresh and herbarium tissues.
(DOCX)
DNA extraction gel images.
(DOCX)
ANOVA on average number of miscoding lesions (per 106 total nucleotides) for each substitution type across fresh and herbarium DNA. Separate analyses were performed for plastid, mitochondrial and nuclear DNA.
(DOCX)
Dried plant herbarium specimens are potentially a valuable source of DNA. Efforts to obtain genetic information from this source are often hindered by an inability to obtain amplifiable DNA as herbarium DNA is typically highly degraded. DNA post-mortem damage may not only reduce the number of amplifiable template molecules, but may also lead to the...
Molecular phylogenetic trees with reconstructed shifts in geographic distribution and flowering patterns (flowering durations and flowering midpoint) indicated. Unless otherwise indicated, shifts in flowering patterns are in the direction consistent with past climatic change; shifts in flowering midpoint are from the summer towards the spring, and...
Table illustrating the degree of shift in flowering phenology in the eighteen Cape clades sampled. Mid-month flowering midpoint character states are indicated by an abbreviation for the month in question, while character states at the boundary between two months are indicated by those two month abbreviations separated by a hyphen. Flowering duratio...
The best documented survival responses of organisms to past climate change on short (glacial-interglacial) timescales are distributional shifts. Despite ample evidence on such timescales for local adaptations of populations at specific sites, the long-term impacts of such changes on evolutionary significant units in response to past climatic change...
Het herkennen van biologische soorten aan de hand van een gestandaardiseerde DNA-barcode heeft de laatste tijd een enorme vlucht genomen. Gedreven door aan de ene kant de biodiversiteitscrises en de mogelijke global change, en aan de andere kant zowel razendsnelle technologische vooruitgang als ook het vooruitzicht dat niet genoeg klassieke taxonom...
Brassicaceae is an important family at both the agronomic and scientific level. The family not only includes several model species, but it is also becoming an evolutionary model at the family level. However, resolving the phylogenetic relationships within the family has been problematic, and a large-scale molecular phylogeny in terms of generic sam...
Butterflies of the Afrotropical genus Cymothoe are characterised by sexual dimorphism. Females of the most common species of the genus, Cymothoe caenis Drury, occur in many different forms in the equatorial zone, while only a single form is present west of the Niger Delta in Nigeria, raising the question as to whether the two populations need taxon...
