Kai F Müller

Kai F Müller
University of Münster | WWU · Institute for Evolution and Biodiversity

Professor Dr.

About

195
Publications
32,268
Reads
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8,908
Citations
Additional affiliations
May 2009 - present
University of Münster
Position
  • Professor (Full)
May 2009 - present
University of Münster
Position
  • Professor (Full)
October 2006 - April 2009
University of Bonn
Position
  • Professor (Assistant)
Education
February 2006 - September 2006
Pennsylvania State University
Field of study
  • Botany
December 2001 - December 2005
University of Bonn
Field of study
  • Botany
September 1996 - January 2001

Publications

Publications (195)
Article
Full-text available
The recently described Linderniaceae are a monophyletic group that emerged in the course of the disintegration of the Scrophulariaceae in the last years. First molecular studies sampled only a small fraction of the genera assigned to the Linderniaceae, but later Lindernia was shown to be non-monophyletic. Here we used a plastid trnK/matK sequence d...
Article
Full-text available
Carnivorous Lentibulariaceae exhibit the most sophisticated implementation of the carnivorous syndrome in plants. Their unusual lifestyle coincides with distinct genomic peculiarities such as the smallest angiosperm nuclear genomes and extremely high nucleotide substitution rates across all genomic compartments. Here, we report the complete plastid...
Article
Full-text available
Nonphotosynthetic plants possess strongly reconfigured plastomes attributable to convergent losses of photosynthesis and housekeeping genes, making them excellent systems for studying genome evolution under relaxed selective pressures. We report the complete plastomes of 10 photosynthetic and nonphotosynthetic parasites plus their nonparasitic sist...
Article
Full-text available
The lifestyle of parasitic plants is associated with peculiar morphological, genetic, and physiological adaptations that existing online plant-specific resources fail to adequately represent. Here, we introduce the Web Application for the Research of Parasitic Plants (WARPP) as an online resource dedicated to advancing research and development of p...
Article
In Zeiten wachsender Naturentfremdung und abnehmender Artenkenntnis können Exkursionen zur ökologischen Grundbildung beitragen. Im vorliegenden Beitrag wird ein Exkursionsmodul beschrieben, dessen Ziel es ist, angehenden Biologie-Lehrerinnen und -Lehrern die Kompetenzen zu vermitteln, die sie später für die Durchführung schulischer Exkursionen benö...
Article
Full-text available
Background: Today a variety of phylogenetic file formats exists, some of which are well-established but limited in their data model, while other more recently introduced ones offer advanced features for metadata representation. Although most currently available software only supports the classical formats with a limited metadata model, it would be...
Article
Besides their alleged therapeutic effects, mistletoes of the genus Viscum L. (Viscaceae) are keystone species in many ecosystems across Europe, Africa, Asia and Australia because of their complex faunal interactions. We here reconstructed the evolutionary history of Viscum based on plastid and nuclear DNA sequence data. We obtained a highly resolve...
Article
Iresine is a neotropical genus of the Amaranthaceae with most of the species diversity in Mexico and Mesoamerica. It has suffered a complex classification history with considerably diverging views on the genus concept. We have carried out a phylogenetic analysis of Iresine and allied genera using sequence data of combined plastid introns (including...
Poster
Full-text available
Phylogenetics, phylogenomics and related fields have become data-intensive due to increasingly cheaper high-throughput sequencing technologies, the digitization of large biological collections or data contributions from citizen science. An increasing number of computationally accessible methods for analyses that produce derived data, like phylogene...
Preprint
Full-text available
Besides their alleged therapeutic effects, mistletoes of the genus Viscum L. (Viscaceae) are keystone species in many ecosystems across Europe, Africa, Asia, and Australia because of their complex faunal interactions. We here reconstructed the evolutionary history of Viscum based on plastid and nuclear DNA sequence data. We obtained a highly resolv...
Article
Full-text available
Bladderworts (Utricularia, Lentibulariaceae, Lamiales) constitute the largest genus of carnivorous plants but only aquatic species (about one fifth of the genus) have so far been thoroughly studied as to their suction trap functioning. In this study, we comparatively investigated trap biomechanics in 19 Utricularia species to examine correlations b...
Article
Aims Taxon identification is an important step in many plant ecological studies. Its efficiency and reproducibility might greatly benefit from partly automating this task. Image-based identification systems exist, but mostly rely on hand-crafted algorithms to extract sets of features chosen a priori to identify species of selected taxa. In conseque...
Poster
Full-text available
In philosophy ontology is defined as the study of the nature and relations of being. Information sciences apply this concept to create naming conventions describing types, properties and interrelationships of certain entities. Ontologies aim to limit complexity and organize information. In phylogenetics they allow scientists to provide semantic inf...
Article
Full-text available
Geraniaceae are known for their unusual plastid genomes (plastomes), with the genus Pelargonium being most conspicuous with regard to plastome size and gene organization as judged by the sequenced plastomes of P. x hortorum and P. alternans. However, the hybrid origin of P. x hortorum and the uncertain phylogenetic position of P. alternans obscure...
Poster
Full-text available
TreeGraph 2 is a user friendly tree editor with the main focus on processing, visualizing and comparing phylogenetic trees carrying numerous annotations. Here, new features added since its initial publication in 2010 are presented. The ability to import and visualize probabilities for ancestral character states (e.g. by pie charts attached to inter...
Conference Paper
Collection and maintenance of biodiversity data is in need for automation. We present first results of an automated and model-free approach to the species identification from herbarium specimens kept in herbaria worldwide. Methodologically, our approach relies on standard methods for the detection and description of so-called interest points and th...
Poster
Full-text available
Today a variety of alignment and tree file formats exist, some of which well-established but limited in their data model, others more recently proposed offer advanced future-orientated features for metadata representation. Most phylogenetic and other bioinformatic software currently only supports one or few different formats, while supporting many...
Article
Full-text available
Because novel environmental conditions alter the selection pressure on genes or entire subgenomes, adaptive and nonadaptive changes will leave a measurable signature in the genomes, shaping their molecular evolution. We present herein a model of the trajectory of plastid genome evolution under progressively relaxed functional constraints during the...
Article
Biodiversity loss is mainly driven by human activity. While concern grows over the fate of hot spots of biodiversity, contemporary species losses still prevail in industrialized nations. Therefore, strategies were formulated to halt or reverse the loss, driven by evidence for its value for ecosystem services. Maintenance of the latter through conse...
Article
Full-text available
We present the model and implementation of a workflow that blazes a trail in systematic biology for the re-usability of character data (data on any kind of characters of pheno- and genotypes of organisms) and their additivity from specimen to taxon level. We take into account that any taxon characterization is based on a limited set of sampled indi...
Poster
Full-text available
TreeGraph 2 is a user friendly and widely used tree editor with the main focus on processing, visualizing and comparing phylogenetic trees carrying numerous annotations. Since its initial publication a number of features have been added. The ability to import and visualize probabilities for ancestral character states (as reconstructed by software p...
Conference Paper
Full-text available
We combine the conventional method of ex situ cultivation and the new molecular DNA-barcoding for the development of the new monitoring tool. With DNA-barcoding of the seed bench it should be possible to determine the current and potential or past plant diversity of a site on a fast, significant and cost-efficient way.
Poster
Full-text available
http://www2.ieb.uni-muenster.de/EvolBiodivPlants/en/Publications/ConferenceContribution?id=100872
Poster
Full-text available
http://www2.ieb.uni-muenster.de/EvolBiodivPlants/en/Publications/ConferenceContribution?id=100873
Article
Full-text available
Background and Aims Some species of Genlisea possess ultrasmall nuclear genomes, the smallest known among angiosperms, and some have been found to have chromosomes of diminutive size, which may explain why chromosome numbers and karyotypes are not known for the majority of species of the genus. However, other members of the genus do not possess ult...
Poster
Full-text available
Several applications currently developed in our group and by cooperators deal with multiple sequence alignments (MSA) or associated raw and meta data, and allow the user to view and edit these in a graphical user interface. Instead of implementing independent solutions for these different tasks, we decided to develop LibrAlign, a Java library provi...
Poster
Full-text available
With a growing number of alternative algorithms for automated multiple sequence alignment (MSA) and different strategies for manual alignment corrections it becomes more and more relevant to visualize the differences between alternative MSAs of the same data set. This allows the researcher to decide which alternative alignments to take into account...
Poster
Full-text available
Several applications currently developed in our group and by our cooperators deal with multiple sequence alignments (MSA) or associated raw and meta data, and allow the user to view and edit it in a graphical user interface (GUI). Instead of implementing independent solutions for these different tasks, we decided to create a library containing powe...
Conference Paper
Full-text available
Sideroxylon comprises about 70 tree and shrub species distributed worldwide (Pennington, 1991), including the well-known argan tree [S. spinosum L. (= Argania spinosa (L.) Skeels)] from Morocco. Sideroxylon canariense Leyens, Lobin & Santos (Figure 1) is a Canary Island endemic of conservation concern. It is considered as “critically endangered” on...
Article
Previous molecular phylogenetic studies of Pelargonium have remained inconclusive with respect to branching patterns of major infrageneric lineages, with the exception of a basalmost generic split that reflects chromosome length differences. Because of this and the lack of clearly distinguishing morphological characters, no subgeneric classificatio...
Article
Full-text available
Genetic diversity patterns of different populations were studied in Sideroxylon canariense, a Canary Island endemic of conservation concern. The species range is composed of a number of very small and isolated populations. Genetic variation of these populations was analyzed using: (1) inter simple sequence repeats (ISSR), a common fingerprinting me...
Poster
Full-text available
http://www2.ieb.uni-muenster.de/EvolBiodivPlants/en/Publications/ConferenceContribution?id=94531
Poster
See also: http://www2.ieb.uni-muenster.de/EvolBiodivPlants/en/Theses/Detail?id=0
Article
Recent phylogenetic analyses revealed a grade with Ranunculales, Sabiales, Proteales, Trochodendrales, and Buxales as first branching eudicots, with the respective positions of Proteales and Sabiales still lacking statistical confidence. As previous analyses of conserved plastid genes remain inconclusive, we aimed to use and evaluate a representati...
Article
The newly described monotypic genus Bardotia, with the new species B. ankaranensis from limestone tsingy in Northern Madagascar, and its differences from Radamaea and Sieversandreas are discussed. The phylogenetic positions of the genera Radamaea, Rhamphicarpa and Sieversandreas are investigated. Bardotia, Radamaea, Rhamphicarpa, and Sieversandreas...
Conference Paper
Non-photosynthetic angiosperms possess highly reduced plastid chromosomes compared to their autotrophic relatives. Deletions of photosynthesis-related genes as well as few housekeeping subunits display prominent convergences in several unrelated non-photosynthetic lineages. However, little is known about the steps of functional and structural genom...
Data
Full-text available
Phylogram of agt1 based on a Bayesian inference of full dataset containing cloned sequences. Phylogram from the Bayesian inference of the agt1 data set with relative substitution rates using the GTR+G+I model and posterior probabilities plotted above the branches. Clades are colored according to Figure 3. The applied data set comprises part I and p...
Data
Primers used for amplification and sequencing of both the nuclear and chloroplast markers applied in this study. Excel file listing primer sequences of the respective gene region that were used for both PCR and sequencing.
Data
Sequence statistics for the coding and non-coding regions for all markers in this study calculated with SeqState. This table provides information about the general characteristics of the coding, and non-coding parts of the study sequences for different sampling densities.
Data
Taxa used in the present study. Excel file listing the species used in this study including voucher information and GenBank accession numbers (provided upon final acceptance of manuscript). For detailed information of origin and collection sites see [49].
Data
Hotspots excluded, due to ambiguous homology assessments. Regions of uncertain sequence homology (hotspots) excluded from the different datasets. Positions are given equivalent to files downloadable from TreeBase.
Data
Results from topology tests. Excel file showing Shimodaira-Hasegawa (SH) test results of different topology/dataset combinations. Asterisk indicates a significant rejection (p ≤ 0.05) of the respective combination.
Article
Full-text available
The rapidly increasing number of available plant genomes opens up almost unlimited prospects for biology in general and molecular phylogenetics in particular. A recent study took advantage of this data and identified a set of nuclear genes that occur in single copy in multiple sequenced angiosperms. The present study is the first to apply genomic s...
Article
Full-text available
• The Cactaceae are a major New World plant family and popular in horticulture. Still, taxonomic units and species limits have been difficult to define, and molecular phylogenetic studies so far have yielded largely unresolved trees, so relationships within Cactaceae remain insufficiently understood. This study focuses on the predominantly epiphyti...
Article
Full-text available
This review bridges functional and evolutionary aspects of plastid chromosome architecture in land plants and their putative ancestors. We provide an overview on the structure and composition of the plastid genome of land plants as well as the functions of its genes in an explicit phylogenetic and evolutionary context. We will discuss the architect...
Article
We used random sequences to determine which alignment methods are most susceptible to aligning sequences so as to create artifactual resolution and branch support in phylogenetic trees derived from those alignments. We compared four alignment methods (progressive pairwise alignment, simultaneous multiple alignment of sequence fragments, local pairw...
Data
Table S1: Taxa, specimens and GenBank acession numbers for sequences used in the 5 gene analysis. Voucher information.
Data
Full-text available
Figure S2: Tree from rbcL analysis. Strict consensus of 100 MP bootstrap replicates performed.
Data
Full-text available
Figure S5: Tree from combined trnK/matK, trnL-F, rps16, rbcL, ndhF analysis. 100 bootstrap replicates performed.
Data
Full-text available
Figure S1: A comparison of decay values. Numbers above branches give decay values from nucleotide data matrix; numbers below branches that from nucleotides plus coded indels.
Data
Full-text available
Figure S3: Tree from ndhF analysis. Strict consensus of 100 MP bootstrap replicates performed.
Data
Full-text available
Figure S4: Tree from angiosperm-wide matK analysis of the Hilu et al. 2003 dataset plus our newly generated Hydrostachys sequence. Strict consensus of 100 MP bootstrap replicates performed.
Article
Full-text available
In the large angiosperm order Lamiales, a diverse array of highly specialized life strategies such as carnivory, parasitism, epiphytism, and desiccation tolerance occur, and some lineages possess drastically accelerated DNA substitutional rates or miniaturized genomes. However, understanding the evolution of these phenomena in the order, and clarif...
Article
Alignment of nucleotide and/or amino acid sequences is a fundamental component of sequence-based molecular phylogenetic studies. Here we examined how different alignment methods affect the phylogenetic trees that are inferred from the alignments. We used simulations to determine how alignment errors can lead to systematic biases that affect phyloge...