Andreas Franzke

Bio: Andreas Franzke is an academic researcher from Heidelberg University. The author has contributed to research in topics: Molecular phylogenetics & Brassicaceae. The author has an hindex of 19, co-authored 23 publications receiving 1738 citations. Previous affiliations of Andreas Franzke include University of Osnabrück.

Molecular phylogenetics, temporal diversification, and principles of evolution in the mustard family (Brassicaceae).

Abstract: Brassicaceae is an important family at both the agronomic and scientific level. The family not only inlcudes 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 sampling and number of genes is still lacking. In particular, the deeper relationships within the family, for example between the three major recognized lineages, prove particularly hard to resolve. Using a slow-evolving mitochondrial marker (nad4 intron 1), we reconstructed a comprehensive phylogeny in generic representation for the family. In addition, and because resolution was very low in previous single marker phylogenies, we adopted a supermatrix approach by concatenating all checked and reliable sequences available on GenBank as well as new sequences for a total 207 currently recognized genera and eight molecular markers representing a comprehensive coverage of all three genomes. The supermatrix was dated under an uncorrelated relaxed molecular clock using a direct fossil calibration approach. Finally, a lineage-through-time-plot and rates of diversification for the family were generated. The resulting tree, the largest in number of genera and markers sampled to date and covering the whole family in a representative way, provides important insights into the evolution of the family on a broad scale. The backbone of the tree remained largely unresolved and is interpreted as the consequence of early rapid radiation within the family. The age of the family was inferred to be 37.6 (24.2–49.4) Ma, which largely agrees with previous studies. The ages of all major lineages and tribes are also reported. Analysis of diversification suggests that Brassicaceae underwent a rapid period of diversification, after the split with the early diverging tribe Aethionemeae. Given the dates found here, the family appears to have originated under a warm and humid climate approximately 37 Ma. We suggest that the rapid radiation detected was caused by a global cooling during the Oligocene coupled with a genome duplication event. This duplication could have allowed the family to rapidly adapt to the changing climate.

Molecular evidence for bicontinental hybridogenous genomic constitution in Lepidium sensu stricto (Brassicaceae) species from Australia and New Zealand.

Abstract: Lepidium sensu stricto (s.s.) (Brassicaceae) (ca. 150 species) is distributed worldwide with endemic species on every continent. It is represented in Australia and New Zealand by 19 and seven native species, respectively. In the present study we used a nuclear ribosomal internal transcribed spacer (ITS) phylogeny in comparison with a cpDNA phylogeny to unravel the origin of Australian/ New Zealand species. Although phylogenetic relationships within Lepidium s.s. were not fully resolved, the cpDNA data were in agreement with a Californian origin of Lepidium species from Australia/New Zealand. Strongly conflicting signals between the cpand nuclear DNA phylogenetic analysis clearly indicated hybridogenous genomic constitution of Australian Lepidium s.s. species: All 18 studied Australian/New Zealand Lepidium s.s. species examined shared a Californian cpDNA type. While eleven Australian/New Zealand species appeared to harbor a Californian ITS type, a group of seven species shared a South African ITS type. This pattern is most likely explained by two trans-oceanic dispersals of Lepidium from California and Africa to Australia/New Zealand and subsequent hybridization followed by homogenization of the ribosomal DNA either to the Californian or South African ITS type in the two different lineages. Calibration of our molecular trees indicates a Pliocene/Pleistocene origin of Lepidium in Australia/New Zealand. Low levels of cpDNA and ITS sequence divergence and unresolved topologies within Australian/New Zealand species suggest a rapid and recent radiation of Lepidium after the hybridization event. This coincides with dramatic climatic changes in that geological epoch shaping the composition of the vegetation.

BrassiBase: Introduction to a Novel Knowledge Database on Brassicaceae Evolution

Abstract: The Brassicaceae family (mustards or crucifers) includes Arabidopsis thaliana as one of the most important model species in plant biology and a number of important crop plants such as the various Brassica species (e.g. cabbage, canola and mustard). Moreover, the family comprises an increasing number of species that serve as study systems in many fields of plant science and evolutionary research. However, the systematics and taxonomy of the family are very complex and access to scientifically valuable and reliable information linked to species and genus names and its interpretation are often difficult. BrassiBase is a continuously developing and growing knowledge database (http://brassibase.cos.uni-heidelberg.de) that aims at providing direct access to many different types of information ranging from taxonomy and systematics to phylo- and cytogenetics. Providing critically revised key information, the database intends to optimize comparative evolutionary research in this family and supports the introduction of the Brassicaceae as the model family for evolutionary biology and plant sciences. Some features that should help to accomplish these goals within a comprehensive taxonomic framework have now been implemented in the new version 1.1.9. A 'Phylogenetic Placement Tool' should help to identify critical accessions and germplasm and provide a first visualization of phylogenetic relationships. The 'Cytogenetics Tool' provides in-depth information on genome sizes, chromosome numbers and polyploidy, and sets this information into a Brassicaceae-wide context.

Arabidopsis family ties: molecular phylogeny and age estimates in Brassicaceae

Abstract: The Brassicaceae family is of great scientific interest because it contains the plant model organism Arabidopsis thaliana. Currently, contemporary plant research activities expand to other Brassicaceae taxa. Despite that, the phylogeny of this family is only partly understood. The present study deepens our understanding of a family-wide phylogeny by using two new approaches in phylogenetic family-wide research. We used a molecular marker from the mitochondrial genome and utilised a relaxed molecular dating method. Our data generally confirms a recent tribal alignment of Brassicaceae. We present for the first time a biogeographical scenario for the broad-scale Brassicaceae evolution. We suggest that Brassicaceae most likely evolved some 19 mya in or near the eastern Mediterranean region from a common ancestor of its sister family Cleomaceae. The early Brassicaceae formed a lineage adapted to more open/drier habitats than its capparoid progenitors. The early Brassicaceae evolution was very rapid and the radiation was most likely driven by climatic changes that created open habitats and the well-documented expansion of open grass-dominated ecosystems. Moreover, our dating suggests that the radiation events correlate with an ancient genome duplication in the early history of the family, which is evidenced by recent genomic studies.

Zinc in plants

Abstract: Zinc (Zn) is an essential component of thousands of proteins in plants, although it is toxic in excess. In this review, the dominant fluxes of Zn in the soil-root-shoot continuum are described, including Zn inputs to soils, the plant availability of soluble Zn(2+) at the root surface, and plant uptake and accumulation of Zn. Knowledge of these fluxes can inform agronomic and genetic strategies to address the widespread problem of Zn-limited crop growth. Substantial within-species genetic variation in Zn composition is being used to alleviate human dietary Zn deficiencies through biofortification. Intriguingly, a meta-analysis of data from an extensive literature survey indicates that a small proportion of the genetic variation in shoot Zn concentration can be attributed to evolutionary processes whose effects manifest above the family level. Remarkable insights into the evolutionary potential of plants to respond to elevated soil Zn have recently been made through detailed anatomical, physiological, chemical, genetic and molecular characterizations of the brassicaceous Zn hyperaccumulators Thlaspi caerulescens and Arabidopsis halleri.

Metal hyperaccumulator plants: a review of the ecology and physiology of a biological resource for phytoremediation of metal-polluted soils

Abstract: The concentrations in plant parts depend both on intrinsic and extrinsic factors and vary greatly for different species and for different metals. Responses by plant species to exposure to metalliferous soils can range from phytotoxicity to survival by exclusion, with only small elevations of metal concentration to survival with accumulated metal constituting a significant percentage of the plant dry matter. The importance of nonvascular transport through laticifers, for example, is also obscure. The extent to which secondary xylem tissues become a long-term repository for accumulated metals is not known. The high degree of endemism to metal-rich soils shown by hyperaccumulating taxa has been related to their survival. The success of many metallophytes in overcoming the adverse edaphic conditions is such that they can exist relatively free from competition. Metal hyperaccumulators have been recognized on the basis of concentrations of metals in leaf dry matter.

Comparative Evolutionary Analysis of Chalcone Synthase and Alcohol Dehydrogenase Loci in Arabidopsis, Arabis, and Related Genera (Brassicaceae)

Abstract: We analyzed sequence variation for chalcone synthase (Chs) and alcohol dehydrogenase (Adh) loci in 28 species in the genera Arabidopsis and Arabis and related taxa from tribe Arabideae. Chs was single-copy in nearly all taxa examined, while Adh duplications were found in several species. Phylogenies constructed from both loci confirmed that the closest relatives of Arabidopsis thaliana include Arabidopsis lyrata, Arabidopsis petraea, and Arabidopsis halleri (formerly in the genus Cardaminopsis). Slightly more distant are the North American n = 7 Arabis (Boechera) species. The genus Arabis is polyphyletic-some unrelated species appear within this taxonomic classification, which has little phylogenetic meaning. Fossil pollen data were used to compute a synonymous substitution rate of 1.5 x 10 substitutions per site per year for both Chs and Adh. Arabidopsis thaliana diverged from its nearest relatives about 5 MYA, and from Brassica roughly 24 MYA. Independent molecular and fossil data from several sources all provide similar estimates of evolutionary timescale in the Brassicaceae.

Advances in the study of polyploidy since Plant speciation

Abstract: Summary Enormous strides have been made in the study of polyploidy over the last 20 yr. Here, we highlight some of these discoveries and note where our understanding of polyploid evolution has changed. Genetic and genomic studies have dramatically altered the polyploidy paradigm. The estimated frequency of polyploidy has increased, and it is now recognized that multiple origins are the rule for most polyploids. Likewise, autopolyploidy is much more common than traditionally maintained. Rapid genomic rearrangements, genomic downsizing, movement of genetic elements across genomes, and the movement of foreign genetic materials into the polyploid genome illustrate the complex dynamics of polyploid genomes. Following polyploidization, both genetic and epigenetic mechanisms may play an important role in altering gene expression. Ecological studies reveal that plant polyploidy can have profound effects on interactions with animal herbivores and pollinators and that polyploidy may trigger changes in the reproductive biology of a species. Despite the recent advances in our understanding of polyploid evolution, many exciting aspects remain under-investigated. Some of these include the consequences of genetic and genomic changes in natural polyploid populations, the physiological and ecological effects of polyploidy, and whether recurrent polyploidy prompts evolution to repeat itself.