Fylogenetické studie polyploidního rodu Curcuma L.

1 Phylogenetic Studies in the Polyploid Genus Curcuma L. SUMMARY Curcuma is genetically one of the most complex genera within the tropical family Zingiberaceae, with hybridization and polyploidization being the major forces in its evolution. In this thesis, I have focused mainly on the genetic background of Curcuma species variation, relationships and overall genome structure, as a key to solve long standing taxonomic problems. Results of my molecular studies on the genus Curcuma performed since 2007 represent an extension of ongoing taxonomic and nomenclatural work started by Jana Leong- Škorničková in 2000. The first part of the thesis consists of a broad, general introduction to the subject to reflect the current state of knowledge, formulate the major problems to be confronted within the genus, and summarise the major results of the studies presented in the second part of the thesis. As the main obstacles in studying Curcuma are consequences of its reticulate evolution, it is also outlines the importance of understanding the genetic background and species relationships using molecular markers. Common molecular methods used for assessing phylogenetic relationships on the intraspecific and infrageneric levels - AFLP and sequencing of selected markers from cpDNA, nrDNA and nDNA - are described, with the...1 Fylogenetické studie polyploidního rodu Curcuma L. SOUHRN Tato práce je souhrnem mých dosavadních molekulárních studií rodu Curcuma, které probíhaly od roku 2007, a je těsně propojena s dříve započatými studiemi tohoto rodu z hlediska jeho taxonomie a nomenklatury (Jana Leong-Škorničková, od roku 2000). Rod Curcuma patří díky své obrovské genetické rozmanitosti mezi nejproblematičtější rody v rámci čeledi Zingiberaceae. Velká část této rozmanitosti vznikla díky speciačním procesům jako je hybridizace či polyploidizace. Neboť z povahy hybridizačních (ale i polyploidizačních) procesů jsou druhy rodu Curcuma často provázány síťovitými vztahy (narozdíl od běžných allopatrických speciačních procesů, kdy jeden druh vzniká pozvolným vylišením z jednoho předka), tyto vztahy lze zpětně odhalit zejména za použití tzv. molekulárních markerů. Náplní této práce je odhalení genetických vztahů v rámci rodu Curcuma a v rámci jeho jednotlivých vývojových linií, za účelem objasnění dlouhodobě nevyřešených taxonomickych otázek. První část práce je věnována obecnému úvodu shrnujícímu současný stav poznání rodu Curcuma a předchází části druhé, ve které jsou prezentovány čtyři případové studie. Jsou zde popsány základní charakteristiky rodu Curcuma, zejména znaky morfologické a cytologické, současné geografické rozšíření, či...Department of BotanyKatedra botanikyFaculty of SciencePřírodovědecká fakult

Study of evolution in Indian Curcuma L.

Katedra botanikyDepartment of BotanyPřírodovědecká fakultaFaculty of Scienc

Performance comparison of two reduced-representation based genome-wide marker-discovery strategies in a multi-taxon phylogeographic framework

Multi-locus genetic data are pivotal in phylogenetics. Today, high-throughput sequencing (HTS) allows scientists to generate an unprecedented amount of such data from any organism. However, HTS is resource intense and may not be accessible to wide parts of the scientific community. In phylogeography, the use of HTS has concentrated on a few taxonomic groups, and the amount of data used to resolve a phylogeographic pattern often seems arbitrary. We explore the performance of two genetic marker sampling strategies and the effect of marker quantity in a comparative phylogeographic framework focusing on six species (arthropods and plants). The same analyses were applied to data inferred from amplified fragment length polymorphism fingerprinting (AFLP), a cheap, non-HTS based technique that is able to straightforwardly produce several hundred markers, and from restriction site associated DNA sequencing (RADseq), a more expensive, HTS-based technique that produces thousands of single nucleotide polymorphisms. We show that in four of six study species, AFLP leads to results comparable with those of RADseq. While we do not aim to contest the advantages of HTS techniques, we also show that AFLP is a robust technique to delimit evolutionary entities in both plants and animals. The demonstrated similarity of results from the two techniques also strengthens biological conclusions that were based on AFLP data in the past, an important finding given the wide utilization of AFLP over the last decades. We emphasize that whenever the delimitation of evolutionary entities is the central goal, as it is in many fields of biodiversity research, AFLP is still an adequate technique.Te present study was co-funded by the Austrian Science Fund (FWF, project P25955 “Origin of steppe fora and fauna in inner-Alpine dry valleys” to P.S.), and the Tiroler Wissenschafsfonds (TWF, UNI-0404/2066,“Comparing information efciency of high- versus low-resolution genome scans for phylogeographic studies” to P.K.). Te computational results presented have been achieved using the HPC infrastructure LEO of the University of Innsbruck

Phylogenetic Studies in the Polyploid Genus Curcuma L.

1 Phylogenetic Studies in the Polyploid Genus Curcuma L. SUMMARY Curcuma is genetically one of the most complex genera within the tropical family Zingiberaceae, with hybridization and polyploidization being the major forces in its evolution. In this thesis, I have focused mainly on the genetic background of Curcuma species variation, relationships and overall genome structure, as a key to solve long standing taxonomic problems. Results of my molecular studies on the genus Curcuma performed since 2007 represent an extension of ongoing taxonomic and nomenclatural work started by Jana Leong- Škorničková in 2000. The first part of the thesis consists of a broad, general introduction to the subject to reflect the current state of knowledge, formulate the major problems to be confronted within the genus, and summarise the major results of the studies presented in the second part of the thesis. As the main obstacles in studying Curcuma are consequences of its reticulate evolution, it is also outlines the importance of understanding the genetic background and species relationships using molecular markers. Common molecular methods used for assessing phylogenetic relationships on the intraspecific and infrageneric levels - AFLP and sequencing of selected markers from cpDNA, nrDNA and nDNA - are described, with the..

Study of evolution in Indian Curcuma L.

Katedra botanikyDepartment of BotanyPřírodovědecká fakultaFaculty of Scienc

Evolution of Indian Curcuma

Department of BotanyKatedra botanikyFaculty of SciencePřírodovědecká fakult

Meeting in Liguria

The Mediterranean Basin is renowned for its extremely rich biota and is considered as one of the 25 Global Biodiversity Hotspots, but its diversity is not homogeneously distributed. Outstanding in the number of (endemic) species are the Ligurian Alps (Italy). At the foot of the Ligurian Alps, little above the Mediterranean Sea, a disjunct occurrence of Italian endemic Euphorbia barrelieri was reported. Using an array of integrative methods ranging from cytogenetic (chromosome number and relative genome size estimation), over phylogenetic approaches (plastid, ITS and RAD sequencing) to multivariate morphometrics we disentangled the origin of these populations that were shown to be tetraploid. We performed phylogenetic analyses of the nuclear ITS and plastid regions of a broad taxonomic sampling of Euphorbia sect. Pithyusa to identify possible species involved in the origin of the tetraploid populations and then applied various analyses of RADseq data to identify the putative parental species. Our results have shown that the Ligurian populations of E. barrelieri are of allotetraploid origin that involved E. barrelieri and western Mediterranean E. nicaeensis as parental species. We thus describe a new species, E. ligustica, and hypothesise that its adaptation to similar environments in which E. barrelieri occurs, triggered development of similar morphology, whereas its genetic composition appears to be closer to that of E. nicaeensis. Our study emphasises the importance of polyploidisation for plant diversification, highlights the value of the Ligurian Alps as a hotspot of biodiversity and endemism and underlines the importance of integrative taxonomic approaches in uncovering cryptic diversity

Dealing with discordant genetic signal caused by hybridisation, incomplete lineage sorting and paucity of primary nucleotide homologies: a case study of closely related members of the genus Picris subsection Hieracioides (Compositae).

We investigated genetic variation and evolutionary history of closely related taxa of Picris subsect. Hieracioides with major focus on the widely distributed P. hieracioides and its closely related congeners, P. hispidissima, P. japonica, P. olympica, and P. nuristanica. Accessions from 140 sample sites of the investigated Picris taxa were analyzed on the infra- and the inter-specific level using nuclear (ITS1-5.8S-ITS2 region) and chloroplast (rpl32-trnL(UAG) region) DNA sequences. Genetic patterns of P. hieracioides, P. hispidissima, and P. olympica were shown to be incongruent and, in several cases, both plastid and nuclear alleles transcended borders of the taxa and genetic lineages. The widespread P. hieracioides was genetically highly variable and non-monophyletic across both markers, with allele groups having particular geographic distributions. Generally, all gene trees and networks displayed only a limited and statistically rather unsupported resolution among ingroup taxa causing their phylogenetic relationships to remain rather unresolved. More light on these intricate evolutionary relationships was cast by the Bayesian coalescent-based analysis, although some relationships were still left unresolved. A combination of suite of phylogenetic analyses revealed the ingroup taxa to represent a complex of genetically closely related and morphologically similar entities that have undergone a highly dynamic and recent evolution. This has been especially affected by the extensive and recurrent gene flow among and within the studied taxa and/or by the maintenance of ancestral variation. Paucity of phylogenetically informative signal further hampers the reconstruction of relationships on the infra- as well as on the inter-specific level. In the present study, we have demonstrated that a combination of various phylogenetic analyses of datasets with extremely complex and incongruent phylogenetic signal may shed more light on the interrelationships and evolutionary history of analysed species groups

Borneocola (Zingiberaceae), a new genus from Borneo

A new genus from Borneo, Borneocola Y.Y.Sam, is described here. The genus currently contains eight species previously classified as members of the Scaphochlamys Baker. The finding is based on the results of the morphological and molecular studies of Scaphochlamys throughout its geographical range and its closely allied sister groups, Distichochlamys M.F.Newman and Myxochlamys A.Takano & Nagam. Borneocola is nested within the tribe Zingibereae and its monophyly is strongly supported by both ITS and matK sequence data. The genus is characterised by several thin, translucent and marcescent floral bracts, absence of coloured streaks on the labellum and capitate stigma with two dorsal knobs. The genus is distributed in northwest Borneo and all species are very rare and highly endemic

Information for the DNA datasets and details on maximum parsimony analyses.

a<p>ITS1 – analysis based on the ITS_1 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0104929#pone.0104929.s003" target="_blank">Alignment S1</a>. ITS_1.</p>b<p>cpDNA - analysis based on the <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0104929#pone.0104929.s005" target="_blank">Alignment S3</a>. cpDNA.</p>c<p>concat - analysis based on the concatenated <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0104929#pone.0104929.s006" target="_blank">Alignment S4</a>. ITS_cpDNA.</p><p>Information for the DNA datasets and details on maximum parsimony analyses.</p