Phylogenetic signal in growth and reproductive traits and in their plasticity: the D escurainia radiation in the C anary I slands

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/106137/1/boj12139.pd

Study of plant dispersal in river corridors using molecular marker

5 Summary The thesis presents how the use of molecular markers (AFLPs and microsatellites) can help when studying plant dispersal in river systems. Analysis and interpretation of the spatial pattern of genetic variation allowed to address and discuss following aspects of long-distance dispersal in these linearly structured systems: (1) the extent of long-distance dispersal, (2) the intensity of vegetative long-distance dispersal, (3) unidirectional transport along the streams, and (4) dispersal among rivers. The first part of the PhD. thesis presents several general aspects of plant dispersal, methodological approaches used to detect dispersal, and possibilities of analysis and interpretation of the molecular data. It also gives a short introduction to the methodology used in the particular studies, summarizes the results of all studies, and discusses how differences detected by molecular markers correspond to dispersal possibility (e.g., by water, by wind) of the selected species. The second part contains a set of four papers, each focusing on a detailed survey of dispersal possibilities of one of four plant species within the river system of the Cidlina, the Mrlina and partly also the Labe Rivers (Czech Republic). Above- mentioned aspects of dispersal in river systems are further discussed in the light..

Studium rostlinného rozptýlení v říčních koridorech pomocí molekulárních markerů

5 Summary The thesis presents how the use of molecular markers (AFLPs and microsatellites) can help when studying plant dispersal in river systems. Analysis and interpretation of the spatial pattern of genetic variation allowed to address and discuss following aspects of long-distance dispersal in these linearly structured systems: (1) the extent of long-distance dispersal, (2) the intensity of vegetative long-distance dispersal, (3) unidirectional transport along the streams, and (4) dispersal among rivers. The first part of the PhD. thesis presents several general aspects of plant dispersal, methodological approaches used to detect dispersal, and possibilities of analysis and interpretation of the molecular data. It also gives a short introduction to the methodology used in the particular studies, summarizes the results of all studies, and discusses how differences detected by molecular markers correspond to dispersal possibility (e.g., by water, by wind) of the selected species. The second part contains a set of four papers, each focusing on a detailed survey of dispersal possibilities of one of four plant species within the river system of the Cidlina, the Mrlina and partly also the Labe Rivers (Czech Republic). Above- mentioned aspects of dispersal in river systems are further discussed in the light...Úvod K šířenírostlin a ýměně genetickéinformacemezi populacemidocházískrze tzv. propagule(částice určenépro šíření)a pyl. Propagule mohou být bud' vegetativní(např' pacibulky nebo turionyJ nebo generativní(semenaneboplody].Různédruhyisoušířenyrůznýmzpůsobem,např.větrem(anemochorie), vodou (hydr.ochorie),zvířaty [zoochorie] nebo díky člověku (antropochorie).Typ a frekvence šíření v'ýznamněovlivňu|erozšířenídruhu a takédistribuci genetickévariability uvnitř a mezi populacemi. Zl]alosttzv' ,dispersalkernel',cožie určenítoho,iak jsou šířenasemenaokolo zdroie,ie zásadnípro porozuměníekologickýmprocesůmnakraiinnéúrovni.PočetšíŤ.enýchsemen,aIei Vzdálenosta směrjejich transportu ie podstatnépro ekologickéotázky. Používáse něko|ik různýchpřístupůke studiu šíření: (lJ sledovánÍ šířených propagulí, (2J chytání šířených propagulí, (3) matematické (empirické, mechanistické)modelypopisuiígípohybpropagulíokoloiejichzdrojůa (4Jpříménebonepi.ímégenetické metody vyrržÍvajícímolekulární informaci fisozymovou, restrikčnífragmenty,DNA sekvence).Protože genetickápodobnostodpovídápříbuznostimeziiedinci,prostorovépatterngenetickévariabilitymůžebýt interpretovánojakovýměnagenetickéinformace,např.šířenípropagulímezipopulacemi. studovatšířenírostlinie obzvláštězajimavév heterogenníkrajině,kde jsoupotenciálnívhodnámísta propoiena...Department of BotanyKatedra botanikyFaculty of SciencePřírodovědecká fakult

HybPhyloMaker: Target Enrichment Data Analysis From Raw Reads to Species Trees

Summary: Hybridization-based target enrichment in combination with genome skimming (Hyb-Seq) is becoming a standard method of phylogenomics. We developed HybPhyloMaker, a bioinformatics pipeline that performs target enrichment data analysis from raw reads to supermatrix-, supertree-, and multispecies coalescent-based species tree reconstruction. HybPhyloMaker is written in BASH and integrates common bioinformatics tools. It can be launched both locally and on a high-performance computer cluster. Compared with existing target enrichment data analysis pipelines, HybPhyloMaker offers the following main advantages: implementation of all steps of data analysis from raw reads to species tree reconstruction, calculation and summary of alignment and gene tree properties that assist the user in the selection of “quality-filtered” genes, implementation of several species tree reconstruction methods, and analysis of the coding regions of organellar genomes. Availability: The HybPhyloMaker scripts, manual as well as a test data set, are available in https://github.com/tomas-fer/HybPhyloMaker/ . HybPhyloMaker is licensed under open-source license GPL v.3 allowing further modifications

An empirical assessment of a single family-wide hybrid capture locus set at multiple evolutionary timescales in Asteraceae

Premise: Hybrid capture with high-throughput sequencing (Hyb-Seq) is a powerful tool for evolutionary studies. The applicability of an Asteraceae family-specific Hyb-Seq probe set and the outcomes of different phylogenetic analyses are investigated here. Methods: Hyb-Seq data from 112 Asteraceae samples were organized into groups at different taxonomic levels (tribe, genus, and species). For each group, data sets of non-paralogous loci were built and proportions of parsimony informative characters estimated. The impacts of analyzing alternative data sets, removing long branches, and type of analysis on tree resolution and inferred topologies were investigated in tribe Cichorieae. Results: Alignments of the Asteraceae family-wide Hyb-Seq locus set were parsimony informative at all taxonomic levels. Levels of resolution and topologies inferred at shallower nodes differed depending on the locus data set and the type of analysis, and were affected by the presence of long branches. Discussion: The approach used to build a Hyb-Seq locus data set influenced resolution and topologies inferred in phylogenetic analyses. Removal of long branches improved the reliability of topological inferences in maximum likelihood analyses. The Astereaceae Hyb-Seq probe set is applicable at multiple taxonomic depths, which demonstrates that probe sets do not necessarily need to be lineage-specific

Relative performance of customized and universal probe sets in target enrichment: A case study in subtribe Malinae

Premise Custom probe design for target enrichment in phylogenetics is tedious and often hinders broader phylogenetic synthesis. The universal angiosperm probe set Angiosperms353 may be the solution. Here, we test the relative performance of Angiosperms353 on the Rosaceae subtribe Malinae in comparison with custom probes that we specifically designed for this clade. We then address the impact of bioinformatically altering the performance of Angiosperms353 by replacing the original probe sequences with orthologs extracted from the Malus domestica genome. Methods To evaluate the relative performance of these probe sets, we compared the enrichment efficiency, locus recovery, alignment length, proportion of parsimony‐informative sites, proportion of potential paralogs, the topology and support of the resulting species trees, and the gene tree discordance. Results Locus recovery was highest for our custom Malinae probe set, and replacing the original Angiosperms353 sequences with a Malus representative improved the locus recovery relative to Angiosperms353. The proportion of parsimony‐informative sites was similar between all probe sets, while the gene tree discordance was lower in the case of the custom probes. Discussion A custom probe set benefits from data completeness and can be tailored toward the specificities of the project of choice; however, Angiosperms353 was equally as phylogenetically informative as the custom probes. We therefore recommend using both a custom probe set and Angiosperms353 to facilitate large‐scale systematic studies, where financially possible

Bringing Together Evolution on Serpentine and Polyploidy: Spatiotemporal History of the Diploid-Tetraploid Complex of <em>Knautia arvensis</em> (Dipsacaceae)

<div><p>Polyploidization is one of the leading forces in the evolution of land plants, providing opportunities for instant speciation and rapid gain of evolutionary novelties. Highly selective conditions of serpentine environments act as an important evolutionary trigger that can be involved in various speciation processes. Whereas the significance of both edaphic speciation on serpentine and polyploidy is widely acknowledged in plant evolution, the links between polyploid evolution and serpentine differentiation have not yet been examined. To fill this gap, we investigated the evolutionary history of the perennial herb <em>Knautia arvensis</em> (Dipsacaceae), a diploid-tetraploid complex that exhibits an intriguing pattern of eco-geographic differentiation. Using plastid DNA sequencing and AFLP genotyping of 336 previously cytotyped individuals from 40 populations from central Europe, we unravelled the patterns of genetic variation among the cytotypes and the edaphic types. Diploids showed the highest levels of genetic differentiation, likely as a result of long term persistence of several lineages in ecologically distinct refugia and/or independent immigration. Recurrent polyploidization, recorded in one serpentine island, seems to have opened new possibilities for the local serpentine genotype. Unlike diploids, the serpentine tetraploids were able to escape from the serpentine refugium and spread further; this was also attributable to hybridization with the neighbouring non-serpentine tetraploid lineages. The spatiotemporal history of <em>K. arvensis</em> allows tracing the interplay of polyploid evolution and ecological divergence on serpentine, resulting in a complex evolutionary pattern. Isolated serpentine outcrops can act as evolutionary capacitors, preserving distinct karyological and genetic diversity. The serpentine lineages, however, may not represent evolutionary ‘dead-ends’ but rather dynamic systems with a potential to further influence the surrounding populations, e.g., via independent polyplodization and hybridization. The complex eco-geographical pattern together with the incidence of both primary and secondary diploid-tetraploid contact zones makes <em>K. arvensis</em> a unique system for addressing general questions of polyploid research.</p> </div

Network of 13 plastid DNA haplotypes found within 77 examined individuals of <i>Knautia arvensis</i> agg.

<p>The size of the circles is proportional to the number of individuals, while their shading indicates the ploidy level and monoploid genome size of the samples (black – relict 2× only, dark grey – relict 2×+4×, light grey – all 2×+4×, white – unique for a single non-relict 2× – haplotypes J and M – or 4× – haplotypes C and K – population). The double line indicates an insertion-deletion. For more detailed information, see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039988#pone-0039988-t001" target="_blank">Table 1</a>.</p

Phylogeographical grouping of 40 analyzed populations of <i>Knautia arvensis</i> agg. in central Europe.

<p>Grouping is according to the nonhierarchical K-means clustering of AFLP phenotypes. Pie charts represent the proportion of individuals belonging to each of the seven detected groups (K1–K7). The size of the pie chart reflects the sample size. The inset displays the situation in the Slavkovský les serpentine area. White ovals denote populations from relict limestone habitats (open pine forests or subalpine grasslands), grey ovals populations from relict serpentine pine forests. Note the presence of several relict diploid populations in the western part of the area (P03, P04, and P05) with the genetic composition highly similar to the surrounding tetraploids. The distribution of chloroplast haplotypes is indicated (A–M).</p