ALLCOPOL: inferring allele co-ancestry in polyploids.

BACKGROUND: Inferring phylogenetic relationships of polyploid species and their diploid ancestors (leading to reticulate phylogenies in the case of an allopolyploid origin) based on multi-locus sequence data is complicated by the unknown assignment of alleles found in polyploids to diploid subgenomes. A parsimony-based approach to this problem has been proposed by Oberprieler et al. (Methods Ecol Evol 8:835-849, 2017), however, its implementation is of limited practical value. In addition to previously identified shortcomings, it has been found that in some cases, the obtained results barely satisfy the applied criterion. To be of better use to other researchers, a reimplementation with methodological refinement appears to be indispensable. RESULTS: We present the AllCoPol package, which provides a heuristic method for assigning alleles from polyploids to diploid subgenomes based on the Minimizing Deep Coalescences (MDC) criterion in multi-locus sequence datasets. An additional consensus approach further allows to assess the confidence of phylogenetic reconstructions. Simulations of tetra- and hexaploids show that under simplifying assumptions such as completely disomic inheritance, the topological errors of reconstructed phylogenies are similar to those of MDC species trees based on the true allele partition. CONCLUSIONS: AllCoPol is a Python package for phylogenetic reconstructions of polyploids offering enhanced functionality as well as improved usability. The included methods are supplied as command line tools without the need for prior programming knowledge.

'At the crossroads towards polyploidy': genomic divergence and extent of homoploid hybridization are drivers for the formation of the ox-eye daisy polyploid complex (Leucanthemum, Compositae-Anthemideae).

Polyploidy plays a paramount role in phytodiversity, but the causes of this evolutionary pathway require further study. Here, we use phylogenetic methods to examine possible polyploidy-promoting factors by comparing diploid representatives of the comprehensive European polyploid complex Leucanthemum with members of its strictly diploid North African counterpart Rhodanthemum. We investigate genetic divergence and gene flow among all diploid lineages of both genera to evaluate the role of genomic differentiation and hybridization for polyploid speciation. To test whether hybridization in Leucanthemum has been triggered by the geological conditions during its diversification, we additionally generate a time-calibrated phylogeny of 46 species of the subtribe Leucantheminae. Leucanthemum shows a significantly higher genetic divergence and hybridization signal among diploid lineages compared with Rhodanthemum, in spite of a similar crown age and diversification pattern during the Quaternary. Our study demonstrates the importance of genetic differentiation among diploid progenitors and their concurrent affinity for natural hybridization for the formation of a polyploid complex. Furthermore, the role of climate-induced range overlaps on hybridization and polyploid speciation during the Quaternary is discussed.

Leucanthemum vulgare lam. crude oil phytoremediation.

Sites with crude oil pollution have been successfully treated using phytoremediation, but expanding the range of plants that can be used and understanding how exposure impacts the plants are two areas of study that are important to continue. Leucanthemum vulgare has been shown to grow well under a variety of stressful conditions. To examine L. vulgare's ability to both survive crude oil exposure and to reduce crude oil concentrations in soil, plants were placed in soil containing 0, 2.5, 5, 7.5, or 10% w/w crude oil. Total petroleum hydrocarbons (TPH) concentration, peroxidase and catalase activity, proline and phenol content in roots and leaves were determined at the start of planting and every 2 months for 6 months. L. vulgare roots were successfully colonized with mycorrhizae under all conditions. Results showed positive correlation between antioxidant compound concentration and crude oil contamination. Also, a significant reduction occurred in TPH content of soil over time in planted pots as compared to controls. The lowest TPH content was recorded after 6 months under all treatments. Results showed L. vulgare could survive crude oil exposure and enhance reducing of crude oil from soil.