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.

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The role of glacial oscillations in shaping plant diversity has been only rarely addressed in endemics of formerly glaciated areas. The Galium pusillum group represents a rare example of an ecologically diverse and ploidy-variable species complex that exhibits substantial diversity in deglaciated northern Europe. Using AFLP and plastid and nuclear DNA sequences of 67 populations from northern, central, and western Europe with known ecological preferences, we elucidate the evolutionary history of lineages restricted to deglaciated areas and identify the eco-geographic partitioning of their genetic variation. We reveal three distinct endemic northern lineages: (i) diploids from southern Sweden + the British Isles, (ii) tetraploids from southern Scandinavia and the British Isles that show signs of ancient hybridization between the first lineage and populations from unglaciated central Europe, and (iii) tetraploids from Iceland + central Norway. Available evidence supports a stepwise differentiation of these three lineages that started at least before the last glacial maximum by processes of genome duplication, interlineage hybridization and/or allopatric evolution in distinct periglacial refugia. We reject the hypothesis of more recent postglacial speciation. Ecological characteristics of the populations under study only partly reflect genetic variation and suggest broad niches of postglacial colonizers. Despite their largely allopatric modern distributions, the north-European lineages of the G. pusillum group do not show signs of rapid postglacial divergence, in contrast to most other northern endemics. Our study suggests that plants inhabiting deglaciated areas outside the Arctic may exhibit very different evolutionary histories compared with their more thoroughly investigated high-arctic counterparts.

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Divergent natural selection is known to facilitate speciation in many taxa. The genus Bolboschoenus (Cyperaceae) is a model group for investigating ecological and homoploid hybrid speciation. Four taxa of Bolboschoenus occur in central Europe: the halophyte B. maritimus and glycophytes B. laticarpus, B. planiculmis and B. yagara. These species differ in their ecological niches. Such ecological and/or geographical isolation is critical for homoploid hybrid speciation. The determination of species of Bolboschoenus is based on morphological characters of the inflorescence and on achene shape and anatomy. On the basis of its intermediate morphology, chromosome number and ecological amplitude B. laticarpus is thought to be a hybrid. In order to determine the validity of morphological species and the possible hybrid origin of B. laticarpus we used amplified fragment length polymorphisms (AFLPs) as molecular markers and compared different genetic groups defined using STRUCTURE analysis with morphological data. The morphological classification of central-European species of Bolboschoenus was confirmed. Plants of heterogeneous genotypes were also found to be intermediate individuals resulting from spontaneous hybridization. Hybrid origin of B. laticarpus, which is genetically and morphologically intermediate between B. yagara and B. planiculmis, was elucidated. Inflorescence characters were less important for determining species than anatomical characters of achenes (widths of the exocarp and mesocarp).K e y w o r d s: AFLP, Bolboschoenus, central Europe, hybridization, model-based clustering, morphometrics, speciation IntroductionThe evolutionary histories of groups of closely related species of plants have been the focus of interest of much research in recent years, especially the process of speciation (Kaplan et al. 2013, Kolář et al. 2014, 2015. Moreover, questions concerning reproductive isolating mechanisms and the genetics and genomics of speciation have been highlighted by a major European initiative as the main subjects for further research (Butlin et al. 2012). Ecological speciation is one of the main modes of speciation (Schluter 2001). It occurs as a result of reproductive isolation due to divergent selection of organisms in different environments and can arise even where species occur sympatrically (Sobel et al. Preslia 89: 17-39, 2017 17 doi: 10.23855/preslia.2017.017 2009). Studying microevolution within groups of closely related species differing in ecology may thus reveal the role of such environmental differences in their origin. Hybridization can result in both gene flow among plant taxa and generation of new species. Some families and genera have relatively high numbers of hybrids, with the family Cyperaceae being one of them (Ellstrand et al. 1996).The European species of Bolboschoenus (Asch.) Palla (Cyperaceae) provide an example of a putative hybrid complex for which ecological selection, geographic isolation and hybridization are thought to have been important in their speciation, with the...

The ecology and species diversity of ephemeral wetland vegetation have been fairly well studied, but the biology of its characteristic species has rarely been investigated holistically. Here we combine previous results on the genetic diversity of a suitable model species (the diploid Cyperus fuscus) with new data on its historical and recent occurrence, its ecological and climatic niche, and the associated vegetation. Analysis of phytosociological relevés from Central Europe revealed a broad ecological niche of C. fuscus with an optimum in the Isoëto-Nanojuncetea class, extending to several other vegetation types. Overall species composition in the relevés highlight C. fuscus as a potential indicator of habitat conditions suitable for a range of other threatened taxa. Analysis of historical records of C. fuscus from the Czech Republic showed an increasing trend in the number of localities since the 1990s. It seems that recent climate warming allows the thermophilous C. fuscus to expand its range into colder regions. Isoëto-Nanojuncetea and Bidentetea species are well represented in the soil seed bank in both riverine and anthropogenic habitats of C. fuscus. Vegetation diversity has a weak negative effect and anthropogenic (compared to riverine) habitats have a strong negative effect on genetic diversity in this species.