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The Eurasian steppes occupy a significant portion of the worldwide land surface and their biota have been affected by specific past range dynamics driven by ice ages-related climatic fluctuations. The dynamic alterations in conditions during the Pleistocene often triggered reticulate evolution and whole genome duplication events. Employing genomic, genetic and cytogenetic tools as well as morphometry we investigate the intricate evolution of Astragalus onobrychis, a widespread Eurasian steppe plant with diploid, tetraploid and octoploid cytotypes. To analyse the heteroploid RADseq dataset we employ both genotype-based and genotype-free methods that result in highly consistent results, and complement our inference with information from the plastid ycf1 region. We uncover a complex and reticulate evolutionary history, including at least one auto-tetraploidization event and two allo-octoploidization events; one of them involved also genetic contributions from other species, most likely A. goktschaicus. The present genetic structure points to the existence of four main clades within A. onobrychis, which only partly correspond to different ploidies. Time-calibrated diffusion models suggest that diversification within A. onobrychis was associated with ice age-related climatic fluctuations during the last million years. We finally argue for the usefulness of uniparentally inherited plastid markers, even in the genomic era, especially when investigating heteroploid systems., (Copyright © 2019 The Authors. Published by Elsevier Inc. All rights reserved.)

Two new genera (Streptosarcina and Streptofilum) and three new species (Streptosarcina arenaria, S. costaricana and Streptofilum capillatum) of streptophyte algae were detected in cultures isolated from terrestrial habitats of Europe and Central America and described using an integrative approach. Additionally, a strain isolated from soil in North America was identified as Hormidiella parvula and proposed as an epitype of this species. The molecular phylogeny based on 18S rRNA and rbcL genes, secondary structure of ITS-2, as well as the morphology of vegetative and reproductive stages, cell ultrastructure, ecology and distribution of the investigated strains were assessed. The new genus Streptosarcina forms a sister lineage to the genus Hormidiella (Klebsormidiophyceae). Streptosarcina is characterized by packet-like (sarcinoid) and filamentous thalli with true branching and a cell organization typical for Klebsormidiophyceae. Streptofilum forms a separate lineage within Streptophyta. This genus represents an easily disintegrating filamentous alga which exhibits a cell coverage of unique structure: layers of submicroscopic scales of piliform shape covering the plasmalemma and exfoliate inside the mucilage envelope surrounding cells. The implications of the discovery of the new taxa for understanding evolutionary tendencies in the Streptophyta, a group of great evolutionary interest, are discussed., (Copyright © 2018 The Author(s). Published by Elsevier GmbH.. All rights reserved.)

Premise of the Study: Clade-specific bursts in diversification are often associated with the evolution of key innovations. However, in groups with no obvious morphological innovations, observed upticks in diversification rates have also been attributed to the colonization of a new geographic environment. In this study, we explore the systematics, diversification dynamics, and historical biogeography of the plant clade Rhinantheae in the Orobanchaceae, with a special focus on the Andean clade of the genus Bartsia., Methods: We sampled taxa from across Rhinantheae, including a representative sample of Andean Bartsia species. Using standard phylogenetic methods, we reconstructed evolutionary relationships, inferred divergence times among the clades of Rhinantheae, elucidated their biogeographic history, and investigated diversification dynamics., Key Results: We confirmed that the South American Bartsia species form a highly supported monophyletic group. The median crown age of Rhinantheae was determined to be ca. 30 Myr, and Europe played an important role in the biogeographic history of the lineages. South America was first reconstructed in the biogeographic analyses around 9 Myr ago, and with a median age of 2.59 Myr, this clade shows a significant uptick in diversification., Conclusions: Increased net diversification of the South American clade corresponds to biogeographic movement into the New World. This movement happened at a time when the Andes were reaching the necessary elevation to host an alpine environment. Although a specific route could not be identified with certainty, we provide plausible hypotheses to how the group colonized the New World., (© 2015 Botanical Society of America.)

Recent phylogenetic studies have shown that Saxifraga, as currently understood, must be divided into two genera: Saxifraga L. sensu stricto and Micranthes Haw. To better understand the evolutionary history of these two genera, we performed phylogenetic analyses inferred from the nuclear ribosomal sequences from the internal transcribed spacer and the sequences of the plastid DNA (rbcL). Our molecular data confirmed the monophyly of the genus Micranthes and the consistency of the existing systematic treatments based on morphological criteria. Moreover, Micranthes species native from the Iberian Peninsula (i.e. M. clusii, M. lepismigena and M. stellaris) should be included into Micranthes sect. Arabisa.

Premise of the Study: The discontinuous North American distribution of Najas gracillima has not been explained satisfactorily. Influences of extirpation, nonindigenous introduction, and postglacial migration on its distribution were evaluated using field, fossil, morphological, and molecular data. Najas is a major waterfowl food, and appropriate conservation measures rely on accurate characterization of populations as indigenous or imperiled. •, Methods: Seed lengths of N. gracillima from native Korean populations, a nonindigenous Italian population, and North American populations were compared using digital image analysis. DNA sequence analyses from these regions provided nine nrITS genotypes and eight cpDNA haplotypes. •, Key Results: Najas gracillima seeds from Eurasia and California are shorter than those from eastern North America. Nuclear and chloroplast DNA sequences of N. gracillima from Korea and Italy were identical to California material but differed from native eastern North American plants. Eastern North American specimens of N. gracillima at localities above the last glacial maximum boundary were identical or similar genetically to material from the northeastern United States and Atlantic Coastal Plain and Piedmont but divergent from plants of the Interior Highlands-Mississippi Embayment region. •, Conclusions: In California, N. gracillima is nonindigenous and introduced from Asia. In eastern North America, populations that colonized deglaciated areas were derived primarily from refugia in the Atlantic Coastal Plain and Piedmont. Genetic data indicate initial postglacial migration to northeastern North America, with subsequent westward dispersal into the Upper Great Lakes. These results differentiate potentially invasive California populations from seriously imperiled indigenous eastern North American populations.

Wild apples (Malus sp.) have been a major food source in the northern Alpine region since prehistory and their use is well understood. The onset of deliberate fruit tree growing in the area is, however, less clear. It is generally assumed that horticulture was practised in Roman times, but it might be even earlier. In the archaeological record seed testa and pericarp remains are particularly frequent at sites with waterlogged preservation such as lakeshore settlements or wells, pits and ditches, but the distinction between wild and domestic plants is not morphologically possible. With waterlogged remains being one main source of information about past fruit cultivation, we have tested the feasibility of analysing ancient DNA from waterlogged preserved bulk samples of testa fragments. We studied apple seeds from three Neolithic and three Roman sites with waterlogged preservation in the Alpine foreland. Chloroplast markers failed in all samples, but nuclear ITS1 (internal transcribed spacer region 1) of the ribosomal DNA was successfully typed in two Roman samples from the site Oedenburg/Biesheim-Kunheim (Haut-Rhin, F). The retrieved ITS1 sequences are identical to each other and are shared with wild Malus sylvestris and Malus sieversii, and with domestic apple cultivars, supporting the potential of using waterlogged remains for identifying the genetic status of apple diachronically., (Copyright © 2011 Elsevier GmbH. All rights reserved.)

Adaptive genetic variation is a key factor in evolutionary biology, but the detection of signatures of natural selection remains challenging in nonmodel organisms. We used a genome scan approach to detect signals of natural selection in the Black alder (Alnus glutinosa), a widespread wind-pollinated tree. Gene flow through pollen dispersal is believed to be high in this species, and we therefore expected to find a clear response to natural selection. In combination with two different landscape genetic approaches, we determined which environmental variables were most associated with the inferred selection. This analysis was performed on a regional scale (northern Belgium) and on a continental scale (Europe). Because climate-related differences are much more pronounced at the continental scale, we expected to find more selection-sensitive genetic markers across Europe than across northern Belgium. At both spatial scales, a substantial number of genetic loci were considered outliers, with respect to neutral expectations, and were therefore identified as selective. Based on results from our combined approach, four putative selective loci (or 2.5%) were recovered with high statistical support. Although these loci seemed to be associated with different environmental variables, they were mainly temperature-related. Our study demonstrates that the use of complementary methods in landscape genetics allows the discovery of selective loci which otherwise might stay hidden. In combination with a genome scan, the selective loci can be verified and the nature of the selection pressure can be identified., (© 2011 Blackwell Publishing Ltd.)

In all, 10 nuclear loci were re-sequenced in four spruce species. Three of the species are boreal species with very large natural ranges: Picea mariana and P. glauca are North American, and P. abies, is Eurasian. The fourth species, P. breweriana, is a Tertiary relict from Northern California, with a very small natural range. Although the boreal species population sizes have fluctuated through the Ice Ages, P. breweriana is believed to have had a rather stable population size through the Quaternary. Indeed, the average Tajima's D was close to zero in this species and negative in the three boreal ones. Reflecting differences in current population sizes, nucleotide diversity was an order of magnitude lower in P. breweriana than in the boreal species. This is in contrast to the similar and high levels of heterozygosity observed in previous studies at allozyme loci across species. As the species have very different histories and effective population sizes, selection at allozyme loci rather than demography appears to be a better explanation for this discrepancy. Parameters of Isolation-with-Migration (IM) models were also estimated for pairs of species. Shared polymorphisms were extensive and fixed polymorphisms few. Divergence times were much shorter than those previously reported. There was also evidence of historical gene flow between P. abies and P. glauca. The latter was more closely related to P. abies than to its sympatric relative P. mariana. This last result suggests that North American and Eurasian species might have been geographically much closer in the recent past than they are today.

Microbotryum violaceum is a basidiomycete that infects the anthers of its Caryophyllaceae host species. Individual fungal isolates are host limited, though they are not morphologically distinct. This study used variable regions of the highly conserved gamma-tubulin, beta-tubulin, and ribosomal RNA-encoding genes to determine the relationships among M. violaceum fungal isolates from different host species and different geographical locations. Phylogenetic trees from intron nucleotide sequences in two protein-coding genes were compared to trees produced from internal transcribed spacers (ITS) of rDNA. Phylogenetic analyses suggested that there are two clades, one from North America and one from Europe. Isolates from both clades grouped according to host species, although in some analyses isolates from closely related host species were placed together. These results are consistent with the view that M. violaceum has experienced cospeciation with its hosts., (2002 Elsevier Science (USA).)

Onopordum L. (Compositae) is an extremely diverse genus of thistles, which includes several species that have become serious pasture weeds in several regions of the world. We present a comparison of the genetic diversity in invasive forms of Onopordum from Australia with several known native European species. A total of 108 polymorphic genetic markers was generated using amplified fragment length polymorphism (AFLP) fingerprinting. Non-metric multidimensional scaling (NMDS) revealed that Australia contained O. acanthium, O. illyricum and a full range of genetic intermediates between these species. Intermediates largely comprised segregating fragments diagnostic for European O. acanthium and O. illyricum with a low frequency of fragments that were diagnostic for other species never recorded in Australia. The current genetic patterns in Australia may be best explained by a combination of processes, both in the native and in the alien range. These include multiple introductions of seed, including hybrid material, and the continuous dispersal in Australia, leading to an increase in the contact among hybridizing taxa. Such processes appear to have produced more widespread hybridization and introgression in Australian Onopordum than is found in Europe.

As part of the European Union program of European Scientist Sequencing Arabidopsis (ESSA), the DNA sequence of a 24.053-bp insert of cosmid clone CC17J13 was determined. The cosmid is located on chromosome 1 at the PFL locus (position 30 cM). Analysis of the sequence and comparison to public databases predicts seven genes in this area, thus approximately one gene every 3.3 kb. Three cDNAs corresponding to genes in this region were also sequenced. The homologies and/or possible functions of the (putative) genes are discussed. Proteins encoded by genes in this region include a polyadenylate-binding protein (PAB-3) and a GTP-binding protein (Rab7) as well as a novel protein, possibly involved in double-stranded RNA unwinding and apoptosis. Intriguingly, the gene encoding the PAB-3 protein, which is very specifically expressed, is flanked by putative matrix attachment regions.