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The history of life has been driven by evolutionary transitions in individuality, that is, the aggregation of autonomous individuals to form a new, higher-level individual. The fungus Neurospora tetrasperma has recently undergone an evolutionary transition in individuality from homokaryosis (one single type of nuclei in the same cytoplasm) to heterokaryosis (two genetically divergent and free-ranging nuclear types). In this species, selection can act at different levels: while nuclei can compete in their replication and transmission into shortlived asexual spores, at the level of the heterokaryotic individual, cooperation between nuclear types is required to produce the long-lived sexual spores. Conflicts can arise between these two levels of selection if the coevolution between nuclear types is disrupted. Here, we investigated the extent of multilevel selection in three strains of N. tetrasperma. We assessed the ratio between nuclear types under different conditions and measured fitness traits of homo-and heterokaryotic mycelia with varying nuclear ratios. We show that the two nuclei have complementary traits, consistent with division of labor and cooperation. In one strain, for which a recent chromosomal introgression was detected, we observed the occurrence of selfish nuclei, enjoying better replication and transmission than sister nuclei at the same time as being detrimental to the heterokaryon. We hypothesize that introgression has disrupted the coevolution between nuclear types in this strain.

Turneraceae, with just over 200 species in 10 genera, is today often included in a widely circumscribed Passifloraceae. The vast majority of the species are found in the New World, whereas generic diversity is largest in the Old World. According to current circumscriptions, three of the genera show trans–Atlantic disjunctions: Turnera with over 135 species in America and two species in Africa (one in the south–western and one in the north–eastern part), Piriqueta with 44 species in America and one in southern Africa, and Erblichia with one species in Central America and four in Madagascar. The phylogeny of Turneraceae is reconstructed based on DNA sequences from plastid trnL–F and nuclear ITS and sampling for all genera, including both New and Old World species for the trans–Atlantic groups to test their monophyly. The genera of Turneraceae form a strongly supported monophyletic group, the Turneraceae clade, within Passifloraceae s.l. The phylogeny is geographically structured, with one clade comprising American species only, except for the two African species of Turnera, and another clade with all other African species plus the Central American Erblichia odorata. Turnera is retrieved as monophyletic with the two African species appearing as close relatives of T. ulmifolia, the type of Turnera. The existence of a trans–Atlantic disjunction in Turnera is therefore supported. It is most likely caused by long–distance dispersal and estimated to be not older than late Miocene. In Piriqueta only the American species are supported as a monophyletic group, whereas the single African species is resolved as a member of the African clade. The trans–Atlantic disjunction in Piriqueta is therefore not supported and the African species is proposed to be placed in a genus of its own, Afroqueta gen. nov., as Afroqueta capensis comb. nov. Erblichia on Madagascar is supported as sister to Mathurina, a genus endemic to Rodrigues Island in the Mascarenes, and does not group with E. odorata in Central America, the type of Erblichia. The trans–Atlantic disjunction in Erblichia is therefore not supported either and the genus Arboa gen. nov. is proposed to accommodate the four Malagasy species, Arboa integrifolia comb. nov., Arboa berneriana comb. nov., Arboa madagascariensis comb. nov., and Arboa antsingyae comb. nov.

BackgroundIncreasing evidence from DNA sequence data has revealed that phylogenies based on different genes may drastically differ from each other. This may be due to either inter- or intralineage processes, or to methodological or stochastic errors. Here we investigate a spectacular case where two parts of the same gene (SlX1/Y1) show conflicting phylogenies within Silene (Caryophyllaceae). SlX1 and SlY1 are sex-linked genes on the sex chromosomes of dioecious members of Silene sect. Elisanthe.ResultsWe sequenced the homologues of the SlX1/Y1 genes in several Sileneae species. We demonstrate that different parts of the SlX1/Y1 region give different phylogenetic signals. The major discrepancy is that Silene vulgaris and S. sect. Conoimorpha (S. conica and relatives) exchange positions. To determine whether gene duplication followed by recombination (an intralineage process) may explain the phylogenetic conflict in the Silene SlX1/Y1 gene, we use a novel probabilistic, multiple primer-pair PCR approach. We did not find any evidence supporting gene duplication/loss as explanation to the phylogenetic conflict.ConclusionThe phylogenetic conflict in the Silene SlX1/Y1 gene cannot be explained by paralogy or artefacts, such as in vitro recombination during PCR. The support for the conflict is strong enough to exclude methodological or stochastic errors as likely sources. Instead, the phylogenetic incongruence may have been caused by recombination of two divergent alleles following ancient interspecific hybridization or incomplete lineage sorting. These events probably took place several million years ago. This example clearly demonstrates that different parts of the genome may have different evolutionary histories and stresses the importance of using multiple genes in reconstruction of taxonomic relationships.

Atocion and Viscaria are two of seven small genera recognised in the tribe Sileneae on the basis of molecular phylogenies. The aim of the present study is to infer phylogenetic relationships among their subordinate taxa, using chloroplast (rps16 intron, psbE‐petG spacer region) and nuclear (ITS and the RNA polymerase gene family) DNA sequences. Relative dating was used to discriminate among intralineage and interlineage processes that cause incongruence among different gene‐tree topologies. Atocion asterias is demonstrated to belong to Viscaria, which contains three species: V. vulgaris (incl. V. atropurpurea), V. alpina, and V. asterias. Infraspecific differentiation of V. alpina is not supported by the sequence data. The traditional sectional delimitation of Atocion taxa within Silene is not supported phylogenetically, and Silene tatarinowii as well as S. hoefftiana do not belong to Atocion, as classified previously. Atocion contains six species: A. armeria, A. compactum, A. lerchenfeldianum, A. reuterianum, A. rupestre, and A. scythicinum (not included in our study). With this circumscription, Atocion and Viscaria, respectively, form monophyletic groups in the cpDNA, ITS, RPD2a and RPD2b trees, but not in the RPA2 tree, where such relationships were possibly distorted by ancient hybridisation. Hybridisation with subsequent chloroplast capture is likely to have taken place in the evolutionary history of A. compactum. Three novel nomenclatural combinations are made: Atocion reuterianum, A. scythicinum and Viscaria asterias.

Direct Sanger sequencing of polymerase chain reaction (PCR)-amplified nuclear genes leads to polymorphic sequences when allelic variation is present. To overcome this problem, most researchers subclone the PCR products to separate alleles. An alternative is to directly sequence the separate alleles using allele-specific primers. We tested two methods to enhance the specificity of allele-specific primers for use in direct sequencing: using short primers and amplification refractory mutation system (ARMS) technique. By shortening the allele-specific primer to 15-13 nucleotides, the single mismatch in the ultimate base of the primer is enough to hinder the amplification of the nontarget allele in direct sequencing and recover only the targeted allele at high accuracy. The deliberate addition of a second mismatch, as implemented in the ARMS technique, was less successful and seems better suited for allele-specific amplification in regular PCR rather than in direct sequencing.

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