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The Finnish population is a unique example of a genetic isolate affected by a recent founder event. Previous studies have suggested that the ancestors of Finnic-speaking Finns and Estonians reached the circum-Baltic region by the 1(st) millennium BC. However, high linguistic similarity points to a more recent split of their languages. To study genetic connectedness between Finns and Estonians directly, we first assessed the efficacy of imputation of low-coverage ancient genomes by sequencing a medieval Estonian genome to high depth (23×) and evaluated the performance of its down-sampled replicas. We find that ancient genomes imputed from >0.1× coverage can be reliably used in principal-component analyses without projection. By searching for long shared allele intervals (LSAIs; similar to identity-by-descent segments) in unphased data for >143,000 present-day Estonians, 99 Finns, and 14 imputed ancient genomes from Estonia, we find unexpectedly high levels of individual connectedness between Estonians and Finns for the last eight centuries in contrast to their clear differentiation by allele frequencies. High levels of sharing of these segments between Estonians and Finns predate the demographic expansion and late settlement process of Finland. One plausible source of this extensive sharing is the 8(th)–10(th) centuries AD migration event from North Estonia to Finland that has been proposed to explain uniquely shared linguistic features between the Finnish language and the northern dialect of Estonian and shared Christianity-related loanwords from Slavic. These results suggest that LSAI detection provides a computationally tractable way to detect fine-scale structure in large cohorts.

Background Traces of interbreeding of Neanderthals and Denisovans with modern humans in the form of archaic DNA have been detected in the genomes of present-day human populations outside sub-Saharan Africa. Up to now, only nuclear archaic DNA has been detected in modern humans; we therefore attempted to identify archaic mitochondrial DNA (mtDNA) residing in modern human nuclear genomes as nuclear inserts of mitochondrial DNA (NUMTs). Results We analysed 221 high-coverage genomes from Oceania and Indonesia using an approach which identifies reads that map both to the nuclear and mitochondrial DNA. We then classified reads according to the source of the mtDNA, and found one NUMT of Denisovan mtDNA origin, present in 15 analysed genomes; analysis of the flanking region suggests that this insertion is more likely to have happened in a Denisovan individual and introgressed into modern humans with the Denisovan nuclear DNA, rather than in a descendant of a Denisovan female and a modern human male. Conclusions Here we present our pipeline for detecting introgressed NUMTs in next generation sequencing data that can be used on genomes sequenced in the future. Further discovery of such archaic NUMTs in modern humans can be used to detect interbreeding between archaic and modern humans and can reveal new insights into the nature of such interbreeding events.

Recent taxonomic and DNA sequence-based studies in several groups of lichen-forming fungi have revealed incongruence between the morphological and molecule-based circumscriptions of species. While the cosmopolitan genus Usnea is well-known and easily recognized by the yellowish beard-like thallus with central cord, delimitation of many Usnea species is difficult due to the high variation and complexity of diagnostic characters. In this study, we assessed the monophyly of 18 species from section Usnea occurring in North America and Europe, including sorediate and sexually reproducing taxa with both pendent and shrubby thalli. Six nuclear markers (ribosomal internal transcribed spacer (ITS) and intergenic spacer (IGS), and protein-coding beta-tubulin, MCM7, RPB1 and RPB2) were sequenced for 144 samples. All analyzed loci show weak genetic structure and short branch lengths in single-locus topologies, suggesting recent diversification history of the sampled taxa. Concatenated, multi-locus analyses conducted in Bayesian and maximum likelihood frameworks, as well as coalescent-based species delimitation and species tree methods, recover several distinct clades, some represent traditional morphology-based species (Usnea cavernosa, U. praetervisa, U. silesiaca, U. wasmuthii), while others form clusters of two or more species (Usnea florida–U. subfloridana, U. fulvoreagens–U. glabrescens, U. barbata–U. chaetophora–U. dasopoga–U. diplotypus, U. barbata–U. intermedia–U. lapponica–U. substerilis). We propose synonymization of U. substerilis under U. lapponica. The status of several other species within intermixed clusters requires further evaluation with more extensive sampling and the inclusion of more variable markers before taxonomic consequences can be considered. A new species, Usnea parafloridana is described from Wisconsin, USA.

WOS: 000365393000021, PubMed ID: 26299211, We studied the evolutionary history of the Parmeliaceae (Lecanoromycetes, Ascomycota), one of the largest families of lichen-forming fungi with complex and variable morphologies, also including several lichenicolous fungi. We assembled a six-locus data set including nuclear, mitochondrial and low-copy protein-coding genes from 293 operational taxonomic units (OTUs). The lichenicolous lifestyle originated independently three times in lichenized ancestors within Parmeliaceae, and a new generic name is introduced for one of these fungi. In all cases, the independent origins occurred c. 24 million yr ago. Further, we show that the Paleocene, Eocene and Oligocene were key periods when diversification of major lineages within Parmeliaceae occurred, with subsequent radiations occurring primarily during the Oligocene and Miocene. Our phylogenetic hypothesis supports the independent origin of lichenicolous fungi associated with climatic shifts at the Oligocene-Miocene boundary. Moreover, diversification bursts at different times may be crucial factors driving the diversification of Parmeliaceae. Additionally, our study provides novel insight into evolutionary relationships in this large and diverse family of lichen-forming ascomycetes., Spanish Ministerio de Ciencia e Innovacion [CGL2010-21646/BOS, CGL2011-25003, CGL2013-42498-P]; Universidad Complutense-Banco Santander [GR3/14]; Comunidad Autonoma de Madrid [REMEDINAL S-2009/AMB-1783]; National Science Foundation [DEB-0949147]; Swedish Research Council [VR621-2009-5372, VR 621-2012-3990]; Academy of Finland [1133858]; Estonian Science Foundation [9109]; European Regional Development Fund (Center of Excellence FIBIR); German Academic Exchange Service (DAAD); Tromso University Museum, We are indebted to Adriano A. Spielmann, Joel Mercado, Robert Egan, Udeni Jayalal and Daniel Sanchez Mata for providing a few samples, and to Rosario G. Gavilan for assisting in collecting expeditions. We also thank editors and anonymous reviewers for valuable comments and suggestions. This work was supported by the Spanish Ministerio de Ciencia e Innovacion (projects CGL2010-21646/BOS, CGL2011-25003 and CGL2013-42498-P), the Universidad Complutense-Banco Santander (GR3/14), Comunidad Autonoma de Madrid (REMEDINAL S-2009/AMB-1783), the National Science Foundation ('Hidden diversity in parmelioid lichens'; DEB-0949147), the Swedish Research Council (VR621-2009-5372 and VR 621-2012-3990), the Academy of Finland (grant 1133858), the Estonian Science Foundation (grant 9109), and the European Regional Development Fund (Center of Excellence FIBIR). G.S. was supported by a fellowship from the German Academic Exchange Service (DAAD). I.K.K.T. was supported by a grant from Tromso University Museum.

Clovis, with its distinctive biface, blade and osseous technologies, is the oldest widespread archaeological complex defined in North America, dating from 11,100 to 10,700 C-14 years before present (BP) (13,000 to 12,600 calendar years BP)(1,2). Nearly 50 years of archaeological research point to the Clovis complex as having developed south of the North American ice sheets from an ancestral technology(3). However, both the origins and the genetic legacy of the people who manufactured Clovis tools remain under debate. It is generally believed that these people ultimately derived from Asia and were directly related to contemporary Native Americans(2). An alternative, Solutrean, hypothesis posits that the Clovis predecessors emigrated from southwestern Europe during the Last Glacial Maximum(4). Here we report the genome sequence of a male infant (Anzick-1) recovered from the Anzick burial site in western Montana. The human bones date to 10,705 +/- 35 C-14 years BP (approximately 12,707-12,556 calendar years BP) and were directly associated with Clovis tools. We sequenced the genome to an average depth of 14.4x and show that the gene flow from the Siberian Upper Palaeolithic Mal'ta population(5) into Native American ancestors is also shared by the Anzick-1 individual and thus happened before 12,600 years BP. We also show that the Anzick-1 individual is more closely related to all indigenous American populations than to any other group. Our data are compatible with the hypothesis that Anzick-1 belonged to a population directly ancestral to many contemporary Native Americans. Finally, we find evidence of a deep divergence in Native American populations that predates the Anzick-1 individual.

The third version of the world list of cetrarioid lichens contains 572 names representing 149 accepted species. It is presented in a new, electronical form, based on a FileMaker-powered database, allowing users to view data in different sets and to perform searches. Type information is added for most of the names, and new information regarding the phylogenetic status of accepted taxa is introduced. Five global taxonomic databases (Catalogue of Life, Encyclopedia of Life, Index Fungorum, LIAS, MycoBank) are compared by scanning the availability of mainly nomenclatural data of 30 selected cetrarioid names (10 accepted names, 10 homotypic and 10 heterotypic synonyms); the significance of digital web resources is discussed.

The vertical gradient of the community structure of epiphytic lichens in forest canopies was studied in southern Estonian coniferous forests. All lichen species on 15 Norway spruces and 15 Scots pines were recorded; age of trees ≥100 years. Species were sampled in height ranges on entire trees from the bottom to the top. The number of lichen species on pine trunks decreased with height from the ground, whereas the number of species on branches increased. There was no significant vertical change in the number of lichen species on spruce trunks; number of species on spruce branches was highest in mid canopy. The mean number of lichen species on a tree was 41 in spruces and 34 in pines; the mean number of species on the first 2 m was 14 in spruces and 12 in pines. According to the results, about two thirds of a tree's lichen species remain unrecorded if only the first 2 m near the ground are surveyed. Many lichen species were found only higher than 2 m, including several common species (e.g. Buellia griseovirens, Lecanora pulicaris, and Melanohalea exasperatula), but also some locally rather rare (Fellhanera subtilis, Micarea nitschkeana, Rinodina efflorescens) or red-listed ones (Evernia mesomorpha, Usnea barbata, U. fulvoreagens, U. substerilis, U. wasmuthii) and one new species for Estonia, Lecanora farinaria. There were also some species, such as Chaenotheca stemonea, Cladonia cenotea and C. norvegica, that were restricted to the lowest 2 m. The results indicate that canopy lichens form a significant part of lichen diversity in coniferous forests, and could add valuable information when estimating forest lichen diversity for conservation and other purposes.

Epiphytic lichen communities were studied in old coniferous forests across Estonia to find out the effect of site openness on the lichen species richness. All lichen species were recorded on the basal 2 m of 105 Picea abies and 105 Pinus sylvetsris trunks. The canopy openness readings were taken with a spherical densiometer around every sampled tree. The number of species on the trunks of both tree species increased significantly with increasing canopy openness. Nine lichen species, e.g. Cladonia cenotea, Lecidea nylanderi, Platismatia glauca, were significantly favoured by higher light availability, and only one species, Coenogonium pineti, by lower light availability. The results demonstrate that in the coniferous forests higher light availability supports higher species richness of epiphytic lichens on the lower trunk of trees.

The delimitation of two morphologically similar and not easily separable Vulpicida species, V. juniperinus and V. tubulosus, is analyzed using nuclear ITS and Mcm7, and mitochondrial SSU DNA sequences. Seventy-nine Vulpicida specimens, most from the two focal taxa, are included in the three-locus gene tree. The results from Bayesian and parsimony analyses are presented. There are strong conflicts between the single locus gene trees. Vulpicida juniperinus and V. tubulosus are divided into two clearly distinguished groups in the ITS and concatenated B/MCMC tree. However, these species are mixed in both clades, appearing polyphyletic. Currently accepted V. juniperinus and V. tubulosus are not distinct according to the loci studied. Vulpicida pinastri appears monophyletic based on the available sequences.

Epiphytic lichen biota on Picea abies and Pinus sylvestris in Estonia was studied. Twenty-one spruce and 21 pine sample plots were located in old forests with long forest continuity, and 12 spruce and 12 pine sample plots in young first-generation forests (

This study focuses on EuropeanUsneaspecies with sorediate shrubby thalli, with the aim to evaluate the morphological and chemical separation of species in the light of molecular data. Twenty-twoUsneaspecies, including widely distributed taxa such asU. diplotypus, U. fulvoreagens, U. glabrescens, U. lapponica, U. subfloridana, U. substerilisandU. wasmuthii, were included in the study using Bayesian and maximum parsimony analyses of nuclear ITS and beta-tubulin sequences. The analyses showed that: 1) most taxa that are morphologically well delimited are also distinct by means of molecular characters, 2) shrubby taxa in the sectionUsneathat are difficult to determine by traditional characters form a group of closely related but still genetically distinct entities, exceptU. diplotypusandU. substeriliswhich appear to be polyphyletic. The branch lengths differed largely between two parts of the ITS tree (sectionsUsneaandCeratinae).Usnea intermediais proposed as the sexually reproducing counterpart for the sorediateU. lapponica. Additionally, some new chemotypes ofUsneaspecies were determined.

UNLABELLED • PREMISE OF THE STUDY Species boundaries in many organism groups are still in a state of flux, and for empirical species delimitation, finding appropriate character sets and analytical tools are among the greatest challenges. In the lichenized fungal genus Vulpicida, six morphologically circumscribed species have been distinguished, but phenotypic characters partly overlap for three of these and intermediate forms occur. We used a combination of phylogenetic strategies to delimit the species in this genus.• METHODS Five DNA loci were sequenced and analyzed. Single-locus gene trees and a five-locus concatenated phylogeny were constructed to assess current Vulpicida species. Species boundaries were inferred from molecular data using two coalescent-based species delimitation methods (BP&P and Brownie) and from species trees reconstructed with three different algorithms (*BEAST, BEST, and STEM).• KEY RESULTS The two species restricted to North America, Vulpicida canadensis and V. viridis, are clearly distinct in all analyses. The four other traditionally accepted species form two strongly supported, closely related species-level lineages within the core group of the genus. On the basis of these results, we propose four instead of the current six species in the genus: V. canadensis, V. juniperinus, V. pinastri, and V. viridis, while V. tilesii and V. tubulosus are reduced to synonymy under V. juniperinus.• CONCLUSIONS Coalescent species delimitation and tree inference give consistent results for fully distinct Vulpicida species but not for diverging populations. Even the inconsistent results were informative, revealing developing isolation despite a complex history of recombination and incomplete lineage sorting.