Publications
NIBIOs employees contribute to several hundred scientific articles and research reports every year. You can browse or search in our collection which contains references and links to these publications as well as other research and dissemination activities. The collection is continously updated with new and historical material.
2021
Forfattere
Ruth Jaén-Molina Águedo Marrero-Rodríguez Juli Caujapé-Castells Dario Isidro Ojeda AlayonSammendrag
With a wide distribution range including Europe and Asia, Lotus (Leguminosae) represents the largest genus within Loteae. It is particularly diverse in the Mediterreanean region and in the five archipelagos of Macaronesia (Atlantic Ocean). However, little is known about the relationships among the 14 sections currently recognized within Lotus and about the timing and patterns of its colonization in the Macaronesian region. In this investigation, we use four DNA regions (nuclear ribosomal ITS plus three plastid regions) in the most comprehensive sampling of Lotus species to date (some endemic species within the Canary Islands were poorly represented in previous phylogenetic analyses) to infer relationships within this genus and to establish patterns of colonization in Macaronesia. Divergence time estimates and habitat reconstruction analyses indicate that Lotus likely diverged about 7.86 Ma from its sister group, but all colonization events to Macaronesia occurred more recently (ranging from the last 0.23 to 2.70 Ma). The diversification of Lotus in Macaronesia involved between four and six independent colonization events from four sections currently distributed in Africa and Europe. A major aspect shaping the current distribution of taxa involved intra-island colonization of mainly new habitats and inter-island colonization of mostly similar habitats, with Gran Canaria and Tenerife as the major sources of diversification and of further colonization events. Section Pedrosia is the most diverse in terms of colonization events, number of species, and habitat heterogeneity, including a back-colonization event to the continent. Subsections within Pedrosia radiated into diverse habitat types recently (late Pleistocene, ca 0.23–0.29 Ma) and additional molecular markers and sampling would be necessary to understand the most recent dispersal events of this group within the Canary Islands and Cape Verde.
Forfattere
Chedly Kastally Alina Katariina Niskanen Annika Perry Sonja T. Kujala Komlan Avia Sandra Cervantes Matti Haapanen Robert Kesälahti Timo A. Kumpula Tiina M. Mattila Dario Isidro Ojeda Alayon Jaakko S. Tyrmi Witold Wachowiak Stephen Cavers Katri Kärkkäinen Outi Savolainen Tanja PyhäjärviSammendrag
Pinus sylvestris (Scots pine) is the most widespread coniferous tree in the boreal forests of Eurasia, with major economic and ecological importance. However, its large and repetitive genome presents a challenge for conducting genome-wide analyses such as association studies, genetic mapping and genomic selection. We present a new 50K single-nucleotide polymorphism (SNP) genotyping array for Scots pine research, breeding and other applications. To select the SNP set, we first genotyped 480 Scots pine samples on a 407 540 SNP screening array and identified 47 712 high-quality SNPs for the final array (called ‘PiSy50k’). Here, we provide details of the design and testing, as well as allele frequency estimates from the discovery panel, functional annotation, tissue-specific expression patterns and expression level information for the SNPs or corresponding genes, when available. We validated the performance of the PiSy50k array using samples from Finland and Scotland. Overall, 39 678 (83.2%) SNPs showed low error rates (mean = 0.9%). Relatedness estimates based on array genotypes were consistent with the expected pedigrees, and the level of Mendelian error was negligible. In addition, array genotypes successfully discriminate between Scots pine populations of Finnish and Scottish origins. The PiSy50k SNP array will be a valuable tool for a wide variety of future genetic studies and forestry applications.
Sammendrag
The complete chloroplast genome sequence of wild sea mallow Malva wigandii (=Lavatera maritima) was determined and characterized in this study. The genome is 158,162 bp long, containing a pair of inverted repeats regions (IRs) of 25,166 bp, which are separated by a large single-copy region of 86,860 bp and a small single-copy region of 20,970 bp. The sea mallow chloroplast genome has 131 known genes, including 85 protein-coding genes, eight ribosomal RNA genes, and 37 tRNA genes. The phylogenomic analysis showed that M. wigandii forms a cluster with Althaea officinalis with a strong bootstrap support and is sister to sequences belonging to the tribe Gossypieae. All of them are grouped in a lineage with other members of the subfamily Malvoideae. This newly sequenced chloroplast genome sequence provides useful genetic information to explore the origin and evolution of the Mediterranean radiation that gave rise to the generic alliance of Malva.
Sammendrag
During a three-day field trip to the Gaupne area, Luster kommune, three main localities were visited in search of lichens. A total of 35 lichens or lichenicolous fungi were found to be new to Sogn og Fjordane, most of which are also rare on a national scale. Three species on rocks, Calogaya biatorina, Lecanora gisleriana and L. subaurea, are red-listed and two species, Blastenia monticola and Caloplaca squamuleoisidiata, are new to Norway. Most of the species new to Sogn og Fjordane are calcicolous or prefer siliceous rocks containing high levels of heavy metals. The area around Gaupne is shown to be a previously unknown lichen hot-spot.
Sammendrag
Population fluctuations of small rodents are often synchronized over larger areas (>100 km) than what could be explained by dispersal, suggesting that the synchronizing factor is weather-related and possibly mediated through changes in food quality. Because bank vole (Myodes glareolus) populations usually peak 1 year after peaks in reproduction of the staple winter food plant bilberry (Vaccinium myrtillus), we tested for a possible link between food and spatial synchrony by comparing the synchrony in bank vole population indices and bilberry seed production indices between three study areas across about 20,000 km2 in South Norway during a four decade period (1979–2019). There were subperiods of spatial synchrony and asynchrony between the study areas in the fluctuations of bank vole numbers and bilberry seed production, with the latter part of the study period displaying more pronounced synchrony than the first and middle part. However, with a few marked exceptions, when vole fluctuations were spatially out of phase across study areas so was bilberry seed production. Thus, we conclude that bilberry seed production to a large extent explained the spatiotemporal synchronicity in bank vole population fluctuations. Although bilberry seed production seems to be a causal driver of vole fluctuations, it remains to be seen to what extent the chemical composition of bilberry plants influences vole performance. Finally, certain weather factors may still influence voles directly, or indirectly by triggering bilberry seed production.
Forfattere
Torstein Kvamme Michail Mandelshtam Мaria Salnitska Dario Isidro Ojeda Alayon Åke LindelövSammendrag
No abstract has been registered
2020
Sammendrag
Red-listed species are often used as target species in selection of sites for conservation. However, limitations to their use have been pointed out, and here we address the problem of expected high spatio-temporal dynamics of red-listed species. We used species data (vascular plants, bryophytes, macrolichens and polypore fungi) from two inventories 17 years apart to estimate temporal turnover of red-listed and non-red-listed species in two forest areas (147 and 195 ha) and of plots (0.25 ha) within each area. Furthermore, we investigated how turnover of species afected the rank order of plots regarding richness of red-listed species, using two diferent national Red List issues (1998 and 2015). In both study areas, temporal turnover was substantial, despite minor changes in the overall number of species. At plot level, temporal turnover in red-listed species was higher than in non-red-listed species, but similar to non-red-listed species of the same frequency of occurrence. Adding the efect of changing identities of species red-listed according to the two Red List issues, further increased the estimated spatio-temporal dynamics. Recorded spatio-temporal turnover also resulted in substantial changes in the rank order of plots regarding richness of red-listed species. Using rare red-listed species for site selection may therefore be accompanied by a higher loss of conservation efectiveness over time than for more common species, and particularly at fner scales. Red-listed species · Site selection · Spatio-temporal dynamics · Temporal turnover
Forfattere
Erik J. M. Koenen Dario Isidro Ojeda Alayon Royce Steeves Jérémy Migliore Freek T. Bakker Jan J. Wieringa Catherine Kidner Olivier J. Hardy R. Toby Pennington Anne Bruneau Colin E. HughesSammendrag
Phylogenomics is increasingly used to infer deep‐branching relationships while revealing the complexity of evolutionary processes such as incomplete lineage sorting, hybridization/introgression and polyploidization. We investigate the deep‐branching relationships among subfamilies of the Leguminosae (or Fabaceae), the third largest angiosperm family. Despite their ecological and economic importance, a robust phylogenetic framework for legumes based on genome‐scale sequence data is lacking. We generated alignments of 72 chloroplast genes and 7621 homologous nuclear‐encoded proteins, for 157 and 76 taxa, respectively. We analysed these with maximum likelihood, Bayesian inference, and a multispecies coalescent summary method, and evaluated support for alternative topologies across gene trees. We resolve the deepest divergences in the legume phylogeny despite lack of phylogenetic signal across all chloroplast genes and the majority of nuclear genes. Strongly supported conflict in the remainder of nuclear genes is suggestive of incomplete lineage sorting. All six subfamilies originated nearly simultaneously, suggesting that the prevailing view of some subfamilies as ‘basal’ or ‘early‐diverging’ with respect to others should be abandoned, which has important implications for understanding the evolution of legume diversity and traits. Our study highlights the limits of phylogenetic resolution in relation to rapid successive speciation.
Forfattere
Boris B. Demenou Jérémy Migliore Myriam Heuertz Franck K. Monthe Dario Isidro Ojeda Alayon Jan J. Wieringa Gilles Dauby Laura Albreht Arthur Boom Olivier J. HardySammendrag
Paleo-environmental data show that the distribution of African rain forests was affected by Quaternary climate changes. In particular, the Dahomey Gap (DG) – a 200 km wide savanna corridor currently separating the West African and Central African rain forest blocks and containing relict rain forest fragments – was forested during the mid-Holocene and possibly during previous interglacial periods, whereas it was dominated by open vegetation (savanna) during glacial periods. Genetic signatures of past population fragmentation and demographic changes have been found in some African forest plant species using nuclear markers, but such events appear not to have been synchronous or shared across species. To better understand the colonization history of the DG by rain forest trees through seed dispersal, the plastid genomes of two widespread African forest legume trees, Anthonotha macrophylla and Distemonanthus benthamianus, were sequenced in 47 individuals for each species, providing unprecedented phylogenetic resolution of their maternal lineages (857 and 115 SNPs, respectively). Both species exhibit distinct lineages separating three regions: 1. Upper Guinea (UG, i.e. the West African forest block), 2. the area ranging from the DG to the Cameroon volcanic line (CVL), and 3. Lower Guinea (LG, the western part of the Central African forest block) where three lineages co-occur. In both species, the DG populations (including southern Nigeria west of Cross River) exhibit much lower genetic diversity than UG and LG populations, and their plastid lineages originate from the CVL, confirming the role of the CVL as an ancient forest refuge. Despite the similar phylogeographic structures displayed by A. macrophylla and D. benthamianus, molecular dating indicates very contrasting ages of lineage divergence (UG diverged from LG since c. 7 Ma and 0.7 Ma, respectively) and DG colonization (probably following the Mid Pleistocene Transition and the Last Glacial Maximum, respectively). The stability of forest refuge areas and repeated similar forest shrinking/expanding events during successive glacial periods might explain why similar phylogeographic patterns can be generated over contrasting timescales.
Forfattere
Manuel de la Estrella Sandra Cervantes Steven B. Janssens Félix Forest Olivier J. Hardy Dario Isidro Ojeda AlayonSammendrag
Aim: The Guineo‐Congolian region in Africa constitutes the second largest area of tropical rainforest (TRF) in the world. It covered an estimated 15–22 million km2 during the late Miocene (55–11 Ma) and it has experienced since a declining trend, currently reaching 3.4 million km2, associated with increasing aridification and the replacement of TRF by savanna habitats. Here, we examine whether rainforest area contraction led to a decrease in net diversification rates linked to increasing extinction, or if it is associated with increasing opportunities for allopatric or ecological speciation during periods of forest fragmentation. Location: Tropical Africa, Guineo‐Congolian region. Taxon: Anthonotha, Englerodendron, Berlinia clade (Leguminosae). Methods: We used a target enrichment approach combined with a complete data set representing all genera within the Berlinia clade. We combined phylogenomic, dating estimates, habitat reconstruction and diversification rate analyses to infer the effect of change in rainforest area coverage at two taxonomic levels: among genera, and within Anthonotha and Englerodendron. Results: We recovered fully resolved and well‐supported relationships among all genera and among species within the two genera. Most genera (87.5%) diverged before the Pleistocene, but Anthonotha and Englerodendron diversified recently, during the most recent cycles of forest contraction and expansion of the Pleistocene. Main conclusions: Our results suggest that the Berlinia clade displays an overall trend of accumulation of species over evolutionary time, suggesting the reduction in TRF area has not decreased net diversification rates. Most habitat shifts to savanna occurred in the Miocene, with no major habitat shifts during the most recent phases of forest expansion–contraction in the Pleistocene. Shifts in habitat from lowland forest to savanna did not trigger diversification rates, but habitat fragmentation might have increased diversification rates through allopatric speciation.