Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

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Plastome based phylogenetics and younger crown node age in Pelargonium
Kerke, Sara J. van de; Shrestha, Bikash ; Ruhlman, Tracey A. ; Weng, Mao Lun ; Jansen, Robert K. ; Jones, Cynthia S. ; Schlichting, Carl D. ; Hosseini, Samin ; Mohammadin, Setareh ; Schranz, M.E. ; Bakker, Freek T. - \ 2019
Molecular Phylogenetics and Evolution 137 (2019). - ISSN 1055-7903 - p. 33 - 43.
Geraniaceae - Pelargonium - Phylogeny - Plastome - Time-calibrated

The predominantly South-African plant genus Pelargonium L'Hér. (Geraniaceae) displays remarkable morphological diversity, several basic chromosome numbers as well as high levels of organelle genomic rearrangements, and represents the 7th largest Cape Floristic Region clade. In this study, we reconstructed a phylogenetic tree based on 74 plastome exons and nuclear rDNA ITS regions for 120 species, which represents 43% taxon coverage for Pelargonium. We also performed a dating analysis to examine the timing of the major radiations in the genus. Phylogenetic analyses of nucleotide, amino acid, and ITS alignments confirmed the previously-documented subgeneric split into five main clades ((C1,C2),(B(A1,A2))) although clade only A1 received low bootstrap support. Using calibration evidence from a range of sources the Pelargonium crown age was estimated to be 9.7 My old, much younger than previous estimates for the genus but similar to recent studies of other Cape Floristic lineages that are part of both Fynbos and Succulent Karoo biomes.

Parastagonosporella fallopiae gen. et sp. nov. (Phaeosphaeriaceae) on Fallopia convolvulus from Iran
Bakhshi, Mounes ; Arzanlou, Mahdi ; Groenewald, Johannes Z. ; Quaedvlieg, William ; Crous, Pedro W. - \ 2019
Mycological Progress 18 (2019)1-2. - ISSN 1617-416X - p. 203 - 214.
2 new taxa - Leaf spot - Phaeosphaeria - Phylogeny - Plant pathogens - Taxonomy

Phaeosphaeriaceae is a species-rich family in the order Pleosporales, encompassing species with diverse lifestyles viz., endophytic, epiphytic, lichenicolous, phytopathogenic, saprobic and even human pathogenic. In a survey on biodiversity of fungal species associated with leaf spot diseases of herbaceous plants in Iran, a coelomycetous fungus was recovered from symptomatic leaves of Fallopia convolvulus. Morphologically, the fungal isolates resembled species in the genus Parastagonospora. Although the phylogenetic analysis based on combined LSU and ITS sequence data placed these isolates within the family Phaeosphaeriaceae, they clustered distinct from presently known genera in the family. The monotypic genus Parastagonosporella (Phaeosphaeriaceae) is therefore introduced, with Parastagonosporella fallopiae as type species. A detailed description is provided, with notes discussing allied genera in the family.

The Colletotrichum dracaenophilum, C. magnum and C. orchidearum species complexes
Damm, U. ; Sato, T. ; Alizadeh, A. ; Groenewald, J.Z. ; Crous, P.W. - \ 2019
Studies in Mycology 92 (2019). - ISSN 0166-0616 - p. 1 - 46.
Anthracnose - Ascomycota - Colletotrichum - Gloeosporium - Glomerella - Phylogeny - Systematics

Although Glomerella glycines, Colletotrichum magnum and C. orchidearum are known as causal agents of anthracnose of soybean, Cucurbitaceae and Orchidaceae, respectively, their taxonomy remains unresolved. In preliminary analyses based on ITS, strains of these species appear basal in Colletotrichum phylogenies, clustering close to C. cliviae, C. brevisporum and other recently described species from tropical or subtropical regions. Phylogenetic analyses (ITS, GAPDH, CHS-1, HIS3, ACT, TUB2) of 102 strains previously identified as Ga. glycines, C. magnum and C. orchidearum as well as other related strains from different culture collections and studies placed these taxa in three species complexes, and distinguished at least 24 species, including 11 new species. In this study, C. magnum, C. orchidearum and C. piperis were epitypified and their taxonomy resolved, while C. cliviicola was proposed as a new name for C. cliviae. Furthermore, a sexual morph was observed for C. yunnanense, while C. brevisporum, C. cliviicola and C. tropicicola were reported from new hosts or countries. Regarding their conidial morphology, species in the C. dracaenophilum, C. magnum and C. orchidearum species complexes are reminiscent of C. gloeosporioides or C. boninense s. lat., and were likely to be confused with them in the past.

Families and genera of diaporthalean fungi associated with canker and dieback of tree hosts
Fan, X.L. ; Bezerra, J.D.P. ; Tian, Cheng Ming ; Crous, P.W. - \ 2018
Persoonia 40 (2018)June. - ISSN 0031-5850 - p. 119 - 134.
Ascomycota - Phylogeny - Sordariomycetes - Taxonomy

In this study we accept 25 families in Diaporthales based on phylogenetic analyses using partial ITS, LSU, rpb2 and tef1-α gene sequences. Four different families associated with canker and dieback of tree hosts are morphologically treated and phylogenetically compared. These include three new families (Diaporthostomata-ceae, Pseudomelanconidaceae, Synnemasporellaceae), and one new genus, Dendrostoma (Erythrogloeaceae). Dendrostoma is newly described from Malus spectabilis, Osmanthus fragrans and Quercus acutissima having fusoid to cylindrical, bicellular ascospores, with three new species namely D. mali, D. osmanthi and D. quercinum. Diaporthostomataceae is characterised by conical and discrete perithecia with bicellular, fusoid ascospores on branches of Machilus leptophylla. Pseudomelanconidaceae is defined by conidiogenous cells with apical collarets and discreet annellations, and the inconspicuous hyaline conidial sheath when mature on Carya cathayensis, compared to morphologically similar families Melanconidaceae and Juglanconidaceae. Synnemasporellaceae is proposed to accommodate fungi with synnematous conidiomata, with descriptions of S. toxicodendri on Toxico-dendron sylvestre and S. aculeans on Rhus copallina.

On the origin of vanillyl alcohol oxidases
Gygli, Gudrun ; Vries, Ronald P. de; Berkel, Willem J.H. van - \ 2018
Fungal Genetics and Biology 116 (2018). - ISSN 1087-1845 - p. 24 - 32.
Dehydrogenase - Flavoprotein - Fungus - Phylogeny - Sequence motif
Vanillyl alcohol oxidase (VAO) is a fungal flavoenzyme that converts a wide range of para-substituted phenols. The products of these conversions, e.g. vanillin, coniferyl alcohol and chiral aryl alcohols, are of interest for several industries. VAO is the only known fungal member of the 4-phenol oxidising (4PO) subgroup of the VAO/PCMH flavoprotein family. While the enzyme has been biochemically characterised in great detail, little is known about its physiological role and distribution in fungi. We have identified and analysed novel, fungal candidate VAOs and found them to be mostly present in Pezizomycotina and Agaricomycotina. The VAOs group into three clades, of which two clades do not have any characterised member. Interestingly, bacterial relatives of VAO do not form a single outgroup, but rather split up into two separate clades. We have analysed the distribution of candidate VAOs in fungi, as well as their genomic environment. VAOs are present in low frequency in species of varying degrees of relatedness and in regions of low synteny. These findings suggest that fungal VAOs may have originated from bacterial ancestors, obtained by fungi through horizontal gene transfer. Because the overall conservation of fungal VAOs varies between 60 and 30% sequence identity, we argue for a more reliable functional prediction using critical amino acid residues. We have defined a sequence motif P-x-x-x-x-S-x-G-[RK]-N-x-G-Y-G-[GS] that specifically recognizes 4PO enzymes of the VAO/PCMH family, as well as additional motifs that can help to further narrow down putative functions. We also provide an overview of fingerprint residues that are specific to VAOs.
Mouse models for human intestinal microbiota research : a critical evaluation
Hugenholtz, Floor ; Vos, Willem M. de - \ 2018
Cellular and Molecular Life Sciences 75 (2018)1. - ISSN 1420-682X - p. 149 - 160.
Diet - Metagenome - Microbiome - Murine models - Phylogeny - Reproducibility
Since the early days of the intestinal microbiota research, mouse models have been used frequently to study the interaction of microbes with their host. However, to translate the knowledge gained from mouse studies to a human situation, the major spatio-temporal similarities and differences between intestinal microbiota in mice and humans need to be considered. This is done here with specific attention for the comparative physiology of the intestinal tract, the effect of dietary patterns and differences in genetics. Detailed phylogenetic and metagenomic analysis showed that while many common genera are found in the human and murine intestine, these differ strongly in abundance and in total only 4% of the bacterial genes are found to share considerable identity. Moreover, a large variety of murine strains is available yet most of the microbiota research is performed in wild-type, inbred strains and their transgenic derivatives. It has become increasingly clear that the providers, rearing facilities and the genetic background of these mice have a significant impact on the microbial composition and this is illustrated with recent experimental data. This may affect the reproducibility of mouse microbiota studies and their conclusions. Hence, future studies should take these into account to truly show the effect of diet, genotype or environmental factors on the microbial composition.
High-resolution phylogeny providing insights towards the epidemiology, zoonotic aspects and taxonomy of sapoviruses
Barry, A.F. ; Durães-Carvalho, R. ; Oliveira-Filho, Edmilson F. ; Alfieri, A. ; Poel, W.H.M. Van der - \ 2017
Infection, Genetics and Evolution 56 (2017). - ISSN 1567-1348 - p. 8 - 13.
Epidemiology - Phylogeny - Sapoviruses - Taxonomy - Zoonoses
The evolution, epidemiology and zoonotic aspects of Sapoviruses (SaV) are still not well explored. In this study, we applied high-resolution phylogeny to investigate the epidemiological and zoonotic origins as well as taxonomic classification of animal and human SaV. Bayesian framework analyses showed an increase in porcine SaV (PoSaV) population dynamics and genetic diversity between 1975 and 1982, resulting in a SaV gene flow and generation of new strains among porcine and human populations. Our results also show the contribution of different animal populations involved in SaV epidemiology and highlight zoonotic aspects, as exemplified by the crucial role that swine, dogs, mink and humans play in SaV spread. Additionally, phylogenetic analysis suggests that bats may play key role in SaV epidemiology. According to our hypothesis, these animals may act as reservoirs or intermediate host species, contributing to viral spread in zoonotic and other epidemiological scenarios and facilitating the generation of new SaV genogroups and genotypes through recombination events. Data from large-scale phylogeny partition based on patristic distance, did not show a correlation between transmission clusters on generation of SaV genogroups, nevertheless we present both important findings about SaV taxonomy and important considerations useful for further taxonomical studies.
PCR and omics based techniques to study the diversity, ecology and biology of anaerobic fungi : Insights, challenges and opportunities
Edwards, Joan E. ; Forster, Robert J. ; Callaghan, Tony M. ; Dollhofer, Veronika ; Dagar, Sumit S. ; Cheng, Yanfen ; Chang, Jongsoo ; Kittelmann, Sandra ; Fliegerova, Katerina ; Puniya, Anil K. ; Henske, John K. ; Gilmore, Sean P. ; O'Malley, Michelle A. ; Griffith, Gareth W. ; Smidt, Hauke - \ 2017
Frontiers in Microbiology 8 (2017). - ISSN 1664-302X - 27 p.
(meta) transcriptomics - Anaerobic fungi - Genomics - Metabolomics - Neocallimastigomycota - Phylogeny - Proteomics - Rumen

Anaerobic fungi (phylum Neocallimastigomycota) are common inhabitants of the digestive tract of mammalian herbivores, and in the rumen, can account for up to 20% of the microbial biomass. Anaerobic fungi play a primary role in the degradation of lignocellulosic plant material. They also have a syntrophic interaction with methanogenic archaea, which increases their fiber degradation activity. To date, nine anaerobic fungal genera have been described, with further novel taxonomic groupings known to exist based on culture-independent molecular surveys. However, the true extent of their diversity may be even more extensively underestimated as anaerobic fungi continue being discovered in yet unexplored gut and non-gut environments. Additionally many studies are now known to have used primers that provide incomplete coverage of the Neocallimastigomycota. For ecological studies the internal transcribed spacer 1 region (ITS1) has been the taxonomic marker of choice, but due to various limitations the large subunit rRNA (LSU) is now being increasingly used. How the continued expansion of our knowledge regarding anaerobic fungal diversity will impact on our understanding of their biology and ecological role remains unclear; particularly as it is becoming apparent that anaerobic fungi display niche differentiation. As a consequence, there is a need to move beyond the broad generalization of anaerobic fungi as fiber-degraders, and explore the fundamental differences that underpin their ability to exist in distinct ecological niches. Application of genomics, transcriptomics, proteomics and metabolomics to their study in pure/mixed cultures and environmental samples will be invaluable in this process. To date the genomes and transcriptomes of several characterized anaerobic fungal isolates have been successfully generated. In contrast, the application of proteomics and metabolomics to anaerobic fungal analysis is still in its infancy. A central problem for all analyses, however, is the limited functional annotation of anaerobic fungal sequence data. There is therefore an urgent need to expand information held within publicly available reference databases. Once this challenge is overcome, along with improved sample collection and extraction, the application of these techniques will be key in furthering our understanding of the ecological role and impact of anaerobic fungi in the wide range of environments they inhabit.

Seed and root endophytic fungi in a range expanding and a related plant species
Geisen, Stefan ; Kostenko, Olga ; Cnossen, Mark C. ; Hooven, Freddy C. ten; Vreš, Branko ; Putten, Wim H. van der - \ 2017
Frontiers in Microbiology 8 (2017). - ISSN 1664-302X - 11 p.
Cultivation - Endophytes - Fungi - Phylogeny - Range expanding plant species - Seeds - Soil - Soil Sterilization

Climate change is accelerating the spread of plants and their associated species to new ranges. The differences in range shift capacity of the various types of species may disrupt long-term co-evolved relationships especially those belowground, however, this may be less so for seed-borne endophytic microbes. We collected seeds and soil of the range-expanding Centaurea stoebe and the congeneric Centaurea jacea from three populations growing in Slovenia (native range of both Centaurea species) and the Netherlands (expanded range of C. stoebe, native range of C. jacea). We isolated and identified endophytic fungi directly from seeds, as well as from roots of the plants grown in Slovenian, Dutch or sterilized soil to compare fungal endophyte composition. Furthermore, we investigated whether C. stoebe hosts a reduced community composition of endophytes in the expanded range due to release from plant-species specific fungi while endophyte communities in C. jacea in both ranges are similar. We cultivated 46 unique and phylogenetically diverse endophytes. A majority of the seed endophytes resembled potential pathogens, while most root endophytes were not likely to be pathogenic. Only one endophyte was found in both roots and seeds, but was isolated from different plant species. Unexpectedly, seed endophyte diversity of southern C. stoebe populations was lower than of populations from the north, while the seed endophyte community composition of northern C. stoebe populations was significantly different southern C. stoebe as well as northern and southern C. jacea populations. Root endophyte diversity was considerably lower in C. stoebe than in C. jacea independent of plant and soil origin, but this difference disappeared when plants were grown in sterile soils. We conclude that the community composition of fungal endophytes not only differs between related plant species but also between populations of plants that expand their range compared to their native habitat. Our results suggest that fungal endophytes of two Centaurea species are not able to systemically infect plants. We highlight that endophytes remain poorly studied and further work should investigate the functional importance of endophytes.

The VAO/PCMH flavoprotein family
Ewing, Tom A. ; Fraaije, Marco W. ; Mattevi, Andrea ; Berkel, Willem J.H. van - \ 2017
Archives of Biochemistry and Biophysics 632 (2017). - ISSN 0003-9861 - p. 104 - 117.
Enzyme mechanism - Flavoprotein - Oxidoreductase - Phylogeny - Protein family
The VAO/PCMH flavoprotein family consists of structurally homologous flavin-dependent enzymes that catalyze a wide range of chemical reactions. Family members share an architecture consisting of a conserved FAD-binding domain and a more variable substrate-binding domain, which enables varying interactions with a range of substrates while maintaining the same cofactor-binding fold. Here, we provide an overview of the current state of our knowledge on the members of the VAO/PCMH family. Based on a phylogenetic analysis, we divide the family into 11 subgroups. We discuss the properties of these subgroups, focusing on recent developments in terms of the discovery of new family members and mechanistic advances. We also highlight open questions that will provide challenges for future research.
Naturalized alien flora of the world : Species diversity, taxonomic and phylogenetic patterns, geographic distribution and global hotspots of plant invasion
Pyšek, Petr ; Pergl, Jan ; Essl, Franz ; Lenzner, Bernd ; Dawson, Wayne ; Kreft, Holger ; Weigelt, Patrick ; Winter, Marten ; Kartesz, John ; Nishino, Misako ; Antonova, Liubov A. ; Barcelona, Julie F. ; Cabezas, Francisco J. ; Cárdenas, Dairon ; Cárdenas-Toro, Juliana ; Castaño, Nicolás ; Chacón, Eduardo ; Chatelain, Cyrille ; Dullinger, Stefan ; Ebel, Aleksandr L. ; Figueiredo, Estrela ; Fuentes, Nicol ; Genovesi, Piero ; Groom, Quentin J. ; Henderson, Lesley ; Inderjit, ; Kupriyanov, Andrey ; Masciadri, Silvana ; Maurel, Noëlie ; Meerman, Jan ; Morozova, Olga ; Moser, Dietmar ; Nickrent, Daniel L. ; Nowak, Pauline M. ; Pagad, Shyama ; Patzelt, Annette ; Pelser, Pieter B. ; Seebens, Hanno ; Shu, Wen Sheng ; Thomas, Jacob ; Velayos, Mauricio ; Weber, Ewald ; Wieringa, Jan J. ; Baptiste, María P. ; Kleunen, Mark Van - \ 2017
Preslia 89 (2017)3. - ISSN 0032-7786 - p. 203 - 274.
Alien species - Distribution - Global Naturalized Alien Flora (GloNAF) database - Invasive species - Islands - Life history - Mainland - Naturalized species - Phylogeny - Plant invasion - Regional floras - Species richness - Taxonomy - Zonobiome
Using the recently built Global Naturalized Alien Flora (GloNAF) database, containing data on the distribution of naturalized alien plants in 483 mainland and 361 island regions of the world, we describe patterns in diversity and geographic distribution of naturalized and invasive plant species, taxonomic, phylogenetic and life-history structure of the global naturalized flora as well as levels of naturalization and their determinants. The mainland regions with the highest numbers of naturalized aliens are some Australian states (with New South Wales being the richest on this continent) and several North American regions (of which California with 1753 naturalized plant species represents the world's richest region in terms of naturalized alien vascular plants). England, Japan, New Zealand and the Hawaiian archipelago harbour most naturalized plants among islands or island groups. These regions also form the main hotspots of the regional levels of naturalization, measured as the percentage of naturalized aliens in the total flora of the region. Such hotspots of relative naturalized species richness appear on both the western and eastern coasts of North America, in north-western Europe, South Africa, south-eastern Australia, New Zealand, and India. High levels of island invasions by naturalized plants are concentrated in the Pacific, but also occur on individual islands across all oceans. The numbers of naturalized species are closely correlated with those of native species, with a stronger correlation and steeper increase for islands than mainland regions, indicating a greater vulnerability of islands to invasion by species that become successfully naturalized. South Africa, India, California, Cuba, Florida, Queensland and Japan have the highest numbers of invasive species. Regions in temperate and tropical zonobiomes harbour in total 9036 and 6774 naturalized species, respectively, followed by 3280 species naturalized in the Mediterranean zonobiome, 3057 in the subtropical zonobiome and 321 in the Arctic. The New World is richer in naturalized alien plants, with 9905 species compared to 7923 recorded in the Old World. While isolation is the key factor driving the level of naturalization on islands, zonobiomes differing in climatic regimes, and socioeconomy represented by per capita GDP, are central for mainland regions. The 11 most widely distributed species each occur in regions covering about one third of the globe or more in terms of the number of regions where they are naturalized and at least 35% of the Earth's land surface in terms of those regions' areas, with the most widely distributed species Sonchus oleraceus occuring in 48% of the regions that cover 42% of the world area. Other widely distributed species are Ricinus communis, Oxalis corniculata, Portulaca oleracea, Eleusine indica, Chenopodium album, Capsella bursa-pastoris, Stellaria media, Bidens pilosa, Datura stramonium and Echinochloa crus-galli. Using the occurrence as invasive rather than only naturalized yields a different ranking, with Lantana camara (120 regions out of 349 for which data on invasive status are known), Calotropis procera (118), Eichhornia crassipes (113), Sonchus oleraceus (108) and Leucaena leucocephala (103) on top. As to the life-history spectra, islands harbour more naturalized woody species (34.4%) thanmainland regions (29.5%), and fewer annual herbs (18.7% compared to 22.3%). Ranking families by their absolute numbers of naturalized species reveals that Compositae (1343 species), Poaceae (1267) and Leguminosae (1189) contribute most to the global naturalized alien flora. Some families are disproportionally represented by naturalized aliens on islands (Arecaceae, Araceae, Acanthaceae, Amaryllidaceae, Asparagaceae, Convolvulaceae, Rubiaceae, Malvaceae), and much fewer so on mainland (e.g. Brassicaceae, Caryophyllaceae, Boraginaceae). Relating the numbers of naturalized species in a family to its total global richness shows that some of the large species-rich families are over-represented among naturalized aliens (e.g. Poaceae, Leguminosae, Rosaceae, Amaranthaceae, Pinaceae), some under-represented (e.g. Euphorbiaceae, Rubiaceae), whereas the one richest in naturalized species, Compositae, reaches a value expected from its global species richness. Significant phylogenetic signal indicates that families with an increased potential of their species to naturalize are not distributed randomly on the evolutionary tree. Solanum (112 species), Euphorbia (108) and Carex (106) are the genera richest in terms of naturalized species; over-represented on islands are Cotoneaster, Juncus, Eucalyptus, Salix, Hypericum, Geranium and Persicaria, while those relatively richer in naturalized species on the mainland are Atriplex, Opuntia, Oenothera, Artemisia, Vicia, Galium and Rosa. The data presented in this paper also point to where information is lacking and set priorities for future data collection. The GloNAF database has potential for designing concerted action to fill such data gaps, and provide a basis for allocating resources most efficiently towards better understanding and management of plant invasions worldwide.
The head of the earwig Forficula auricularia (Dermaptera) and its evolutionary implications
Neubert, David ; Simon, Sabrina ; Beutel, Rolf G. ; Wipfler, Benjamin - \ 2017
Arthropod Systematics and Phylogeny 75 (2017)1. - ISSN 1863-7221 - p. 99 - 124.
Morphology - Musculature - Phylogeny - Polyneoptera
The external and internal head morphology including the musculature of the common earwig Forficula auricularia is described in detail. We specified and corrected previous descriptions and provided a detailed documentation. The head of Forficula is characterized by prognathism, generalized mandibles with a mesal cutting edge distally of the mola and its drop-shaped appearance. We added the following new apomorphies for Dermaptera to the various previously reported ones: (I) coronal and frontal cleavage lines with corresponding strong internal strengthening ridges; (II) the division of the praementum into a basal and a distal sclerite; (III) the presence of a bumpulus at the tip of the paraglossa; (IV) the presence of large distal palpilla on the terminal maxillary and labial palpomeres and (V) the origin of M. tentoriohypopharyngealis on the submentum. Another potential apomorphy are the lateral lobes on the distal hypopharynx which are most likely not homologous to the superlingua of apterygote insect. Other characters such as the prominent ball-and-socket joint between scapus and pedicellus or the unique antennal heart are poorly studied within Dermaptera and therefore cannot be phylogenetically polarized. In contrast to the various ordinarial apomorphies, the dermapteran head exhibits only one potential synapomorphy with other polyneopteran orders: the absence of the linguactual tendon and the associated muscle that is shared with Plecoptera and/or Zoraptera. Our results show that additional studies of the presumingly basal splits of Dermaptera are required to understand the head evolution of the group.
Ecological determinants of butterfly vulnerability across the European continent
Essens, Tijl ; Langevelde, Frank van; Vos, Rutger A. ; Swaay, Chris A.M. van; Wallis de Vries, Michiel - \ 2017
Journal of Insect Conservation 21 (2017)3. - ISSN 1366-638X - p. 439 - 450.
Butterflies - Conservation - Life-history traits - Phylogeny - Red List - Vulnerability

In drawing up Red Lists, the extinction risks of butterflies and other insects are currently assessed mainly by using information on trends in distribution and abundance. Incorporating information on species traits may increase our ability to predict species responses to environmental change and, hence, their vulnerability. We summarized ecologically relevant life-history and climatic niche traits in principal components, and used these to explain the variation in five vulnerability indicators (Red List status, Endemicity, Range size, Habitat specialisation index, Affinity for natural habitats) for 397 European butterfly species out of 482 species present in Europe. We also evaluated a selection of 238 species to test whether phylogenetic correction affected these relationships. For all but the affinity for natural habitats, climatic niche traits predicted more variation in vulnerability than life-history traits; phylogenetic correction had no relevant influence on the findings. The life-history trait component reflecting mobility, development rate, and overwintering stage, proved the major non-climatic determinant of species vulnerability. We propose that this trait component offers a preferable alternative to the frequently used, but ecologically confusing generalist-specialist continuum. Our analysis contributes to the development of trait-based approaches to prioritise vulnerable species for conservation at a European scale. Further regional scale analyses are recommended to improve our understanding of the biological basis of species vulnerability.

Colonization and diversification of aquatic insects on three Macaronesian archipelagos using 59 nuclear loci derived from a draft genome
Rutschmann, Sereina ; Detering, Harald ; Simon, Sabrina ; Funk, David H. ; Gattolliat, Jean Luc ; Hughes, Samantha J. ; Raposeiro, Pedro M. ; DeSalle, Rob ; Sartori, Michel ; Monaghan, Michael T. - \ 2017
Molecular Phylogenetics and Evolution 107 (2017). - ISSN 1055-7903 - p. 27 - 38.
Baetidae - Island radiation - Multispecies coalescent - Phylogeny - Phylogeography

The study of processes driving diversification requires a fully sampled and well resolved phylogeny, although a lack of phylogenetic markers remains a limitation for many non-model groups. Multilocus approaches to the study of recent diversification provide a powerful means to study the evolutionary process, but their application remains restricted because multiple unlinked loci with suitable variation for phylogenetic or coalescent analysis are not available for most non-model taxa. Here we identify novel, putative single-copy nuclear DNA (nDNA) phylogenetic markers to study the colonization and diversification of an aquatic insect species complex, Cloeon dipterum L. 1761 (Ephemeroptera: Baetidae), in Macaronesia. Whole-genome sequencing data from one member of the species complex were used to identify 59 nDNA loci (32,213 base pairs), followed by Sanger sequencing of 29 individuals sampled from 13 islands of three Macaronesian archipelagos. Multispecies coalescent analyses established six putative species. Three island species formed a monophyletic clade, with one species occurring on the Azores, Europe and North America. Ancestral state reconstruction indicated at least two colonization events from the mainland (to the Canaries, respectively Azores) and one within the archipelago (between Madeira and the Canaries). Random subsets of the 59 loci showed a positive linear relationship between number of loci and node support. In contrast, node support in the multispecies coalescent tree was negatively correlated with mean number of phylogenetically informative sites per locus, suggesting a complex relationship between tree resolution and marker variability. Our approach highlights the value of combining genomics, coalescent-based phylogeography, species delimitation, and phylogenetic reconstruction to resolve recent diversification events in an archipelago species complex.

Comparative genomics of campylobacter iguaniorum to unravel genetic regions associated with reptilian hosts
Gilbert, Maarten J. ; Miller, William G. ; Yee, Emma ; Kik, Marja ; Zomer, Aldert L. ; Wagenaar, Jaap A. ; Duim, Birgitta - \ 2016
Genome Biology and Evolution 8 (2016)9. - ISSN 1759-6653 - p. 3022 - 3029.
Campylobacter Iguaniorum - Comparative Genomics - Evolution - Phylogeny - Recombination - Reptile

Campylobacter iguaniorum is most closely related to the species C. fetus, C. hyointestinalis, andC. lanienae. Reptiles, chelonians and lizards in particular, appear to be a primary reservoir of this Campylobacter species. Here we report the genome comparison of C. iguaniorumstrain 1485E, isolated from a bearded dragon (Pogona vitticeps), and strain 2463D, isolated froma green iguana (Iguana iguana), with the genomes of closely related taxa, in particular with reptile-Associated C. fetus subsp.Testudinum. In contrast to C. fetus, C. iguaniorum is lacking an S-layer encoding region. Furthermore, a defined lipooligosaccharide biosynthesis locus, encoding multiple glycosyltransferases and bounded by waa genes, is absent from C. iguaniorum. Instead, multiple predicted glycosylation regionswere identified inC. iguaniorum.One of these regions is>50 kb withdeviantG+Ccontent, suggesting acquisition via lateral transfer. These similar, but non-homologous glycosylation regions were located at the same position on the genome in both strains. Multiple genes encoding respiratory enzymes not identified to date within the C. fetus clade were present. C. iguaniorum shared highest homology with C. hyointestinalis and C. fetus. As in reptile-Associated C. fetus subsp.Testudinum, a putative tricarballylate catabolism locus was identified. However, despite colonizing a shared host, no recent recombination between both taxa was detected. This genomic study provides a better understanding of host adaptation, virulence, phylogeny, and evolution of C. iguaniorum and related Campylobacter taxa.

Prospects of herbivore egg-killing plant defenses for sustainable crop protection
Fatouros, Nina E. ; Cusumano, Antonino ; Danchin, Etienne G.J. ; Colazza, Stefano - \ 2016
Ecology and Evolution 6 (2016)19. - ISSN 2045-7758 - p. 6906 - 6918.
Egg deposition - Egg parasitoids - Hypersensitive response - Oviposition-induced plant volatiles - Phylogeny

Due to a growing demand of food production worldwide, new strategies are suggested to allow for sustainable production of food with minimal effects on natural resources. A promising alternative to the application of chemical pesticides is the implementation of crops resistant to insect pests. Plants produce compounds that are harmful to a wide range of attackers, including insect pests; thus, exploitation of their natural defense system can be the key for the development of pest-resistant crops. Interestingly, some plants possess a unique first line of defense that eliminates the enemy before it becomes destructive: egg-killing. Insect eggs can trigger (1) direct defenses, mostly including plant cell tissue growth or cell death that lead to eggs desiccating, being crushed or falling off the plant or (2) indirect defenses, plant chemical cues recruiting natural enemies that kill the egg or hatching larvae (parasitoids). The consequences of plant responses to eggs are that insect larvae do not hatch or that they are impeded in development, and damage to the plant is reduced. Here, we provide an overview on the ubiquity and evolutionary history of egg-killing traits within the plant kingdom including crops. Up to now, little is known on the mechanisms and on the genetic basis of egg-killing traits. Making use of egg-killing defense traits in crops is a promising new way to sustainably reduce losses of crop yield. We provide suggestions for new breeding strategies to grow egg-killing crops and improve biological control.

Take-all or nothing
Hernández-Restrepo, M. ; Groenewald, J.Z. ; Elliott, M.L. ; Canning, G. ; McMillan, V.E. ; Crous, P.W. - \ 2016
Studies in Mycology 83 (2016). - ISSN 0166-0616 - p. 19 - 48.
Cryptic species - Gaeumannomyces graminis - Magnaporthaceae - Phylogeny - Triticum

Take-all disease of Poaceae is caused by Gaeumannomyces graminis (Magnaporthaceae). Four varieties are recognised in G. graminis based on ascospore size, hyphopodial morphology and host preference. The aim of the present study was to clarify boundaries among species and varieties in Gaeumannomyces by combining morphology and multi-locus phylogenetic analyses based on partial gene sequences of ITS, LSU, tef1 and rpb1. Two new genera, Falciphoriella and Gaeumannomycella were subsequently introduced in Magnaporthaceae. The resulting phylogeny revealed several cryptic species previously overlooked within Gaeumannomyces. Isolates of Gaeumannomyces were distributed in four main clades, from which 19 species could be delimited, 12 of which were new to science. Our results show that the former varieties Gaeumannomyces graminis var. avenae and Gaeumannomyces graminis var. tritici represent species phylogenetically distinct from G. graminis, for which the new combinations G. avenae and G. tritici are introduced. Based on molecular data, morphology and host preferences, Gaeumannomyces graminis var. maydis is proposed as a synonym of G. radicicola. Furthermore, an epitype for Gaeumannomyces graminis var. avenae was designated to help stabilise the application of that name.

‘High-co-occurrence genera’: weak but consistent relationships with global richness, niche partitioning, hybridization and decline
Prinzing, Andreas ; Powrie, Leslie W. ; Hennekens, S.M. ; Bartish, Igor V. ; Ozinga, W.A. - \ 2016
Global Ecology and Biogeography 25 (2016)1. - ISSN 1466-822X - p. 55 - 64.
Angiosperms - Biodiversity - Community assembly - Hybridization - Macroevolution and microecology - Niche breadth - Niche variation - Phylogeny - Random sampling - Species decline

Aim: Many biologists explain the global richness of lineages and local co-occurrence of lineage members by distinct processes: speciation/extinction versus ecological interactions. Moreover, allopatric distribution, rarity and local competition limit local co-occurrence of species even within species-rich lineages. However, whether and why the global richness of lineages relates to local co-occurrence of lineage members has not been tested. We study angiosperms, and hypothesize that in globally species-rich genera species frequently encounter congeners locally, reflecting (1) random sampling of species pools into local communities and (2) processes of global species production and local survival such as hybridization, niche filling and a reduced risk of extinction. Location: Netherlands, South Africa, world-wide. Methods: Analysing more than 350,000 plots we quantify per species the observed number of co-occurring congeners as well as the null expectation based on random sampling from species pools. From the literature we quantify the global species richness of genera, and abiotic niche positions and breadths, hybrid status and regional species declines. Results: In some genera species frequently encounter congeners locally, while in others congeners are rarely encountered. This is independent of the total number of species encountered, and is consistent between the Netherlands and South Africa. 'High-co-occurrence genera' are particularly species rich across the globe, consistently so in most families and even after controlling for niche positions, age and regional richness of genera. Species in high-co-occurrence genera tend to occupy niches that are large and close to congeners' niches. These species are more often hybrids and rarely decline. Relationships explain little variance (

Environmental gradients and the evolution of successional habitat specialization : A test case with 14 Neotropical forest sites
Letcher, Susan G. ; Lasky, Jesse R. ; Chazdon, Robin L. ; Norden, Natalia ; Wright, S.J. ; Meave, Jorge A. ; Pérez-García, Eduardo A. ; Muñoz, Rodrigo ; Romero-Pérez, Eunice ; Andrade, Ana ; Balvanera, Patricia ; Bongers, Frans ; Lohbeck, Madelon - \ 2015
Journal of Ecology 103 (2015)5. - ISSN 0022-0477 - p. 1276 - 1290.
Determinants of plant community diversity and structure - Functional traits - Life-history evolution - Phylogeny - Pioneer species - Precipitation gradient - Tropical dry forest - Tropical wet forest

Successional gradients are ubiquitous in nature, yet few studies have systematically examined the evolutionary origins of taxa that specialize at different successional stages. Here we quantify successional habitat specialization in Neotropical forest trees and evaluate its evolutionary lability along a precipitation gradient. Theoretically, successional habitat specialization should be more evolutionarily conserved in wet forests than in dry forests due to more extreme microenvironmental differentiation between early and late-successional stages in wet forest. We applied a robust multinomial classification model to samples of primary and secondary forest trees from 14 Neotropical lowland forest sites spanning a precipitation gradient from 788 to 4000 mm annual rainfall, identifying species that are old-growth specialists and secondary forest specialists in each site. We constructed phylogenies for the classified taxa at each site and for the entire set of classified taxa and tested whether successional habitat specialization is phylogenetically conserved. We further investigated differences in the functional traits of species specializing in secondary vs. old-growth forest along the precipitation gradient, expecting different trait associations with secondary forest specialists in wet vs. dry forests since water availability is more limiting in dry forests and light availability more limiting in wet forests. Successional habitat specialization is non-randomly distributed in the angiosperm phylogeny, with a tendency towards phylogenetic conservatism overall and a trend towards stronger conservatism in wet forests than in dry forests. However, the specialists come from all the major branches of the angiosperm phylogeny, and very few functional traits showed any consistent relationships with successional habitat specialization in either wet or dry forests. Synthesis. The niche conservatism evident in the habitat specialization of Neotropical trees suggests a role for radiation into different successional habitats in the evolution of species-rich genera, though the diversity of functional traits that lead to success in different successional habitats complicates analyses at the community scale. Examining the distribution of particular lineages with respect to successional gradients may provide more insight into the role of successional habitat specialization in the evolution of species-rich taxa.

Phylogenetic patterns are not proxies of community assembly mechanisms (they are far better)
Gerhold, Pille ; Cahill, J.F. ; Winter, Marten ; Bartish, I.V. ; Prinzing, Andreas - \ 2015
Functional Ecology 29 (2015)5. - ISSN 0269-8463 - p. 600 - 614.
Coexistence - Competition - Evolution - Functional traits - Habitat filtering - Inter-actions - Lineage-pool - Macroevolutionary diversification - Phylogeny

The subdiscipline of 'community phylogenetics' is rapidly growing and influencing thinking regarding community assembly. In particular, phylogenetic dispersion of co-occurring species within a community is commonly used as a proxy to identify which community assembly processes may have structured a particular community: phylogenetic clustering as a proxy for abiotic assembly, that is habitat filtering, and phylogenetic overdispersion as a proxy for biotic assembly, notably competition. We challenge this approach by highlighting (typically) implicit assumptions that are, in reality, only weakly supported, including (i) phylogenetic dispersion reflects trait dispersion; (ii) a given ecological function can be performed only by a single trait state or combination of trait states; (iii) trait similarity causes enhanced competition; (iv) competition causes species exclusion; (v) communities are at equilibrium with processes of assembly having been completed; (vi) assembly through habitat filtering decreases in importance if assembly through competition increases, such that the relative balance of the two can be thus quantified by a single parameter; and (vii) observed phylogenetic dispersion is driven predominantly by local and present-day processes. Moreover, technical sophistication of the phylogenetic-patterns-as-proxy approach trades off against sophistication in alternative, potentially more pertinent approaches to directly observe or manipulate assembly processes. Despite concerns about using phylogenetic dispersion as a proxy for community assembly processes, we suggest there are underappreciated benefits of quantifying the phylogenetic structure of communities, including (i) understanding how coexistence leads to the macroevolutionary diversification of habitat lineage-pools (i.e. phylogenetic-patterns-as-result approach); and (ii) understanding the macroevolutionary contingency of habitat lineage-pools and how it affects present-day species coexistence in local communities (i.e. phylogenetic-patterns-as-cause approach). We conclude that phylogenetic patterns may be little useful as proxy of community assembly. However, such patterns can prove useful to identify and test novel hypotheses on (i) how local coexistence may control macroevolution of the habitat lineage-pool, for example through competition among close relatives triggering displacement and diversification of characters, and (ii) how macroevolution within the habitat lineage-pool may control local coexistence of related species, for example through origin of close relatives that can potentially enter in competition. 2015 British Ecological Society.

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