| 1. |
- Dahlin, Sigrun, et al.
(författare)
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Mulch N recycling in green manure leys under Scandinavian conditions
- 2011
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Ingår i: Nutrient cycling in agroecosystems. - : Springer Science and Business Media LLC. - 1385-1314 .- 1573-0867. ; 91, s. 119-129
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Tidskriftsartikel (refereegranskat)abstract
- Nitrogen (N) recycling to the regrowth of mulched red clover (Trifolium pratense L.) and mulched mixed red clover/perennial ryegrass (Lolium perenne L.) leys was determined in field experiments during three consecutive years using (15)N-labelled shoot material. Nitrogen recycling was greater in the pure clover stands than in the mixed stands in the beginning of the growing season, but increased successively in the mixed stands so that it was similar (14-15.5%) in both stands at the end of the season. This recycling of N from the mulch led to increased biomass accumulation but did not alter stand composition in the mixed stands. Mulch-derived N was incorporated into the soil organic N in both pure clover and mixed stands which thus contributed to building up soil fertility. An approximately similar proportion of N remained unaccounted for in mulched pure clover and mixed stand leys and presumably represented gaseous losses. To exploit the benefits of green manure leys in the humid temperate zone while minimising the negative environmental impact, these should be harvested rather than mulched.
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| 2. |
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| 3. |
- Bruneau, Anne, et al.
(författare)
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Advances in Legume Systematics 14. Classification of Caesalpinioideae. Part 2: Higher-level classification
- 2024
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Ingår i: PhytoKeys. - Sofia : Pensoft Publishers. - 1314-2011 .- 1314-2003. ; 240, s. 1-552
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Tidskriftsartikel (refereegranskat)abstract
- Caesalpinioideae is the second largest subfamily of legumes (Leguminosae) with ca. 4680 species and 163 genera. It is an ecologically and economically important group formed of mostly woody perennials that range from large canopy emergent trees to functionally herbaceous geoxyles, lianas and shrubs, and which has a global distribution, occurring on every continent except Antarctica. Following the recent re-circumscription of 15 Caesalpinioideae genera as presented in Advances in Legume Systematics 14, Part 1, and using as a basis a phylogenomic analysis of 997 nuclear gene sequences for 420 species and all but five of the genera currently recognised in the subfamily, we present a new higher-level classification for the subfamily. The new classification of Caesalpinioideae comprises eleven tribes, all of which are either new, reinstated or re-circumscribed at this rank: Caesalpinieae Rchb. (27 genera / ca. 223 species), Campsiandreae LPWG (2 / 5-22), Cassieae Bronn (7 / 695), Cera-tonieae Rchb. (4 / 6), Dimorphandreae Benth. (4 / 35), Erythrophleeae LPWG (2 /13), Gleditsieae Nakai (3 / 20), Mimoseae Bronn (100 / ca. 3510), Pterogyneae LPWG (1 / 1), Schizolobieae Nakai (8 / 42-43), Sclerolobieae Benth. & Hook. f. (5 / ca. 113). Although many of these lineages have been recognised and named in the past, either as tribes or informal generic groups, their circumscriptions have varied widely and changed over the past decades, such that all the tribes described here differ in generic membership from those previously recognised. Importantly, the approximately 3500 species and 100 genera of the former subfamily Mimosoideae are now placed in the reinstated, but newly circumscribed, tribe Mimoseae. Because of the large size and ecological importance of the tribe, we also provide a clade-based classification system for Mimoseae that includes 17 named lower-level clades. Fourteen of the 100 Mimoseae genera remain unplaced in these lower-level clades: eight are resolved in two grades and six are phylogenetically isolated monogeneric lineages. In addition to the new classification, we provide a key to genera, morphological descriptions and notes for all 163 genera, all tribes, and all named clades. The diversity of growth forms, foliage, flowers and fruits are illustrated for all genera, and for each genus we also provide a distribution map, based on quality-controlled herbarium specimen localities. A glossary for specialised terms used in legume morphology is provided. This new phylogenetically based classification of Caesalpinioideae provides a solid system for communication and a framework for downstream analyses of biogeography, trait evolution and diversification, as well as for taxonomic revision of still understudied genera.
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| 4. |
- de Boer, Hugo J., et al.
(författare)
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Synopsis of Trichosanthes (Cucurbitaceae) based on recent molecular phylogenetic data
- 2012
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Ingår i: PhytoKeys. - : Pensoft Publishers. - 1314-2011 .- 1314-2003. ; 12, s. 23-33
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Tidskriftsartikel (refereegranskat)abstract
- The snake gourd genus, Trichosanthes, is the largest genus in the Cucurbitaceae family, with over 90 species. Recent molecular phylogenetic data have indicated that the genus Gymnopetalum is to be merged with Trichosanthes to maintain monophyly. A revised infrageneric classification of Trichosanthes including Gymnopetalum is proposed with two subgenera, (I) subg. Scotanthus comb. nov. and (II) subg. Trichosanthes, eleven sections, (i) sect. Asterospermae, (ii) sect. Cucumeroides, (iii) sect. Edulis, (iv) sect. Foliobracteola, (v) sect. Gymnopetalum, (vi) sect. Involucraria, (vii) sect. Pseudovariifera sect. nov., (viii) sect. Villosae star. nov., (ix) sect. Trichosanthes, (x) sect. Tripodanthera, and (xi) sect. Truncata. A synopsis of Trichosanthes with the 91 species recognized here is presented, including four new combinations, Trichosanthes orientalis, Trichosanthes tubiflora, Trichosanthes scabra var. pectinata, Trichosanthes scabra var. penicaudii, and a clarified nomenclature of Trichosanthes costata and Trichosanthes scabra.
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| 5. |
- Eggens, Frida, et al.
(författare)
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Phylogeny and species delimitation in Silene sect. Arenosae (Caryophyllaceae): a new section
- 2020
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Ingår i: Phytokeys. - : Pensoft Publishers. - 1314-2011 .- 1314-2003. ; :159, s. 1-34
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Tidskriftsartikel (refereegranskat)abstract
- A putatively monophyletic group of annual Silene species is revised taxonomically and described as the new section S. sect. Arenosae. The species of this section were previously treated as a part of a widely circumscribed and polyphyletic S. sect. Rigidulae. Silene sect. Arenosae as circumscribed here consists of nine species. Members of the section show a predominantly E Mediterranean to SW Asian distribution pattern from Turkey southward to Egypt and eastward to Iran and Pakistan, although most of the species have a limited distribution range. The species of S. sect. Arenosae are characterized by narrowly lanceolate calyx teeth, which are often highly polymorphic, and lanceolate to oblanceolate (non-spathulate) basal leaves. The provided taxonomic revision is based on morphological characters and supported by phylogenetic analyses of two nuclear loci (nrITS and an intron of the RPB2 gene) and one chloroplast locus (the intron of the rps16 gene). The species descriptions are formalized using a novel implementation of the Prometheus Description Model.
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| 6. |
- Groppo, Milton, et al.
(författare)
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Chilean Pitavia more closely related to Oceania and Old World Rutaceae than to Neotropical groups: evidence from two cpDNA non-coding regions, with a new subfamilial classification of the family
- 2012
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Ingår i: PhytoKeys. - : Pensoft Publishers. - 1314-2011 .- 1314-2003. ; 19, s. 9-29
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Tidskriftsartikel (refereegranskat)abstract
- The position of the plant genus Pitavia within an infrafamilial phylogeny of Rutaceae (rue, or orange family) was investigated with the use of two non-coding regions from cpDNA, the trnL-trnF region and the rps16 intron. The only species of the genus, Pitavia punctata Molina, is restricted to the temperate forests of the Coastal Cordillera of Central-Southern Chile and threatened by loss of habitat. The genus traditionally has been treated as part of tribe Zanthoxyleae (subfamily Rutoideae) where it constitutes the monogeneric tribe Pitaviinae. This tribe and genus are characterized by fruits of 1 to 4 fleshy drupelets, unlike the dehiscent fruits typical of the subfamily. Fifty-five taxa of Rutaceae, representing 53 genera (nearly one-third of those in the family) and all subfamilies, tribes, and almost all subtribes of the family were included. Parsimony and Bayesian inference were used to infer the phylogeny; six taxa of Meliaceae, Sapindaceae, and Simaroubaceae, all members of Sapindales, were also used as out-groups. Results from both analyses were congruent and showed Pitavia as sister to Flindersia and Lunasia, both genera with species scattered through Australia, Philippines, Moluccas, New Guinea and the Malayan region, and phylogenetically far from other Neotropical Rutaceae, such as the Galipeinae (Galipeeae, Rutoideae) and Pteleinae (Toddalieae, former Toddalioideae). Additionally, a new circumscription of the subfamilies of Rutaceae is presented and discussed. Only two subfamilies (both monophyletic) are recognized: Cneoroideae (including Dictyolomatoideae, Spathelioideae, Cneoraceae, and Ptaeroxylaceae) and Rutoideae (including not only traditional Rutoideae but also Aurantioideae, Flindersioideae, and Toddalioideae). As a consequence, Aurantioideae (Citrus and allies) is reduced to tribal rank as Aurantieae.
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| 7. |
- Kainulainen, Kent, et al.
(författare)
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Chapelieria magna, a new species of Rubiaceae from eastern Madagascar
- 2015
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Ingår i: PhytoKeys. - : Pensoft Publishers. - 1314-2011 .- 1314-2003. ; 44, s. 89-95
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Tidskriftsartikel (refereegranskat)abstract
- A new species of Chapelieria was discovered during a recent field trip to the Masoala National Park in eastern Madagascar, and is described here as Chapelieria magna Kainul., sp. nov. This species is readily distinguishable from previously described species of the genus by its quadrangular shoots, triangular-calyptrate stipules, sessile leaves, pubescent styles, and ridged fruits. It also differs in the larger number of ovules and the much larger size of leaves and fruits.
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| 8. |
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| 9. |
- Razafimandimbison, Sylvain, 1964-
(författare)
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Four new endemic genera of Rubiaceae (Pavetteae) from Madagascar represent multiple radiations into drylands
- 2018
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Ingår i: PhytoKeys. - Bulgaria : Pensoft Publishers. - 1314-2011 .- 1314-2003. ; :99, s. 1-66
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Tidskriftsartikel (refereegranskat)abstract
- The taxonomic positions and phylogenetic relationships of six Pavetteae species endemic to Madagascar were tested with a phylogenetic study of the Afro-Madagascan representatives of the tribe Pavetteae based on sequence data from six markers rps16, trnT-F, petD, accD-psa1, PI and ITS. The six species were resolved into four well-supported and morphologically distinct clades which we here formally recognise at generic level. The new genera are the monospecific Exallosperma and Pseudocoptosperma, each with a single species, and Helictosperma and Tulearia, each with two species. Each genus is characterised by one or more autapomorphies or by a unique combination of plesiomorphic characters. Mostly, the distinguishing characters are found in fruit and seed; Exallosperma differs from all other Pavetteae genera by the fruit consisting of two stony pyrenes, each with a single laterally flattened seed with irregularly distributed ridges on the surface; Helictosperma is unique by its single spherical seed rolled-in on itself in the shape of a giant pill-millipede. Pseudocoptosperma is characterised by the combination of three ovules pendulous from a small placenta and triangular stipules with a strongly developed awn, whereas Tulearia is characterised by robust sericeous flowers, small leaves, uni- or pauciflorous inflorescences and fruits with two pyrenes, each with a single ruminate seed. The four new genera show marked adaptations to the dry habitats in which they grow. They represent multiple radiations into drylands and highlight the importance of the dry forest and scrub vegetation in western, southern and northern Madagascar for plant biodiversity. The description of the four new genera shows that the tribe Pavetteae exhibits the same pattern as many plant groups in Madagascar, which are characterised by a high proportion of endemic genera comprising a single or a few species.
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| 10. |
- Razafimandimbison, Sylvain, 1964-
(författare)
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Phylogeny, infrageneric classification and species delimitation in the Malagasy Impatiens (Balsaminaceae)
- 2018
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Ingår i: PhytoKeys. - Bulgaria : Pensoft Publishers. - 1314-2011 .- 1314-2003. ; 110, s. 51-67
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Tidskriftsartikel (refereegranskat)abstract
- The species-rich genus Impatiens (Balsaminaceae) is represented in Madagascar by no less than 260 species. We conducted molecular phylogenetic analyses of the Malagasy Impatiens based on nuclear and plastid data and 52 accessions (representing 33 species) to: 1) reassess the monophyly of the Malagasy Impatiens; 2) assess the monophyly of the sections Preimpatiens (Humblotianae and Vulgare groups) with spurs and Trimorphopetalum without spurs as delimited by Perrier de la Bâthie, as well as that of the subgenera Impatiens and Trimorphopetalum as defined by Fischer and Rahelivololona; 3) infer the current status of some morphologically variable species; and 4) test whether the species of Impatiens from the Marojejy National Park form a monophyletic group. The Malagasy Impatiens are further confirmed to be paraphyletic with respect of the Comorian I. auricoma. The present sectional and subgeneric classifications of the Malagasy Impatiens are partly supported, with strong support for the monophyly of the sect. or subgen. Trimorphopetalum. Section Preimpatiens was not supported as monophyletic and neither the Humblotianae group nor the Vulgare group is monophyletic. Impatiens elatostemmoides, I.“hammarbyoides”, I. inaperta, I. lyallii and I. manaharensis are either para- or polyphyletic and may represent morpho-species. The Impatiens species from the Marojejy National Park do not form a monophyletic group and therefore are suggested to be derived from numerous independent colonisation events from all over Madagascar followed by subsequent diversifications.
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| 11. |
- Saez, L., et al.
(författare)
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Re-establishment of Silene neglecta Ten. (Caryophyllaceae) with taxonomic notes on some related taxa
- 2022
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Ingår i: Phytokeys. - : Pensoft Publishers. - 1314-2011 .- 1314-2003. ; :195, s. 143-160
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Tidskriftsartikel (refereegranskat)abstract
- Silene neglecta has been misunderstood and confused with S. nocturna, although several morphological characters (petal shape, calyx indumentum, hairiness of stamen filaments, seed size, seed-coat surface and shape) allow separation of these species. Moreover, S. mutabilis (which has been considered conspecific with S. neglecta) and S. martinolii (an alleged endemic species to south-western Sardinia) are considered here as taxonomic synonyms of S. nocturna and S. neglecta, respectively. These taxonomic conclusions are strongly supported by multivariate morphometric analyses of 21 characters.
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| 12. |
- Ulloa, U., Carmen, et al.
(författare)
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A new species of Symplocos (Symplocaceae) from southern Ecuador
- 2015
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Ingår i: PhytoKeys. - : Pensoft Publishers. - 1314-2011 .- 1314-2003. ; 56, s. 41-46
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Tidskriftsartikel (refereegranskat)abstract
- A new species from Ecuador, Symplocos limonensis, is here described and illustrated. It resembles S.clethrifolia but differs by having larger leaves with evident (i.e., not concealed) areoles on lower surface, sessile inflorescences, smaller white corollas, and fewer stamens. The species is only known from three collections in the Andean forests of Morona-Santiago Province in southern Ecuador.
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| 13. |
- Karlsson, Dave, et al.
(författare)
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The data of the Swedish Malaise Trap Project, a countrywide inventory of Sweden's insect fauna
- 2020
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Ingår i: Biodiversity Data Journal. - : Pensoft Publishers. - 1314-2836 .- 1314-2828. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- Despite Sweden's strong entomological tradition, large portions of its insect fauna remain poorly known. As part of the Swedish Taxonomy Initiative, launched in 2002 to document all multi-cellular species occurring in the country, the first taxonomically-broad inventory of the country's insect fauna was initiated, the Swedish Malaise Trap Project (SMTP). In total, 73 Malaise traps were deployed at 55 localities representing a wide range of habitats across the country. Most traps were run continuously from 2003 to 2006 or for a substantial part of that time period. The total catch is estimated to contain 20 million insects, distributed over 1,919 samples (Karlsson et al. 2020). The samples have been sorted into more than 300 taxonomic units, which are made available for expert identification. Thus far, more than 100 taxonomists have been involved in identifying the sorted material, recording the presence of 4,000 species. One third of these had not been recorded from Sweden before and 700 have tentatively been identified as new to science.Here, we describe the SMTP dataset, published through the Global Biodiversity Information Facility (GBIF). Data on the sorted material are available in the "SMTP Collection Inventory" dataset. It currently includes more than 130,000 records of taxonomically-sorted samples. Data on the identified material are published using the Darwin Core standard for sample-based data. That information is divided up into group-specific datasets, as the sample set processed for each group is different and in most cases non-overlapping. The current data are divided into 79 taxonomic datasets, largely corresponding to taxonomic sorting fractions. The orders Diptera and Hymenoptera together comprise about 90% of the specimens in the material and these orders are mainly sorted to family or subfamily. The remaining insect taxa are mostly sorted to the order level. In total, the 79 datasets currently available comprise around 165,000 specimens, that is, about 1% of the total catch. However, the data are now accumulating rapidly and will be published continuously. The SMTP dataset is unique in that it contains a large proportion of data on previously poorly-known taxa in the Diptera and Hymenoptera.
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| 14. |
- Clairambault, Jean, et al.
(författare)
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A survey of adaptive cell population dynamics models of emergence of drug resistance in cancer, and open questions about evolution and cancer
- 2019
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Ingår i: Biomath. - : Biomath Forum. - 1314-684X .- 1314-7218. ; 8:1
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Tidskriftsartikel (refereegranskat)abstract
- This article is a proceeding survey (deepening a talk given by the first author at the BioMath 2019 International Conference on Mathematical Models and Methods, held in Będlewo, Poland) of mathematical models of cancer and healthy cell population adaptive dynamics exposed to anticancer drugs, to describe how cancer cell populations evolve toward drug resistance. Such mathematical models consist of partial differential equations (PDEs) structured in continuous phenotypes coding for the expression of drug resistance genes; they involve different functions representing targets for different drugs, cytotoxic and cytostatic, with complementary effects in limiting tumour growth. These phenotypes evolve continuously under drug exposure, and their fate governs the evolution of the cell population under treatment. Methods of optimal control are used, taking inevitable emergence of drug resistance into account, to achieve the best strategies to contain the expansion of a tumour. This evolutionary point of view, which relies on biological observations and resulting modelling assumptions, naturally extends to questioning the very nature of cancer as evolutionary disease, seen not only at the short time scale of a human life, but also at the billion year-long time scale of Darwinian evolution, from unicellular organisms to evolved multicellular organs such as animals and man. Such questioning, not so recent, but recently revived, in cancer studies, may have consequences for understanding and treating cancer. Some open and challenging questions may thus be (non exhaustively) listed as: • May cancer be defined as a spatially localised loss of coherence between tissues in the same multicellular organism, ‘spa-tially localised’ meaning initially starting from a given organ in the body, but also possibly due to flaws in an individual’s epigenetic landscape such as imperfect control of differentiation genes? • If one assumes that “The genes of cellular cooperation that evolved with multicellularity about a billion years ago are the same genes that malfunction in can-cer.” (Davies and Lineweaver, 2011), how can these genes be systematically investigated, looking for zones of fragility-that depend on individuals-in the ‘tinker-ing’ (F. Jacob, 1977) evolution is made of, tracking local defaults of coherence? • What is such coherence made of and to what extent is the immune system responsible for it (the self and differentiation within the self)? Related to this question of self, what parallelism can be established between the development of multicellularity in different species proceeding from the same origin and the development of the immune system in these different species?.
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| 15. |
- Karlsson, Dave, et al.
(författare)
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The Swedish Malaise Trap Project: a 15 year retrospective on a countrywide inventory.
- 2020
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Ingår i: Biodiversity Data Journal. - 1314-2836 .- 1314-2828. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- The Swedish Malaise Trap Project (SMTP) is one of the most ambitious insect inventories ever attempted. The project was designed to target poorly known insect groups across a diverse range of habitats in Sweden. The field campaign involved the deployment of 73 Malaise traps at 55 localities across the country for three years (2003-2006). Over the past 15 years, the collected material has been hand sorted by trained technicians into over 300 taxonomic fractions suitable for expert attention. The resulting collection is a tremendous asset for entomologists around the world, especially as we now face a desperate need for baseline data to evaluate phenomena like insect decline and climate change. Here, we describe the history, organisation, methodology and logistics of the SMTP, focusing on the rationale for the decisions taken and the lessons learned along the way. The SMTP represents one of the early instances of community science applied to large-scale inventory work, with a heavy reliance on volunteers in both the field and the laboratory. We give estimates of both staff effort and volunteer effort involved. The project has been funded by the Swedish Taxonomy Initiative; in total, the inventory has cost less than 30 million SEK (approximately 3.1 million USD). Based on a subset of the samples, we characterise the size and taxonomic composition of the SMTP material. Several different extrapolation methods suggest that the material comprises around 20 million specimens in total. The material is dominated by Diptera (75% of the specimens) and Hymenoptera (15% of specimens). Amongst the Diptera, the dominant groups are Chironomidae (37% of specimens), Sciaridae (15%), Phoridae (13%), Cecidomyiidae (9.5%) and Mycetophilidae (9.4%). Within Hymenoptera, the major groups are Ichneumonidae (44% of specimens), Diaprioidea (19%), Braconidae (9.6%), Platygastroidea (8.5%) and Chalcidoidea (7.9%). The taxonomic composition varies with latitude and season. Several Diptera and Hymenoptera groups are more common in non-summer samples (collected from September to April) and in the North, while others show the opposite pattern. About 1% of the total material has been processed and identified by experts so far. This material represents over 4,000 species. One third of these had not been recorded from Sweden before and almost 700 of them are new to science. These results reveal the large amounts of taxonomic work still needed on Palaearctic insect faunas. Based on the SMTP experiences, we discuss aspects of planning and conducting future large-scale insect inventory projects using mainly traditional approaches in relation to more recent approaches that rely on molecular techniques.
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| 16. |
- Roslin, Tomas
(författare)
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Biodiversity inventories in high gear: DNA barcoding facilitates a rapid biotic survey of a temperate nature reserve
- 2015
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Ingår i: Biodiversity Data Journal. - 1314-2828. ; 3
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundComprehensive biotic surveys, or 'all taxon biodiversity inventories' (ATBI), have traditionally been limited in scale or scope due to the complications surrounding specimen sorting and species identification. To circumvent these issues, several ATBI projects have successfully integrated DNA barcoding into their identification procedures and witnessed acceleration in their surveys and subsequent increase in project scope and scale. The Biodiversity Institute of Ontario partnered with the rare Charitable Research Reserve and delegates of the 6th International Barcode of Life Conference to complete its own rapid, barcode-assisted ATBI of an established land trust in Cambridge, Ontario, Canada.New informationThe existing species inventory for the rare Charitable Research Reserve was rapidly expanded by integrating a DNA barcoding workflow with two surveying strategies - a comprehensive sampling scheme over four months, followed by a one-day bioblitz involving international taxonomic experts. The two surveys resulted in 25,287 and 3,502 specimens barcoded, respectively, as well as 127 human observations. This barcoded material, all vouchered at the Biodiversity Institute of Ontario collection, covers 14 phyla, 29 classes, 117 orders, and 531 families of animals, plants, fungi, and lichens. Overall, the ATBI documented 1,102 new species records for the nature reserve, expanding the existing long-term inventory by 49%. In addition, 2,793 distinct Barcode Index Numbers (BINs) were assigned to genus or higher level taxonomy, and represent additional species that will be added once their taxonomy is resolved. For the 3,502 specimens, the collection, sequence analysis, taxonomic assignment, data release and manuscript submission by 100+ co-authors all occurred in less than one week. This demonstrates the speed at which barcode-assisted inventories can be completed and the utility that barcoding provides in minimizing and guiding valuable taxonomic specialist time. The final product is more than a comprehensive biotic inventory - it is also a rich dataset of fine-scale occurrence and sequence data, all archived and cross-linked in the major biodiversity data repositories. This model of rapid generation and dissemination of essential biodiversity data could be followed to conduct regional assessments of biodiversity status and change, and potentially be employed for evaluating progress towards the Aichi Targets of the Strategic Plan for Biodiversity 2011-2020.
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