| 1. |
- Bertrand, Yann, et al.
(författare)
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Taxonomic surrogacy in biodiversity assessments, and the meaning of Linnaean ranks
- 2006
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Ingår i: Systematics and Biodiversity. ; 4:2, s. 149-159
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Tidskriftsartikel (refereegranskat)abstract
- The majority of biodiversity assessments use species as the base unit. Recently, a series of studies have suggested replacing numbers of species with higher ranked taxa (genera, families, etc.); a method known as taxonomic surrogacy that has an important potential to save time and resources in assesments of biological diversity. We examine the relationships between taxa and ranks, and suggest that species/higher taxon exchanges are founded on misconceptions about the properties of Linnaean classification. Rank allocations in current classifications constitute a heterogeneous mixture of various historical and contemporary views. Even if all taxa were monophyletic, those referred to the same rank would simply denote separate clades without further equivalence. We conclude that they are no more comparable than any other, non-nested taxa, such as, for example, the genus Rattus and the phylum Arthropoda, and that taxonomic surrogacy lacks justification. These problems are also illustrated with data of polychaetous annelid worms from a broad-scale study of benthic biodiversity and species distributions in the Irish Sea. A recent consensus phylogeny for polychaetes is used to provide three different family-level classifications of polychaetes. We use families as a surrogate for species, and present Shannon–Wiener diversity indices for the different sites and the three different classifications, showing how the diversity measures rely on subjective rank allocations
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| 2. |
- Kruys, Åsa, et al.
(författare)
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Phylogenetic relationships and an assessment of traditionally used taxonomic characters in the Sporormiaceae (Pleosporales, Dothideomycetes, Ascomycota), utilising multi-gene phylogenies
- 2009
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Ingår i: Systematics and Biodiversity. - 1477-2000 .- 1478-0933. ; 7:4, s. 465-478
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Tidskriftsartikel (refereegranskat)abstract
- The family Sporormiaceae (Pleosporales, Dothideomycetes, Ascomycota) occur worldwide and a majority of the species are coprophilous. The taxonomy and classification of the family are based on a small number of morphological and ecological characters. Several taxa are easily confused by their shared morphological features, and the relationships between genera are poorly known and in need of critical study. The aims of this study were to resolve the phylogenetic relationships within the Sporormiaceae, test the current generic classification, and study the utility of traditional characters for the taxonomy in the group. To resolve these questions, we analysed combined data sets of ITS-nLSU rDNA, mtSSU rDNA and beta-tubulin sequences with parsimony and Bayesian methods. The results showed that many characters, which previously have been used in the taxonomy and classification of the Sporormiaceae, such as the substrate choice, presence or absence of an ostiole, and presence or absence of germ slits, were all homoplastic and not useful for circumscribing monophyletic groups. A number of characters may be useful for circumscribing smaller clades if used in combination with other features, such as the shape of the ascus with the shape of the ascospores. Our phylogenetic analyses show that Preussia and Sporormiella are non-monophyletic, and a constrained analysis forcing these genera into monophyly resulted in significantly worse trees. Spororminula is nested in Preussia s. lat., and Eremodothis and Pycnidiophora are nested within Westerdykella. Finally, we suggest a new generic classification for the family Sporormiaceae, including Sporormia, Preussia (including Sporomiella and Spororminula) and Westerdykella (including Eremodothis and Pycnidiophora). We also propose 14 new combinations: Preussia alloiomera (S.I. Ahmed & Cain) Kruys, Preussia antarctica (Speg.) Kruys, Preussia bipartis (Cain) Kruys, Preussia borealis (I.Egeland) Kruys, Preussia dubia (S.I. Ahmed & Cain) Kruys, Preussia lignicola (W. Phillips & Plowr.) Kruys, Preussia longisporopsis (S.I. Ahmed & Cain) Kruys, Preussia minipascua (S.I. Ahmed & Cain) Kruys, Preussia octomera (Auersw.) Kruys, Preussia splendens (Cain) Kruys, Preussia tenerifae (Arx & Aa) Kruys, Preussia tetramera (S.I. Ahmed & Cain) Kruys, Westerdykella angulata (A.C. Das) Kruys and Westerdykella aurantiaca (J.N. Rai & J.P. Tewari) Kruys.
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| 3. |
- Binder, M., et al.
(författare)
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The phylogenetic distribution of resupinate forms across the major clades of mushroom-forming fungi (Homobasidiomycetes)
- 2005
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Ingår i: Systematics and Biodiversity. - 1477-2000. ; 3:2, s. 113-157
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Tidskriftsartikel (refereegranskat)abstract
- Phylogenetic relationships of resupinate Homobasidiomycetes (Corticiaceae s. lat. and others) were studied using ribosomal DNA (rDNA) sequences from a broad sample of resupinate and nonresupinate taxa. Two datasets were analysed using parsimony, a core dataset of 142 species, each of which is represented by four rDNA regions (mitochondrial and nuclear large and small subunits), and a full dataset of 656 species, most of which were represented only by nuclear large subunit rDNA sequences. Both datasets were analysed using traditional heuristic methods with bootstrapping, and the full dataset was also analysed with the Parsimony Ratchet, using equal character weights and six-parameter weighted parsimony. Analyses of both datasets supported monophyly of the eight major clades of Homobasidiomycetes recognised by Hibbett and Thorn, as well as independent lineages corresponding to the Gloeophyllum clade, corticioid clade and Jaapia argillacea. Analyses of the full dataset resolved two additional groups, the athelioid clade and trechisporoid clade (the latter may be nested in the polyporoid clade). Thus, there are at least 12 independent clades of Homobasidiomycetes. Higher-level relationships among the major clades are not resolved with confidence. Nevertheless, the euagarics clade, bolete clade, athelioid clade and Jaapia argillacea are consistently resolved as a monophyletic group, whereas the cantharelloid clade, gomphoid-phalloid clade and hymenochaetoid clade are placed at the base of the Homobasidiomycetes, which is consistent with the preponderance of imperforate parenthesomes in those groups. Resupinate forms occur in each of the major clades of Homobasidiomycetes, some of which are composed mostly or exclusively of resupinate forms (athelioid clade, corticioid clade, trechisporoid clade, Jaapia). The largest concentrations of resupinate forms occur in the polyporoid clade, russuloid clade and hymenochaetoid clade. The cantharelloid clade also includes many resupinate forms, including some that have traditionally been regarded as heterobasidiomycetes (Sebacinaceae, Tulasnellales, Ceratobasidiales). The euagarics clade, which is by far the largest clade in the Homobasidiomycetes, has the smallest fraction of resupinate species. Results of the present study are compared with recent phylogenetic analyses, and a table summarising the phylogenetic distribution of resupinate taxa is presented, as well as notes on the ecology of resupinate forms and related Homobasidiomycetes
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| 4. |
- Hebbeln, Dierk, et al.
(författare)
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Late Holocene coastal hydrographic and climate changes in the eastern North Sea
- 2006
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Ingår i: The Holocene. - : SAGE Publications. - 0959-6836 .- 1477-0911. ; 16:7, s. 987-1001
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Tidskriftsartikel (refereegranskat)abstract
- We present a high-resolution palaeoenvironmental reconstruction covering the late Holocene from the Skagerrak and other sites in the North Sea area. The data, which are based on the analyses of marine sediment cores, reveal a marked environmental shift that took place between AD 700 and AD 1100, with the most pronounced changes occurring at AD 900. Both surface and bottom waters in the Skagerrak were subject to major circulation and productivity changes at this time due to an enhanced advection of Atlantic waters to the North Sea marking the beginning of the 'Mediaeval Warm Period' (MWP). The observed increase in bottom current strength is especially remarkable as there is hardly any comparable signal in the older part of the record going back to 1000 BC. At the transition to the 'Little Ice Age' (LIA) the bottom current strength remains at a high level, now probably forced by atmospheric circulation. Thus, despite opposite temperature forcing, these two consecutive climate scenarios are apparently able to generate distinctly stronger bottom currents in the Skagerrak than observed in the preceding 2000 years, and demonstrate the significance of climatic forcing in shaping the marine environment. Indeed, both the MWP and the LIA are reported as strong climatic signals in northwest Europe, being the warmest (except the late twentieth century) and coldest periods, respectively, during at least the last 2000 years.
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| 5. |
- Mazier, Florence, et al.
(författare)
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Multidisciplinary approach to reconstructing local pastoral activities : an example from the Pyrenean Mountains (Pays Basqueq)
- 2009
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Ingår i: The Holocene. - : SAGE Publications. - 0959-6836 .- 1477-0911. ; 19:2, s. 171-188
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Tidskriftsartikel (refereegranskat)abstract
- In this study archaeology, history and palaeoecology (modern and fossil data sets of pollen and non-pollen palynomorphs) were used to reconstruct small-scale pastoral activities in the Pyrenees Mountain during the last two millennia. Modern pollen assemblages from the major vegetation units (both natural and anthropogenic) are studied on one restricted watershed area. A correlative model (RDA) of 61 modern pollen spectra and 35 external variables distinguishes two groups of taxa, providing information on the nature and spatial extent of human impact on the landscape. The first pool indicates local pastoral activities, and the second one implies regional input from outside the studied watershed, and is not characteristic of a specific land use. These pools are described as 'Local Pastoral Pollen Indicators' (LPPI) for this particular mountain region on crystalline bedrock and 'Regional Human Activities Pollen Indicators' (RHAPI). The modern data set is used to aid interpretation of the local pollen sequence of Sourzay that covers the last 2000 calendar years BP, using RDA reconstructions, and best modern analogues as a means of comparing modern and fossil spectra. The study also demonstrates agreement between the independent interpretations of two fossil proxies, LPPI and corophilous fungi.
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| 6. |
- Urowitz, M B, et al.
(författare)
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Clinical manifestations and coronary artery disease risk factors at diagnosis of systemic lupus erythematosus: data from an international inception cohort
- 2007
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Ingår i: Lupus. - : SAGE Publications. - 0961-2033 .- 1477-0962. ; 16:9, s. 731-735
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Tidskriftsartikel (refereegranskat)abstract
- Systemic Lupus International Collaborating Clinics (SLICC) comprises 27 centres from 11 countries. An inception cohort of 918 SLE patients has been assembled according to a standardized protocol between 2000 and 2006. Clinical features, classic coronary artery disease (CAD) risk factors, as well as other potential risk factors were collected. Of the 918 patients 89% were females, and of multi racial origin. Less than half the patients were living in a permanent relationship, 58% had post secondary education and 51% were employed. Eight percent had family history of SLE. At enrolment, with at mean age of diagnosis of 34.5 years, a significant number of patients already had CAD risk factors, such as hypertension (33%) and hypercholesterolemia (36%). Only 15% of the patients were postmenopausal, 16% were current smokers and 3.6% had diabetes at entry to the SLICC-RAS (Registry for Atherosclerosis). A number of patients in this multi-racial, multi-ethnic inception cohort of lupus patients have classic CAD risk factors within a mean of 5.4 months from diagnosis. This cohort will be increased to 1500 patients to be followed yearly for 10 years. This will provide a unique opportunity to evaluate risk factors for accelerated atherosclerosis in SLE.
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| 7. |
- Gedda, Björn
(författare)
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Terrestrial mollusc succession and stratigraphy of a Holocene calcareous tufa deposit from the Fyledalen valley, southern Sweden
- 2006
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Ingår i: The Holocene. - : SAGE Publications. - 0959-6836 .- 1477-0911. ; 16:1, s. 137-147
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Tidskriftsartikel (refereegranskat)abstract
- A Holocene calcareous tufa deposit in the Fyledalen Valley in southern Sweden was investigated with respect to molluscs, pollen, plant macrofossils and Coleoptera remains. The investigation recovered four mollusc species that today are severely threatened and included in the Swedish Red List of Endangered Species and/or the European Community's Natura 2000 programme. These include Vertigo genesii (Gredler), Vertigo geyeri Lindholm, Cochlicopa nitens (Gallenstein) and Vertigo moulinsiana (Dupuy). Tufa formation was initiated in the early Preboreal (after 11 500 cal. BP), when an open birchpine forest dominated the area and stopped in the late Boreal (after 8800 cal. BP) when deciduous trees had become established. The presence of the molluscan species Vallonia pulchella (Muller), Columella columella (Martens). Vertigo genesii, Pupilla muscorum (L.) and Euconulus alderi (Gray), coupled with an almost complete lack of shade-demanding taxi, suggests an open marsh environment throughout the time of tufa deposition. The mollusc succession shows evidence of increasing temperature. Columella columella, commonly associated with open arctic-alpine habitats is present at the base of the profile in the early Preboreal, whilst Vertigo genesii, which commonly is associated with open arctic-alpine habitats or calcareous springs, persists until the mid-Boreal (similar to 8800 cal. BP). The tufa deposition ends when the regional groundwater levels rise, approximately 8800 cal. BP, more thermophilous molluscs, such as Vertigo moulinsiana and V angustior Jeffreys and the aquatic Bithynia tentaculata (L.). Radii peregra (Muller) and Planorbis planorbis (L.) colonize the site. Stratigraphic correlations. as well as faunal and floral comparisons, are made with nearby sites.
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| 8. |
- Fossum, M., et al.
(författare)
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Autologous in vitro cultured urothelium in hypospadias repair{star, open}
- 2007
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Ingår i: Journal of Pediatric Urology. - : Elsevier BV. - 1477-5131 .- 1873-4898. ; 3:1, s. 10-18
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Tidskriftsartikel (refereegranskat)abstract
- Objective: To treat severe hypospadias with a transplant of autologous in vitro cultured urothelial cells on acellular dermis. Patients and methods: During 2000-2002 six patients aged 14-44 months with severe hypospadias were treated surgically with autologous urothelial cell transplants. All were born with scrotal or perineal hypospadias and pronounced chordee. All patients were subjected to a two-staged procedure starting with repair of the chordee. Urothelial cell harvesting via bladder lavage was performed during the first operation. The neourethra was constructed by using a transplant with cultured urothelium in an on-lay fashion. Patients have been followed 3-5.5 years. Results: All six boys are voiding through their neourethra without straining and have no residual urine after micturition. Five patients are using a standing voiding position and present bell shaped, urinary flow curves. One developed a stricture treated conservatively with persisting good effect (after more than 5 years). Two developed a fistula requiring surgical correction that was uneventful. The last patient developed an obstruction in the proximal anastomosis that was treated with an internal urethrotomy. Cosmetic appearance is good in all cases with good parental satisfaction. Urethroscopy in all patients show a wide penile neourethra. Biopsies indicate a mucosal lining consisting of urothelial cells in three cases. Conclusion: This technique is feasible for treatment of a selected group of hypospadias where pronounced chordee and shortage of preputial and penile skin complicates the creation of a neourethra. It may have other clinical implications including disorders such as bladder exstrophy and cloacal malformations, as well as mutilating traumatic injuries or cancer therapy. © 2006 Journal of Pediatric Urology Company.
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