| 1. |
- Anderberg, A. A., et al.
(author)
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Maesaceae, a new primuloid family in the order Ericales s.l.
- 2000
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In: Taxon. - Vienna, Austria : IAPT. - 0040-0262 .- 1996-8175. ; 49:2, s. 183-187
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Journal article (peer-reviewed)abstract
- Evidence from morphology and molecular sequence data from three chloroplast genes, rbcL, ndhF, and atpB, have shown that the genus Maesa constitutes an evolutionary lineage separate from the other three primuloid families, Theophrastaceae, Myrsinaceae, and Primulaceae. The new family Maesaceae is here formally recognised, its taxonomic status being changed from a subfamily of Myrsinaceae. The new family comprises a single genus, Maesa Forssk., with some 100 species of trees or shrubs; it is diagnosed by characters such as flower pedicels with two bracteoles, a semi-inferior ovary, and indehiscent fruits with many seeds. A key to the major groups of primuloid taxa is presented.
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| 2. |
- Ekström, Magnus, et al.
(author)
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Logistic regression for clustered data from environmental monitoring programs
- 2018
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In: Ecological Informatics. - : Elsevier. - 1574-9541 .- 1878-0512. ; 43, s. 165-173
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Journal article (peer-reviewed)abstract
- Large-scale surveys, such as national forest inventories and vegetation monitoring programs, usually have complex sampling designs that include geographical stratification and units organized in clusters. When models are developed using data from such programs, a key question is whether or not to utilize design information when analyzing the relationship between a response variable and a set of covariates. Standard statistical regression methods often fail to account for complex sampling designs, which may lead to severely biased estimators of model coefficients. Furthermore, ignoring that data are spatially correlated within clusters may underestimate the standard errors of regression coefficient estimates, with a risk for drawing wrong conclusions. We first review general approaches that account for complex sampling designs, e.g. methods using probability weighting, and stress the need to explore the effects of the sampling design when applying logistic regression models. We then use Monte Carlo simulation to compare the performance of the standard logistic regression model with two approaches to model correlated binary responses, i.e. cluster-specific and population-averaged logistic regression models. As an example, we analyze the occurrence of epiphytic hair lichens in the genus Bryoria; an indicator of forest ecosystem integrity. Based on data from the National Forest Inventory (NFI) for the period 1993-2014 we generated a data set on hair lichen occurrence on > 100,000 Picea abies trees distributed throughout Sweden. The NFI data included ten covariates representing forest structure and climate variables potentially affecting lichen occurrence. Our analyses show the importance of taking complex sampling designs and correlated binary responses into account in logistic regression modeling to avoid the risk of obtaining notably biased parameter estimators and standard errors, and erroneous interpretations about factors affecting e.g. hair lichen occurrence. We recommend comparisons of unweighted and weighted logistic regression analyses as an essential step in development of models based on data from large-scale surveys.
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| 3. |
- Esseen, Per-Anders, et al.
(author)
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Broad-scale distribution of epiphytic hair lichens correlates more with climate and nitrogen deposition than with forest structure
- 2016
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In: Canadian Journal of Forest Research. - : Canadian Science Publishing. - 0045-5067 .- 1208-6037. ; 46:11, s. 1348-1358
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Journal article (peer-reviewed)abstract
- Hair lichens are strongly influenced by forest structure at local scales, but their broad-scale distributions are less understood. We compared the occurrence and length of Alectoria sarmentosa (Ach.) Ach., Bryoria spp., and Usnea spp. in the lower canopy of > 5000 Picea abies (L.) Karst. trees within the National Forest Inventory across all productive forest in Sweden. We used logistic regression to analyse how climate, nitrogen deposition, and forest variables influence lichen occurrence. Distributions overlapped, but the distribution of Bryoria was more northern and that of Usnea was more southern, with Alectoria's distribution being intermediate. Lichen length increased towards northern regions, indicating better conditions for biomass accumulation. Logistic regression models had the highest pseudo R2 value for Bryoria, followed by Alectoria. Temperature and nitrogen deposition had higher explanatory power than precipitation and forest variables. Multiple logistic regressions suggest that lichen genera respond differently to increases in several variables. Warmingdecreased the odds for Bryoria occurrence at all temperatures. Corresponding odds for Alectoria and Usnea decreased in warmer climates, but in colder climates, they increased. Nitrogen addition decreased the odds for Alectoria and Usnea occurrence under high deposition, but under low deposition, the odds increased. Our analyses suggest major shifts in the broad-scale distribution of hair lichens with changes in climate, nitrogen deposition, and forest management.
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| 4. |
- Esseen, Per-Anders, et al.
(author)
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Multiple drivers of large-scale lichen decline in boreal forest canopies
- 2022
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In: Global Change Biology. - : John Wiley & Sons. - 1354-1013 .- 1365-2486. ; 28:10, s. 3293-3309
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Journal article (peer-reviewed)abstract
- Thin, hair-like lichens (Alectoria, Bryoria, Usnea) form conspicuous epiphyte communities across the boreal biome. These poikilohydric organisms provide important ecosystem functions and are useful indicators of global change. We analyse how environmental drivers influence changes in occurrence and length of these lichens on Norway spruce (Picea abies) over 10 years in managed forests in Sweden using data from >6000 trees. Alectoria and Usnea showed strong declines in southern-central regions, whereas Bryoria declined in northern regions. Overall, relative loss rates across the country ranged from 1.7% per year in Alectoria to 0.5% in Bryoria. These losses contrasted with increased length of Bryoria and Usnea in some regions. Occurrence trajectories (extinction, colonization, presence, absence) on remeasured trees correlated best with temperature, rain, nitrogen deposition, and stand age in multinomial logistic regression models. Our analysis strongly suggests that industrial forestry, in combination with nitrogen, is the main driver of lichen declines. Logging of forests with long continuity of tree cover, short rotation cycles, substrate limitation and low light in dense forests are harmful for lichens. Nitrogen deposition has decreased but is apparently still sufficiently high to prevent recovery. Warming correlated with occurrence trajectories of Alectoria and Bryoria, likely by altering hydration regimes and increasing respiration during autumn/winter. The large-scale lichen decline on an important host has cascading effects on biodiversity and function of boreal forest canopies. Forest management must apply a broad spectrum of methods, including uneven-aged continuous cover forestry and retention of large patches, to secure the ecosystem functions of these important canopy components under future climates. Our findings highlight interactions among drivers of lichen decline (forestry, nitrogen, climate), functional traits (dispersal, lichen colour, sensitivity to nitrogen, water storage), and population processes (extinction/colonization).
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| 5. |
- Ferm, Julia, et al.
(author)
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A revised classification of the neotropical genus Zapoteca (Caesalpinioideae; Fabaceae), with one new subgenus and two new species combinations
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Other publication (other academic/artistic)abstract
- Based on analyses of new and previously published ETS, ITS and trnL-trnF DNA-sequences, a revised classification of the neotropical legume genus Zapoteca is presented. Subgenus Ravenia is included in subg. Zapoteca, Z. quichoi is transferred from subg. Amazonica to subg. Zapoteca, Z. sousae is included in subg. Zapoteca, one new subgenus, subg. Subamazonica, is described to accomodate the species Z. filipes and Z. scutellifera and the new combinations Z. schottiiand Z. gracilis are made, based on Z. formosa subsp. schottii and Z. formosa subsp. gracilis. An artifical key to the subgenera is provided and a brief phytogeographic overview of Zapoteca is prestented.
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| 6. |
- Ferm, Julia, et al.
(author)
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A Revised Subgeneric Classification of the Neotropical Genus Zapoteca (Caesalpinioideae; Fabaceae)
- 2022
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In: Systematic Botany. - : American Society of Plant Taxonomists. - 0363-6445 .- 1548-2324. ; 47:1, s. 208-214
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Journal article (peer-reviewed)abstract
- The subgeneric classification of the neotropical legume genus Zapoteca is revised based on an analysis of the nuclear ETS and ITS, and the plastid trnL-trnF DNA regions. Zapoteca subgenus Ravenia is included in Z. subgenus Zapoteca, Z. quichoi is transferred from Z. subgenus Amazonica to Z. subgenus Zapoteca, Z. sousae is included in Z. subgenus Zapoteca, and the new subgenus Zapoteca subgenus Subamazonica is described to accommodate the species Z. filipes and Z. scutellifera. A key to the subgenera is presented.
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| 7. |
- Ferm, Julia
(author)
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On Ingeae Systematics of synandrous mimosoids
- 2020
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Doctoral thesis (other academic/artistic)abstract
- Background: The Ingeae tribe (Caesalpiniodeae, Fabaceae) has a long history of taxonomic complexity with genera being merged and split, and many species with former placements in several different genera. Moreover, phylogenetic studies have shown that the tribe is non-monophyletic with the genus Acacia (of tribe Acacieae) nested within Ingeae. This problem of non-monophyly is also reflected at the generic and specific level of ingoid taxa. Phylogenetic relationships have been difficult to resolve, with unsettled generic delimitations as a result. In this thesis, I investigated the systematics and phylogeny of the Ingeae-Acacia complex, with reflections on taxonomy and biogeography. Methods: Molecular data of plastid (matK, psbA, trnL-trnF, ycf1) and nuclear (ETS, ITS) DNA sequences were analysed using Bayesian inference and Ultrafast Bootstrap in order to investigate phylogenetic relationships of the Ingeae-Acacia complex. Results: In paper I, Marmaroxylon was shown to be included in Zygia and Zygia inundata in Inga. Marmaroxylon magdalenae, M. ocumarense and Zygia sabatieri were not recovered in the Zygia-Marmaroxylon clade and therefore left without a placement in any genus. In paper II, Zapoteca was shown to be monophyletic but the subgenera comprising more than one species, and four species, were non-monophyletic. In paper III, a new subgeneric classification of Zapoteca and an identification key to the subgenera are presented, as well as a phytogeographical review of the genus. Zapoteca formosa subsp. schottii and Z. formosa subsp. gracilis were recognized as distinct species. In paper IV, Afrocalliandra and Calliandra were recovered as the earliest diverging lineage within the Ingeae-Acacia complex, and the other taxa possessing the same pod-type as Calliandra, i.e. Sanjappa, Thailentadopsis, Viguieranthus and Zapoteca, were shown to be more closely related to each other and other ingoid genera than to Calliandra. Discussion and conclusions: Phylogenetic relationships of the Ingeae-Acacia complex are possible to resolve with a broad sampling and a combination of several nuclear and plastid informative DNA sequences. Taxonomic revisions are, however, needed for several ingoid genera, as well as for the entire Ingeae tribe since it currently is non-monophyletic with respect to Acacia. Shared morphological characters are not always indicative of common ancestry and older morphology-based classifications do not always reflect the evolutionary history of the group. One example is the “Calliandra-pod” fruit type. While it has often been argued to indicate close relationships, I show that this seemingly specific type of pod occurs in several unrelated genera.
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| 8. |
- Ferm, Julia, et al.
(author)
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Phylogenetic relationships of the mimosoid Ingeae–Acacia complex (Fabaceae), based on plastid and nuclear data
-
Other publication (other academic/artistic)abstract
- Modern phylogenetic analyses based on molecular data have shown that the current classification of the Ingeae tribe (Caesalpinioideae, Fabaceae) do not always reflect evolutionary relationships. Many genera that are currently defined based on morphological characters do not constitute monophyletic groups and generic relationships within the tribe are not fully known. Moreover, the Ingeae tribe itself does not comprise a monophyletic group since the genus Acacia (tribe Acacieae) is nested among the ingoid species. We investigated phylogenetic relationships of the Ingeae−Acacia complex on a generic level. We put special emphasis on genera with a taxonomic history in Calliandra s.l., i.e. Calliandra s.s., Afrocalliandra, Sanjappa, Viguieranthus and Zapoteca, and also the genus Faidherbia, which has been shown to be closely related to these genera in previous phylogenetic studies. We included samples from 32 ingoid genera, samples of Acacia and Senegalia (tribe Acacieae), and Vachellia farnesiana, which was used for rooting the trees. Datasets included the nuclear ETS and ITS, and the plastid matK, trnL-trnF and ycf1 DNA regions and were analysed with Bayesian inference and Ultrafast Bootstrap. The results show that the species of the Ingeae−Acacia complex are resolved in three major clades. Calliandra s.s. together with Afrocalliandra (Clade 1) is the sister to all remaining species of Ingeae and Acacia (Clades 2 and 3). Clade 2 comprises Faidherbia, Sanjappa, Thailentadopsis, Viguieranthus and Zapoteca. Clade 2 and Clade 3 are sisters, and thus the genera of Clade 2 are more closely related to each other and to the taxa of Clade 3, than to Calliandra s.s. and Afrocalliandra (Clade 1). The genera of Clades 1 and 2 all have the same type of pod, the typical “Calliandra-pod”, with Faidherbia being the only exception. Our results show that the “Calliandra-pod” is not a sign of evolutionary relationship within the Ingeae-Acacia complex. Rather this character evolved independently several times, also in clades outside of the Ingeae−Acacia complex. Another example is seen in the leaf structure within the Ingeae−Acacia complex. The possession of pinnate leaves defines the genus Inga (Clade 3) but is also present in the other two major clades (Clades 1 and 2) within the Ingeae−Acacia complex. It seems like the occurrence of pinnate leaves evolved at least three times within the Ingeae-Acacia complex. Another possibility is that the possession of pinnate leaves represents the ancestral state. However, within the mimosoids bipinnate leaves is the most common leaf morphology and the logical conclusion is that bipinnate leaves is the ancestral state. The most common polyad structure within the Ingeae−Acacia complex is 16-grained acalymmate polyads, but exceptions to this is present in Calliandra s.s., Afrocalliandra, Faidherbia and Acacia. Moreover, Calliandra s.s. is the only genus with calymmate polyads. Polyad structure could be useful for the generic classification of the Ingeae−Acacia complex but needs to be combined with other morphological characters. It seems likely that the ancestral state of polyad structure within the Ingeae-Acacia complex is acalymmate polyads and thus that the calymmate polyads seen in Calliandra are secondarily derived.
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| 9. |
- Ferm, Julia, et al.
(author)
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Phylogeny of the Neotropical legume genera Zygia and Marmaroxylon and close relatives
- 2019
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In: Taxon. - : International Association for Plant Taxonomy. - 0040-0262 .- 1996-8175. ; 68:4, s. 661-672
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Journal article (peer-reviewed)abstract
- The Neotropical legume genera Zygia and Marmaroxylon have traditionally been considered closely related and are sometimes treated as congeners. They have been referred to the mimosoid tribe Ingeae based on their possession of flowers with basally fused stamen filaments. However, their systematic status and position have not been analysed in a phylogenetic context. This study provides the first molecular phylogeny of Zygia and Marmaroxylon and closely related mimosoid legume genera, particularly from the tribe Ingeae. DNA sequence data were derived from the nuclear external transcribed spacer (ETS) and the internal transcribed spacer (ITS), and from the chloroplast psbA-trnH and trnL-trnF regions, and were analysed using Bayesian inference. In all, 29 species of Zygia and 7 species of Marmaroxylon were included in the study along with representative species from the closely related genera Abarema, Acacia s.str., Archidendropsis, Calliandra, Chloroleucon, Cojoba, Faidherbia, Havardia, Hydrochorea, Inga, Leucochloron, Macrosamanea, Pithecellobium, Pseudosamanea, Samanea, Senegalia, Vachellia and Zapoteca. The results show that neither Zygia nor Marmaroxylon are monophyletic as presently circumscribed. Furthermore, these two genera are not monophyletic together. None of the nine presently recognized sections of Zygia that contain more than one species are shown to be monophyletic. Two of the monospecific sections of Zygia, sect. Ingopsis (Z. inundata) and sect. Pseudocojoba (Z. sabatieri), were found in a clade together with species of Inga. Marmaroxylon ocumarense and M. magdalenae, previously treated as synonyms (as Zygia), are not conspecific, and are found in a clade with Macrosamanea and in a clade with species of Abarema and Hydrochorea, respectively. Our results also show the Inga alliance to be non-monophyletic. In correspondence with the results presented, all species referred to Marmaroxylon, except for M. ocumarense and M. magdalenae, are here included in Zygia, and Z. inundata is treated in Inga, in which genus it was first described.
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| 10. |
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