| 1. |
- Armstrong, Kate E., et al.
(författare)
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Patterns of diversification amongst tropical regions compared: a case study in Sapotaceae.
- 2014
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Ingår i: Frontiers in Genetics. - : Frontiers Media SA. - 1664-8021. ; 5:362
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Tidskriftsartikel (refereegranskat)abstract
- Species diversity is unequally distributed across the globe,with the greatest concentration occurring in the tropics. Even within the tropics, there are significant differences in the numbers of taxa found in each continental region. Manilkara is a pantropical genus of trees in the Sapotaceae comprising c.78 species. Its distribution allows for biogeographic investigation and testing of whether rates of diversification differ amongst tropical regions. The age and geographical origin of Manilkara are inferred to determine whether Gondwanan break-up, boreotropical migration or long distance dispersal have shaped its current disjunct distribution. Diversification rates through time are also analyzed to determine whether the timing and tempo of speciation on each continent coincides with geoclimatic events. Bayesian analyses of nuclear (ITS) and plastid (rpl32-trnL,rps16-trnK,and trnS-trnFM) sequences were used to reconstruct a species level phylogeny of Manilkara and related genera in the tribe Mimusopeae. Analyses of the nuclear data using a fossil-calibrated relaxed molecular clock indicate that Manilkara evolved 32–29 million years ago (Mya) in Africa. Lineages within the genus dispersed to the Neotropics 26–18 Mya and to Asia 28–15 Mya. Higher speciation rates are found in the Neotropical Manilkara clade than in either African or Asian clades. Dating of regional diversification correlates with known palaeoclimatic events. In South America, the divergence between Atlantic coastal forest and Amazonian clades coincides with the formation of drier Cerrado and Caatinga habitats between them. In Africa diversification coincides with Tertiary cycles of aridification an duplif tof the east African plateaux. In South east Asia dispersal may have been limited by the relatively recent emergence of land in New Guinea and islands further east c.10 Mya.
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| 2. |
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| 3. |
- Gautier, Laurent, et al.
(författare)
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A new species, genus and tribe of Sapotaceae, endemic to Madagascar
- 2013
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Ingår i: Taxon. - 0040-0262 .- 1996-8175. ; 62, s. 972-983
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Tidskriftsartikel (refereegranskat)abstract
- Phylogenetic relationships of the two Malagasy Sapotaceae endemic genera Capurodendron and Tsebona have been unclear until now. Recent collections from Madagascar, as well as a better representation of the tribe Isonandreae, altogether 95 terminals, were used to estimate a phylogeny of subfamily Sapotoideae. We analysed sequences of nrDNA (ITS) and cpDNA (trnH-psbA) with Bayesian inference and parsimony jackknifing. As in previous analyses, Sapoteae and Sideroxyleae are recovered monophyletic. In addition, Isonandreae, distributed in the Indo-Pacific, is for the first time resolved as monophy- letic and sister to Sapoteae. All Malagasy accessions of Capurodendron, Tsebona, and a new species are grouped in another well-supported clade. This clade is accommodated in a new tribe Tseboneae characterized by caducous stipules, 5-merous flowers with quincuncial sepals, contorted aestivation of corolla lobes, absence of corolla appendages, one or three stamens opposite each corolla lobe, villous staminodes, seeds with an adaxial scar and plano-convex cotyledons, lacking endosperm. The new species is described in the new genus Bemangidia (B. lowryi) because it has a unique leaf venation for the tribe and combines different morphological features from Capurodendron and Tsebona. All three genera are well-supported monophy- letic groups. Bemangidia lowryi is threatened with extinction due to extensive ongoing forest destruction and is assigned a preliminary conservation status of Critically Endangered.
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| 4. |
- Smedmark, Jenny E. E., et al.
(författare)
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A Phylogeny of Urophylleae (Rubiaceae) based on rps16 intron data
- 2008
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Ingår i: Taxon. - 0040-0262. ; 57:1, s. 24-32
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Tidskriftsartikel (refereegranskat)abstract
- This is the first study of phylogenetic relationships within the pantropical group Urophylleae. Previous studies have included few representatives from this group and little is known about its phylogeny. Here we use sequence data from the rps16 intron to address the question of where the four genera Temnopteryx, Pentaloncha, Pleiocarpidia, and Poecilocalyx, which have sometimes been classified in this group belong. By using different outgroups we show that there is conflict regarding the resolution among lineages in Rubioideae, which partly affects the support for relationships within Urophylleae. Urophylleae is shown to consist of two sister groups, one larger consisting only of Old World taxa and one smaller including the New World genera Amphidasya and Raritebe, and as sister of these two groups the African monotypic genus Temnopteryx. Pentaloncha, Pleiocarpidia, and Poecilocalyx all belong in the large Old World clade, which only comprises taxa included in the original circumscription of Urophylleae. Relationships within this group are not completely resolved, but Poecilocalyx is found to be the sister of Stelechantha and Pleiocarpidia to be the sister of Urophyllum leucophleum. Urophyllum is paraphyletic, as it seems to include Maschalocorymbus, Pleiocarpidia, Praravinia, and Pravinaria. It is not clear from the present analysis whether Pauridiantha is monophyletic or not.
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| 5. |
- Smedmark, Jenny E. E., et al.
(författare)
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Divergence time uncertainty and historical biogeography reconstruction - an example from Urophylleae (Rubiaceae)
- 2010
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Ingår i: Journal of Biogeography. - : Wiley. - 0305-0270 .- 1365-2699. ; 37:12, s. 2260-2274
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Tidskriftsartikel (refereegranskat)abstract
- Aim When hypotheses of historical biogeography are evaluated, age estimates of individual nodes in a phylogeny often have a direct impact on what explanation is concluded to be most likely. Confidence intervals of estimated divergence times obtained in molecular dating analyses are usually very large, but the uncertainty is rarely incorporated in biogeographical analyses. The aim of this study is to use the group Urophylleae, which has a disjunct pantropical distribution, to explore how the uncertainty in estimated divergence times affects conclusions in biogeographical analysis. Two hypotheses are evaluated: (1) long-distance dispersal from Africa to Asia and the Neotropics, and (2) a continuous distribution in the boreotropics, probably involving migration across the North Atlantic Land Bridge, followed by isolation in equatorial refugia. Location Tropical and subtropical Asia, tropical Africa, and central and southern tropical America. Methods This study uses parsimony and Bayesian phylogenetic analyses of chloroplast DNA and nuclear ribosomal DNA data from 56 ingroup species, beast molecular dating and a Bayesian approach to dispersal-vicariance analysis (Bayes-DIVA) to reconstruct the ancestral area of the group, and the dispersal-extinction-cladogenesis method to test biogeographical hypotheses. Results When the two models of geographic range evolution were compared using the maximum likelihood (ML) tree with mean estimates of divergence times, boreotropical migration was indicated to be much more likely than long-distance dispersal. Analyses of a large sample of dated phylogenies did, however, show that this result was not consistent. The age estimate of one specific node had a major impact on likelihood values and on which model performed best. The results show that boreotropical migration provides a slightly better explanation of the geographical distribution patterns of extant Urophylleae than long-distance dispersal. Main conclusions This study shows that results from biogeographical analyses based on single phylogenetic trees, such as a ML or consensus tree, can be misleading, and that it may be very important to take the uncertainty in age estimates into account. Methods that account for the uncertainty in topology, branch lengths and estimated divergence times are not commonly used in biogeographical inference today but should definitely be preferred in order to avoid unwarranted conclusions.
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| 6. |
- Smedmark, Jenny E. E., et al.
(författare)
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Inferring geographic range evolution of a pantropical tribe in the coffee family (Lasiantheae, Rubiaceae) in the face of topological uncertainty
- 2014
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Ingår i: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1055-7903 .- 1095-9513. ; 70, s. 182-194
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Tidskriftsartikel (refereegranskat)abstract
- In this study we explore what historical biogeographic events are responsible for the wide and disjunct distribution of extant species in Lasiantheae, a pantropical group of trees and shrubs in the coffee family. Three of the genera in the group, Lasianthus, Saldinia, and Trichostachys, are found to be monophyletic, while there are indications that the fourth, Ronabea, is paraphyletic. We also address how the uncertainty in topology and divergence times affects the level of confidence in the biogeographic reconstruction. A data set consisting of chloroplast and nuclear ribosomal DNA data was analyzed using a Bayesian relaxed molecular clock approach to estimate phylogenetic relationships and divergence times, and the dispersal-extinction-cladogenesis (DEC) method to reconstruct geographic range evolution. Our results show that the Lasiantheae stem lineage originated in the neotropics, and the group expanded its range to the palaeotropics during the Eocene, either by continental migration through the boreotropics or by transatlantic long-distance dispersal. Two cases of Oligocene/Miocene over water-dispersal were also inferred, once from the paleotropics to the neotropics within Lasianthus, and once to Madagascar, concurrent with the origin of Saldinia. A lot of the diversification within Lasianthus took place during the Miocene and may have been influenced by climatic factors such as a period of markedly warm and moist climate in Asia and the aridification of the interior of the African continent. When biogeographic reconstructions were averaged over a random sample of 1000 dated phylogenies, the confidence in the biogeographic reconstruction decreased for most nodes, compared to when a single topology was used. A good understanding of phylogenetic relationships is necessary to understand the biogeographic history of a group, bit since the phylogeny is rarely completely known it is important to include phylogenetic uncertainty in biogeographic analysis. For nodes where the resolution is uncertain, the use of a single best topology as a basis for biogeographic analysis will result in inflated confidence in a biogeographic reconstruction which may be just one of several possible reconstructions.
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| 7. |
- Smedmark, Jenny E. E., et al.
(författare)
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Molecular systematics and incongruent gene trees of Urophylleae (Rubiaceae)
- 2011
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Ingår i: Taxon. - 0040-0262 .- 1996-8175. ; 60:5, s. 1397-1406
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Tidskriftsartikel (refereegranskat)abstract
- The phylogeny of the Pantropical tribe Urophylleae is poorly understood. Earlier phylogenetic work has identified major evolutionary lineages within the group, each geographically restricted to a single continent, but relationships among taxa within these lineages are so far largely unresolved. This study uses parsimony and Bayesian phylogenetic analyses of chloroplast DNA (cpDNA) and nuclear ribosomal DNA (nrDNA) to resolve phylogenetic relationships within Urophylleae. The results show that there are conflicts between cpDNA and nrDNA regarding species-level relationships within Pauridiantha, Urophyllum, and Amphidasya, which provides evidence of a complex genetic history. Different types of tests are used to explore the magnitude of the incongruence and locate the exact nodes in the two gene trees that are in conflict. This approach makes it possible to use the topology from the combined analysis, despite the separate datasets being strongly incongruent, since areas of the tree that are free from conflict can be identified. Based on the results presented in this study, Urophylleae is indicated to consist of Temnopteryx, Raritebe, Amphidasya, Urophyllum s.l., Pauridiantha s.l., and Pentaloncha. Several genera are shown to be nested inside Pauridiantha, two of which have already been included in Pauridiantha based on other data (Pamplethantha, Commitheca), and two which are included in this genus here (Poecilocalyx, Stelechantha). Likewise, three genera are shown to be ingroups in Urophyllum (Pravinaria, Maschalocorymbus, Pleiocarpidia), and are therefore subsumed under this genus. New combinations under Pauridiantha are proposed for three species in Poecilocalyx and three species in Stelechantha, as well as new combinations under Urophyllum for two species in Pravinaria and 17 species in Pleiocarpidia. For one of the latter species a new name is presented to avoid homonymy.
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| 8. |
- Smedmark, Jenny E. E., 1972-
(författare)
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The evolutionary history of Geum (Rosaceae, Colurieae) : a study of ancient allopolyploid speciation
- 2004
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Allopolyploid speciation plays an important role in flowering plant evolution. Its contribution to diversity has been suggested to be significant in Geum. In this thesis the evolutionary history of Geum and its closest relatives was investigated by phylogenetic analysis of sequence data from the trnL-trnF region of the chloroplast, the ITS region of nuclear ribosomal DNA, and the nuclear low-copy gene GBSSI. The data were analysed using parsimony, Bayesian inference, and maximum likelihood. The phylogenies were used to test hypotheses about allopolyploid speciation, to investigate the evolution of some fruit characters and the implications for the taxonomy of the group. The GBSSI phylogenies indicated that allopolyploid speciation has occurred in the history of Geum. However, earlier hypotheses based on cytogenetic data about the allopolyploid ancestry of certain species were rejected. One tetraploid species and a morphologically diverse group of hexaploids, likely also including species with higher ploidy levels, were suggested to be of allopolyploid origin. A hypothesis of reticulate organismal relationships, including two instances where new lineages have been formed by allopolyploidy, was proposed based on the gene trees. A molecular dating analysis indicated that these reticulations occurred several million years ago. None of the previously suggested circumscriptions of Geum, Acomastylis, or Sieversia sensu lato were found to be monophyletic. Nested within Geum sensu lato were Waldsteinia, Coluria, and Taihangia and therefore Geum was recircumscribed to include these taxa. Colurieae, the former Dryadeae (in part), was recircumscribed and given a phylogenetic definition. According to this classification, Colurieae includes Fallugia, Sieversia sensu stricto, and Geum. Morphological evolution within the putative allopolyploid group appears to be homoplasious. Initial optimisation of the presence of a "joint", an abscission layer where the style, or part of it, is shed at maturity, on the gene trees indicated that it evolved four times from persistent, elongating styles. However, scanning electron microscopy showed that the development of the various types of fruits with jointed styles is similar, indicating that the joint and the deciduous segment of the style, of different lineages are homologous. The joint was thus hypothesised to have originated in the ancestral lineage of Waldsteinia and Coluria and to have been passed on via hybridisation to the polyploids. It is, however, only expressed in some lineages among the polyploids.
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| 9. |
- Wikström, Niklas, et al.
(författare)
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A Revised Time Tree of the Asterids : Establishing a Temporal Framework For Evolutionary Studies of the Coffee Family (Rubiaceae)
- 2015
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 10:5
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Tidskriftsartikel (refereegranskat)abstract
- Divergence time analyses in the coffee family (Rubiaceae) have all relied on the same Gentianales crown group age estimate, reported by an earlier analysis of the asterids, for defining the upper age bound of the root node in their analyses. However, not only did the asterid analysis suffer from several analytical shortcomings, but the estimate itself has been used in highly inconsistent ways in these Rubiaceae analyses. Based on the original data, we here reanalyze the divergence times of the asterids using relaxed-clock models and 14 fossil-based minimum age constraints. We also expand the data set to include an additional 67 taxa from Rubiaceae sampled across all three subfamilies recognized in the family. Three analyses are conducted: a separate analysis of the asterids, which completely mirrors the original asterid analysis in terms of taxon sample and data; a separate analysis of the Gentianales, where the result from the first analysis is used for defining a secondary root calibration point; and a combined analysis where all taxa are analyzed simultaneously. Results are presented in the form of a time-calibrated phylogeny, and age estimates for asterid groups, Gentianales, and major groups of Rubiaceae are compared and discussed in relation to previously published estimates. Our updated age estimates for major groups of Rubiaceae provide a significant step forward towards the long term goal of establishing a robust temporal framework for the divergence of this biologically diverse and fascinating group of plants.
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| 10. |
- Richardson, James E., et al.
(författare)
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The influence of tectonics, sea-level changes and dispersal on migration and diversification of Isonandreae (Sapotaceae)
- 2014
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Ingår i: Botanical journal of the Linnean Society. - : Wiley-Blackwell. - 0024-4074 .- 1095-8339. ; 174:1, s. 130-140
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Tidskriftsartikel (refereegranskat)abstract
- Internal transcribed spacer (ITS) ribosomal DNA sequence data were generated for 80 of the c. 200 species of Isonandreae and were added to data from African and Neotropical representatives in subfamily Sapotoideae and outgroups in Sapotaceae. Bayesian dating and ancestral area reconstruction indicated that Isonandreae are derived from within an African grade. Multiple Australasian species or lineages are derived from Sundanian lineages in South-East Asia with stem ages originating from the late Oligocene. Sri Lankan and Indian lineages are also derived from Sundanian lineages. Our results are consistent with migration from Africa into Sundania followed by numerous over-water dispersal events across Wallace's Line into Australasia and migration from Sundania to the Indian subcontinent. Pleistocene speciation indicates that sea-level changes during that epoch could have been responsible for some species diversification in Sundania.
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