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- 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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| 2. |
- 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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| 3. |
- 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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