Introduction and synthesis: Plant phylogeny and the origin of major biomes

Royal Botanic Garden Edinburgh, 20a Inverleith Row, Edinburgh EH3 5LR, UK.
Philosophical Transactions of The Royal Society B Biological Sciences (Impact Factor: 7.06). 11/2004; 359(1450):1455-64. DOI: 10.1098/rstb.2004.1539
Source: PubMed


Phylogenetic trees based upon DNA sequence data, when calibrated with a dimension of time, allow inference of: (i) the pattern of accumulation of lineages through time; (ii) the time of origin of monophyletic groups; (iii) when lineages arrived in different geographical areas; (iv) the time of origin of biome-specific morphologies. This gives a powerful new view of the history of biomes that in many cases is not provided by the incomplete plant fossil record. Dated plant phylogenies for angiosperm families such as Leguminoaceae (Fabaceae), Melastomataceae sensu stricto, Annonaceae and Rhamnaceae indicate that long-distance, transoceanic dispersal has played an important role in shaping their distributions, and that this can obscure any effect of tectonic history, previously assumed to have been the major cause of their biogeographic patterns. Dispersal from other continents has also been important in the assembly of the Amazonian rainforest flora and the Australian flora. Comparison of dated biogeographic patterns of plants and animals suggests that recent long-distance dispersal might be more prevalent in plants, which has major implications for community assembly and coevolution. Dated plant phylogenies also reveal the role of past environmental changes on the evolution of lineages in species-rich biomes, and show that recent Plio-Pleistocene diversification has contributed substantially to their current species richness. Because of the critical role of fossils and morphological characters in assigning ages to nodes in phylogenetic trees, future studies must include careful morphological consideration of fossils and their extant relatives in a phylogenetic context. Ideal study systems will be based upon DNA sequence data from multiple loci and multiple fossil calibrations. This allows cross-validation both of age estimates from different loci, and from different fossil calibrations. For a more complete view of biome history, future studies should emphasize full taxon sampling in ecologically important groups, and should focus on geographical areas for which few species-level phylogenies are available, such as tropical Africa and Asia. These studies are urgent because understanding the history of biomes can both inform conservation decisions, and help predict the effects of future environmental changes at a time when biodiversity is being impacted on an unprecedented scale.

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Available from: James E Richardson, Mar 03, 2015
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    • "Specifically, both over-and underestimation of species richness would be reduced compared to a single global relationship. Furthermore , since biomes capture both evolutionary history and ecosystem productivity (Pennington et al., 2004), biomes should better explain species richness than do floristic kingdoms. "
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    ABSTRACT: Aim The species–area relationship (SAR) is a prominent concept for predicting species richness and biodiversity loss. A key step in defining SARs is to accurately estimate the slope of the relationship, but researchers typically apply only one global (canonical) slope. We hypothesized that this approach is overly simplistic and investigated how geographically varying determinants of SARs affect species richness estimates of vascular plants at the global scale. Location Global. Methods We used global species richness data for vascular plants from 1032 geographical units varying in size and shape. As possible determinants of geographical variation in SARs we chose floristic kingdoms and biomes as biogeographical provinces, and land cover as a surrogate for habitat diversity. Using simultaneous autoregressive models we fitted SARs to each set of determinants, compared their ability to predict the observed data and large-scale species richness patterns, and determined the extent to which varying SARs differed from the global relationship. Results Incorporating variation into SARs improved predictions of global species richness patterns. The best model, which accounts for variation due to biomes, explained 46.1% of the species richness variation. Moreover, fitting SARs to biomes produced better results than fitting them to floristic kingdoms, supporting the hypothesis that energy availability complements evolutionary history in generating species richness patterns. Land cover proved to be less important than biomes, explaining only 36.4% of the variation, possibly owing to the high uncertainty in the data set. The incorporation of second-order interactions of area, land cover and biomes did not improve the predictive ability of the models. Main conclusions Our study contributes to a deeper understanding of SARs and improves the applicability of SARs through regionalization. Future models should explicitly consider geographically varying determinants of SARs in order to improve our assessment of the impact of global change scenarios on species richness patterns.
    Journal of Biogeography 10/2013; 41(2):261-273. DOI:10.1111/jbi.12213 · 4.59 Impact Factor
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    • "Thus, 'appropriate' characters may be selected for phylogeny reconstruction . Pennington et al. (2004) noted a tendency in many studies to assign fossils to the stem of the clade that they belong to and, as they emphasized, this will lead to underestimates of divergence times. Smith et al. (2010, p. 5897) also criticized 'the default practice of assigning fossils to the stem of the most inclusive crown clade to which they probably belong, thereby possibly biasing estimated ages (possibly throughout the tree) to be younger'. "
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    ABSTRACT: The crucial step in Bayesian dating of phylogenies is the selection of prior probability curves for clade ages. In studies on regions derived from Gondwana, many authors have used steep priors, stipulating that clades can only be a little older than their oldest known fossil. These studies have ruled out vicariance associated with Gondwana breakup, but only because of the particular priors that were adopted. The use of non-flat priors for fossil-based ages is not justified and is unnecessary. Tectonic calibrations can be integrated with fossil calibrations that are used to give minimum clade ages only.
    Journal of Biogeography 10/2012; 39(10):1749-1756. DOI:10.2307/41687707 · 4.59 Impact Factor
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    • "First, unlike the southern hemisphere landmasses, there have been multiple land routes between these landmasses over the past 50 my, each with a different lifespan , climate and latitude (Tiffney 1985a,b; Wen 1999; Donoghue et al., 2001; Milne & Abbott 2002), and accurate divergence time data can thus distinguish between these as putative routes between continents. Second, divergence time data has led to the rejection of vicariance explanations for all but a handful of major southern hemisphere disjunctions (Renner et al., 2001; Givnish & Renner, 2004; Pennington et al., 2004; Renner, 2004, 2005; Sanmartin & Ronquist, 2004; de Queiroz, 2005; McGlone, 2005), and because of this Tertiary relict floras might provide the best example of a major disjunction , involving large numbers of genera, that came about by vicariance. Finally, for many N America–E Asia disjuncts among Tertiary relict floras, calculated divergence times are generally in the range of 3–15 mya (Xiang et al., 2000; Donoghue et al., 2001). "
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    ABSTRACT: Abstract  A universal method of molecular dating that can be applied to all families and genera regardless of their fossil records, or lack thereof, is highly desirable. A possible method for eudicots is to use a large phylogeny calibrated using deep fossils including tricolpate pollen as a fixed (124 mya) calibration point. This method was used to calculate node ages within three species-poor disjunct basal eudicot genera, Caulophyllum, Podophyllum and Pachysandra, and sensitivity of these ages to effects such as taxon sampling were then quantified. By deleting from one to three accessions related to each genus in 112 different combinations, a confidence range describing variation due only to taxon sampling was generated. Ranges for Caulophyllum, Podophyllum and Pachysandra were 8.4–10.6, 7.6–20.0, and 17.6–25.0 mya, respectively. However, the confidence ranges calculated using bootstrapping were much wider, at 3–19, 0–32 and 11–32 mya, respectively. Furthermore, deleting 10 adjacent taxa had a large effect in Pachysandra only, indicating that undersampling effects are significant among Buxales. Changes to sampling density in neighboring clades, or to the position of the fixed fossil calibration point had small to negligible effects. Non-parametric rate smoothing was more sensitive to taxon sampling effects than was penalized likelihood. The wide range for Podophyllum, compared to the other two genera, was probably due to a high degree of rate heterogeneity within this genus. Confidence ranges calculated by this method could be narrowed by sampling more individuals within the genus of interest, and by sequencing multiple DNA regions from all species in the phylogeny.
    Journal of Systematics and Evolution 08/2009; 47(5):383 - 401. DOI:10.1111/j.1759-6831.2009.00038.x · 1.49 Impact Factor
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