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Journal ArticleDOI

Southern Hemisphere Biogeography Inferred by Event-Based Models: Plant versus Animal Patterns

01 Apr 2004-Systematic Biology (Oxford University Press)-Vol. 53, Iss: 2, pp 216-243
TL;DR: The results confirm the hybrid origin of the South American biota: there has been surprisingly little biotic exchange between the northern tropical and the southern temperate regions of South America, especially for animals.
Abstract: The Southern Hemisphere has traditionally been considered as having a fundamentally vicariant history. The common trans-Pacific disjunctions are usually explained by the sequential breakup of the supercontinent Gondwana during the last 165 million years, causing successive division of an ancestral biota. However, recent biogeographic studies, based on molecular estimates and more accurate paleogeographic reconstructions, indicate that dispersal may have been more important than traditionally assumed. We examined the relative roles played by vicariance and dispersal in shaping Southern Hemisphere biotas by analyzing a large data set of 54 animal and 19 plant phylogenies, including marsupials, ratites, and southern beeches (1,393 terminals). Parsimony-based tree fitting in conjunction with permutation tests was used to examine to what extent Southern Hemisphere biogeographic patterns fit the breakup sequence of Gondwana and to identify concordant dispersal patterns. Consistent with other studies, the animal data are congruent with the geological sequence of Gondwana breakup: (Africa(New Zealand(southern South America, Australia))). Trans-Antarctic dispersal (Australia southern South America) is also significantly more frequent than any other dispersal event in animals, which may be explained by the long period of geological contact between Australia and South America via Antarctica. In contrast, the dominant pattern in plants, (southern South America(Australia, New Zealand)), is better explained by dispersal, particularly the prevalence of trans-Tasman dispersal between New Zealand and Australia. Our results also confirm the hybrid origin of the South American biota: there has been surprisingly little biotic exchange between the northern tropical and the southern temperate regions of South America, especially for animals.

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Journal ArticleDOI
28 Nov 2014-Science
TL;DR: Diversity of most fungal groups peaked in tropical ecosystems, but ectomycorrhizal fungi and several fungal classes were most diverse in temperate or boreal ecosystems, and manyfungal groups exhibited distinct preferences for specific edaphic conditions (such as pH, calcium, or phosphorus).
Abstract: Fungi play major roles in ecosystem processes, but the determinants of fungal diversity and biogeographic patterns remain poorly understood. Using DNA metabarcoding data from hundreds of globally distributed soil samples, we demonstrate that fungal richness is decoupled from plant diversity. The plant-to-fungus richness ratio declines exponentially toward the poles. Climatic factors, followed by edaphic and spatial variables, constitute the best predictors of fungal richness and community composition at the global scale. Fungi show similar latitudinal diversity gradients to other organisms, with several notable exceptions. These findings advance our understanding of global fungal diversity patterns and permit integration of fungi into a general macroecological framework.

2,346 citations

Journal ArticleDOI
12 Nov 2010-Science
TL;DR: It is shown that Andean uplift was crucial for the evolution of Amazonian landscapes and ecosystems, and that current biodiversity patterns are rooted deep in the pre-Quaternary.
Abstract: The Amazonian rainforest is arguably the most species-rich terrestrial ecosystem in the world, yet the timing of the origin and evolutionary causes of this diversity are a matter of debate. We review the geologic and phylogenetic evidence from Amazonia and compare it with uplift records from the Andes. This uplift and its effect on regional climate fundamentally changed the Amazonian landscape by reconfiguring drainage patterns and creating a vast influx of sediments into the basin. On this “Andean” substrate, a region-wide edaphic mosaic developed that became extremely rich in species, particularly in Western Amazonia. We show that Andean uplift was crucial for the evolution of Amazonian landscapes and ecosystems, and that current biodiversity patterns are rooted deep in the pre-Quaternary.

1,790 citations

Journal ArticleDOI
TL;DR: The present analysis indicates that Hemiphractinae are not related to the other three hylid subfamilies and are therefore removed from the family and tentatively considered a subfamily of the paraphyletic Leptodactylidae.
Abstract: Hylidae is a large family of American, Australopapuan, and temperate Eurasian treefrogs of approximately 870 known species, divided among four subfamilies. Although some groups of Hylidae have been addressed phylogenetically, a comprehensive phylogenetic analysis has never been presented. The first goal of this paper is to review the current state of hylid systematics. We focus on the very large subfamily Hylinae (590 species), evaluate the monophyly of named taxa, and examine the evidential basis of the existing taxonomy. The second objective is to perform a phylogenetic analysis using mostly DNA sequence data in order to (1) test the monophyly of the Hylidae; (2) determine its constituent taxa, with special attention to the genera and species groups which form the subfamily Hylinae, and c) propose a new, monophyletic taxonomy consistent with the hypothesized relationships. We present a phylogenetic analysis of hylid frogs based on 276 terminals, including 228 hylids and 48 outgroup taxa. Includ...

927 citations

Journal ArticleDOI
TL;DR: A likelihood framework for inferring the evolution of geographic range on phylogenies that models lineage dispersal and local extinction in a set of discrete areas as stochastic events in continuous time is described.
Abstract: At a time when historical biogeography appears to be again expanding its scope after a period of focusing primarily on discerning area relationships using cladograms, new inference methods are needed to bring more kinds of data to bear on questions about the geographic history of lineages. Here we describe a likelihood framework for inferring the evolution of geographic range on phylogenies that models lineage dispersal and local extinction in a set of discrete areas as stochastic events in continuous time. Unlike existing methods for estimating ancestral areas, such as dispersal-vicariance analysis, this approach incorporates information on the timing of both lineage divergences and the availability of connections between areas (dispersal routes). Monte Carlo methods are used to estimate branch-specific transition probabilities for geographic ranges, enabling the likelihood of the data (observed species distributions) to be evaluated for a given phylogeny and parameterized paleogeographic model. We demonstrate how the method can be used to address two biogeographic questions: What were the ancestral geographic ranges on a phylogenetic tree? How were those ancestral ranges affected by speciation and inherited by the daughter lineages at cladogenesis events? For illustration we use hypothetical examples and an analysis of a Northern Hemisphere plant clade (Cercis), comparing and contrasting inferences to those obtained from dispersal-vicariance analysis. Although the particular model we implement is somewhat simplistic, the framework itself is flexible and could readily be modified to incorporate additional sources of information and also be extended to address other aspects of historical biogeography.

801 citations


Cites background from "Southern Hemisphere Biogeography In..."

  • ...In broad outline it is thus similar to the more familiar task of evaluating the likelihood of an organismal trait (character) on a phylogeny, given an evolutionary model for that character (e.g., Pagel 1994; Schluter 1995)....

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Journal ArticleDOI
TL;DR: In conclusion, EcM fungi are phylogenetically highly diverse, and molecular surveys particularly in tropical and south temperate habitats are likely to supplement to the present figures.
Abstract: The ectomycorrhizal (EcM) symbiosis involves a large number of plant and fungal taxa worldwide During studies on EcM diversity, numerous misidentifications, and contradictory reports on EcM status have been published This review aims to: (1) critically assess the current knowledge of the fungi involved in the EcM by integrating data from axenic synthesis trials, anatomical, molecular, and isotope studies; (2) group these taxa into monophyletic lineages based on molecular sequence data and published phylogenies; (3) investigate the trophic status of sister taxa to EcM lineages; (4) highlight other potentially EcM taxa that lack both information on EcM status and DNA sequence data; (5) recover the main distribution patterns of the EcM fungal lineages in the world Based on critically examining original reports, EcM lifestyle is proven in 162 fungal genera that are supplemented by two genera based on isotopic evidence and 52 genera based on phylogenetic data Additionally, 33 genera are highlighted as potentially EcM based on habitat, although their EcM records and DNA sequence data are lacking Molecular phylogenetic and identification studies suggest that EcM symbiosis has arisen independently and persisted at least 66 times in fungi, in the Basidiomycota, Ascomycota, and Zygomycota The orders Pezizales, Agaricales, Helotiales, Boletales, and Cantharellales include the largest number of EcM fungal lineages Regular updates of the EcM lineages and genera therein can be found at the UNITE homepage http://uniteutee/EcM_lineages The vast majority of EcM fungi evolved from humus and wood saprotrophic ancestors without any obvious reversals Herbarium records from 11 major biogeographic regions revealed three main patterns in distribution of EcM lineages: (1) Austral; (2) Panglobal; (3) Holarctic (with or without some reports from the Austral or tropical realms) The holarctic regions host the largest number of EcM lineages; none are restricted to a tropical distribution with Dipterocarpaceae and Caesalpiniaceae hosts We caution that EcM-dominated habitats and hosts in South America, Southeast Asia, Africa, and Australia remain undersampled relative to the north temperate regions In conclusion, EcM fungi are phylogenetically highly diverse, and molecular surveys particularly in tropical and south temperate habitats are likely to supplement to the present figures Due to great risk of contamination, future reports on EcM status of previously unstudied taxa should integrate molecular identification tools with axenic synthesis experiments, detailed morphological descriptions, and/or stable isotope investigations We believe that the introduced lineage concept facilitates design of biogeographical studies and improves our understanding about phylogenetic structure of EcM fungal communities

791 citations


Cites background or methods from "Southern Hemisphere Biogeography In..."

  • ...Data on distribution of lineages were retrieved from published and unpublished reports of fruit-bodies (and Cenococcum sclerotia) from major biogeographic regions of the world (Sanmartin et al. 2001; Sanmartin and Ronquist 2004)....

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  • ...Interestingly, none of the EcM fungal lineages are restricted to tropical regions, a pattern that is common in many animal and plant taxa, including EcM plant hosts (Sanmartin and Ronquist 2004)....

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  • ...The grouping of the austral regions (Australia, Southern South America, and New Zealand) on the basis of their EcM lineages is in agreement with geological, plant, and animal area cladograms that link Gondwanan regions (Sanmartin and Ronquist 2004)....

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References
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01 Jan 1959

16,220 citations

Journal ArticleDOI
TL;DR: A revised and updated classification for the families of the flowering plants is provided in this paper, which includes Austrobaileyales, Canellales, Gunnerales, Crossosomatales and Celastrales.

7,299 citations

Journal ArticleDOI
TL;DR: The metric presented in this paper makes possible the comparison of the many nonbinary phylogenetic trees appearing in the literature, and provides an objective procedure for comparing the different methods for constructing phylogenetics trees.
Abstract: A metric on general phylogenetic trees is presented. This extends the work of most previous authors, who constructed metrics for binary trees. The metric presented in this paper makes possible the comparison of the many nonbinary phylogenetic trees appearing in the literature. This provides an objective procedure for comparing the different methods for constructing phylogenetic trees. The metric is based on elementary operations which transform one tree into another. Various results obtained in applying these operations are given. They enable the distance between any pair of trees to be calculated efficiently. This generalizes previous work by Bourque to the case where interior vertices can be labeled, and labels may contain more than one element or may be empty.

2,519 citations


"Southern Hemisphere Biogeography In..." refers methods in this paper

  • ...To calculate the degree of congruence (similarity) between the area cladogram and the biogeographic patterns, we used a modification of the method of Robinson and Foulds (1981) for calculating the metric distance between two phylogenetic trees (see Fig....

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Journal ArticleDOI
TL;DR: This work presents a new biogeographic method, dispersal-vicariance analysis, which reconstructs the ancestral distributions in a given phylogeny without any prior assumptions about the form of area relationships, and describes the algorithms that find the optimal reconstruction.
Abstract: Quantification in historical biogeography has usually been based on the search for a single branching relationship among areas of endemism. Unlike organisms, however, areas rarely have a unique hierarchical history. Dispersal barriers appear and disappear and may have differ- ent effects on different species. As a result, the biota of an area may consist of several components with separate histories, each of which may be reticulate rather than branching. In an attempt to address these problems, I present a new biogeographic method, dispersal-vicariance analysis, which reconstructs the ancestral distributions in a given phylogeny without any prior assumptions about the form of area relationships. A three-dimensional step matrix based on a simple biogeo- graphic model is used in the reconstruction. Speciation is assumed to subdivide the ranges of widespread species into vicariant components; the optimal ancestral distributions are those that minimize the number of implied dispersal and extinction events. Exact algorithms that find the optimal reconstruction(s) are described. In addition to their use in taxon biogeography, the in- ferred distribution histories of individual groups serve as a basis for the study of general patterns in historical biogeography, particularly if the relative age of the nodes in the source cladograms is known. (Cladistic biogeography; comparative phylogeography; dispersal; extinction; historical biogeography; optimization; vicariance; widespread species.) In historical biogeography, whether fo- cused on patterns below the species level (comparative phylogeography) or above the species level, there is a need for quan- titative methods to assess the likelihood of alternative hypotheses. Most methods used today are based on the assumption that there is a single branching pattern among areas of endemism caused by vi-

1,529 citations


"Southern Hemisphere Biogeography In..." refers background or methods in this paper

  • ...In contrast, recent event-based methods (Page, 1995; Ronquist, 1997, 1998) are derived from explicit (although not strict probabilistic) process models and reconstruct both ancestral distributions and biogeographic events....

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  • ...Dispersal–vicariance analysis (DIVA; Ronquist, 1997) is an event-based biogeographic inference method that does not force vicariance events to conform to a hierarchical pattern....

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