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Journal Article•DOI•

Phylogeny, adaptive radiation, and historical biogeography in Bromeliaceae: Insights from an eight-locus plastid phylogeny

Thomas J. Givnish1, Michael H. J. Barfuss2, Benjamin W. van Ee1, Benjamin W. van Ee3, Ricarda Riina1, Ricarda Riina4, Katharina Schulte5, Katharina Schulte6, Ralf Horres, Philip A. Gonsiska1, Rachel S. Jabaily7, Rachel S. Jabaily1, Darren M. Crayn5, J. Andrew C. Smith8, Klaus Winter9, Gregory K. Brown10, Timothy M. Evans11, Bruce K. Holst12, Harry E. Luther12, Walter Till2, Georg Zizka6, Paul E. Berry4, Kenneth J. Sytsma1 •
University of Wisconsin-Madison1, University of Vienna2, Harvard University3, University of Michigan4, James Cook University5, Goethe University Frankfurt6, Old Dominion University7, University of Oxford8, Smithsonian Tropical Research Institute9, University of Wyoming10, Grand Valley State University11, Marie Selby Botanical Gardens12
01 May 2011-American Journal of Botany (Botanical Society of America)-Vol. 98, Iss: 5, pp 872-895
TL;DR: A bromeliad phylogeny based on eight plastid regions is used to analyze relationships within the family, test a new, eight-subfamily classification, infer the chronology of b romeliad evolution and invasion of different regions, and provide the basis for future analyses of trait evolution and rates of diversification.
Abstract:  Premise : Bromeliaceae form a large, ecologically diverse family of angiosperms native to the New World. We use a bromeliad phylogeny based on eight plastid regions to analyze relationships within the family, test a new, eight-subfamily classifi cation, infer the chronology of bromeliad evolution and invasion of different regions, and provide the basis for future analyses of trait evolution and rates of diversifi cation.  Methods : We employed maximum-parsimony, maximum-likelihood, and Bayesian approaches to analyze 9341 aligned bases for four outgroups and 90 bromeliad species representing 46 of 58 described genera. We calibrate the resulting phylogeny against time using penalized likelihood applied to a monocot-wide tree based on plastid ndhF sequences and use it to analyze patterns of geographic spread using parsimony, Bayesian inference, and the program S-DIVA.  Results : Bromeliad subfamilies are related to each other as follows: (Brocchinioideae, (Lindmanioideae, (Tillandsioideae, (Hechtioideae, (Navioideae, (Pitcairnioideae, (Puyoideae, Bromelioideae))))))). Bromeliads arose in the Guayana Shield ca. 100 million years ago (Ma), spread centrifugally in the New World beginning ca. 16 – 13 Ma, and dispersed to West Africa ca. 9.3 Ma. Modern lineages began to diverge from each other roughly 19 Ma.  Conclusions : Nearly two-thirds of extant bromeliads belong to two large radiations: the core tillandsioids, originating in the Andes ca. 14.2 Ma, and the Brazilian Shield bromelioids, originating in the Serro do Mar and adjacent regions ca. 9.1 Ma.

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Citations
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Journal Article•DOI•
Biological evidence supports an early and complex emergence of the Isthmus of Panama

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Christine D. Bacon1, Christine D. Bacon2, Daniele Silvestro3, Carlos Jaramillo2, Brian Tilston Smith4, Prosanta Chakrabarty5, Alexandre Antonelli1 •
University of Gothenburg1, Smithsonian Tropical Research Institute2, Swiss Institute of Bioinformatics3, American Museum of Natural History4, Louisiana State University5
12 May 2015-Proceedings of the National Academy of Sciences of the United States of America
TL;DR: It is shown that biotic migrations across the Isthmus of Panama began several million years earlier than commonly assumed, indicating that the dramatic biotic turnover associated with the Great American Biotic Interchange was a long and complex process that began as early as the Oligocene–Miocene transition.
Abstract: The linking of North and South America by the Isthmus of Panama had major impacts on global climate, oceanic and atmospheric currents, and biodiversity, yet the timing of this critical event remains contentious. The Isthmus is traditionally understood to have fully closed by ca. 3.5 million years ago (Ma), and this date has been used as a benchmark for oceanographic, climatic, and evolutionary research, but recent evidence suggests a more complex geological formation. Here, we analyze both molecular and fossil data to evaluate the tempo of biotic exchange across the Americas in light of geological evidence. We demonstrate significant waves of dispersal of terrestrial organisms at approximately ca. 20 and 6 Ma and corresponding events separating marine organisms in the Atlantic and Pacific oceans at ca. 23 and 7 Ma. The direction of dispersal and their rates were symmetrical until the last ca. 6 Ma, when northern migration of South American lineages increased significantly. Variability among taxa in their timing of dispersal or vicariance across the Isthmus is not explained by the ecological factors tested in these analyses, including biome type, dispersal ability, and elevation preference. Migration was therefore not generally regulated by intrinsic traits but more likely reflects the presence of emergent terrain several millions of years earlier than commonly assumed. These results indicate that the dramatic biotic turnover associated with the Great American Biotic Interchange was a long and complex process that began as early as the Oligocene–Miocene transition.

458 citations

Journal Article•DOI•
A quantitative review of pollination syndromes: do floral traits predict effective pollinators?

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Víctor Rosas-Guerrero1, Víctor Rosas-Guerrero2, Ramiro Aguilar3, Silvana Martén-Rodríguez, Lorena Ashworth3, Martha Lopezaraiza-Mikel1, Martha Lopezaraiza-Mikel2, Jesús M. Bastida2, Mauricio Quesada2 •
Autonomous University of Guerrero1, National Autonomous University of Mexico2, National University of Cordoba3
01 Mar 2014-Ecology Letters
TL;DR: The first systematic review of pollination syndromes that quantitatively tests whether the most effective pollinators for a species can be inferred from suites of floral traits for 417 plant species supports the syndrome concept.
Abstract: The idea of pollination syndromes has been largely discussed but no formal quantitative evaluation has yet been conducted across angiosperms. We present the first systematic review of pollination syndromes that quantitatively tests whether the most effective pollinators for a species can be inferred from suites of floral traits for 417 plant species. Our results support the syndrome concept, indicating that convergent floral evolution is driven by adaptation to the most effective pollinator group. The predictability of pollination syndromes is greater in pollinator-dependent species and in plants from tropical regions. Many plant species also have secondary pollinators that generally correspond to the ancestral pollinators documented in evolutionary studies. We discuss the utility and limitations of pollination syndromes and the role of secondary pollinators to understand floral ecology and evolution.

356 citations

Journal Article•DOI•
The systematic distribution of vascular epiphytes – a critical update

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Gerhard Zotz1, Gerhard Zotz2•
Smithsonian Tropical Research Institute1, University of Oldenburg2
01 Mar 2013-Botanical Journal of the Linnean Society
TL;DR: A compilation of epiphytic diversity derived from a vast number of sources is presented, meant to be an important tool for studies on the ecology and evolution ofEpiphytes, but also for comparative studies with a focus on other life forms.

320 citations

Journal Article•DOI•
Adaptive radiation, correlated and contingent evolution, and net species diversification in Bromeliaceae

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Thomas J. Givnish1, Michael H. J. Barfuss2, Benjamin W. van Ee3, Ricarda Riina4, Katharina Schulte5, Katharina Schulte6, Ralf Horres, Philip A. Gonsiska1, Rachel S. Jabaily7, Darren M. Crayn6, J. Andrew C. Smith8, Klaus Winter9, Gregory K. Brown10, Timothy M. Evans11, Bruce K. Holst12, Harry E. Luther13, Walter Till2, Georg Zizka5, Paul E. Berry14, Kenneth J. Sytsma1 •
University of Wisconsin-Madison1, University of Vienna2, Black Hills State University3, Spanish National Research Council4, Goethe University Frankfurt5, James Cook University6, Rhodes College7, University of Oxford8, Smithsonian Tropical Research Institute9, University of Wyoming10, Grand Valley State University11, Marie Selby Botanical Gardens12, National Parks Board13, University of Michigan14
01 Feb 2014-Molecular Phylogenetics and Evolution
TL;DR: This study is among the first to test a priori hypotheses about the relationships among phylogeny, phenotypic evolution, geographic spread, and net species diversification, and to argue for causality to flow from functional diversity to spatial expansion to species diversity.

295 citations

Cites background or methods from "Phylogeny, adaptive radiation, and ..."

  • ...They show little variation in chromosome number and have centers of diversity in four mountainous regions, including Central America, the Andes, the tepuis of the Guayana Shield, and the Serra do Mar and nearby coastal ranges of the Brazilian Shield in South America (Givnish et al., 2011)....

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  • ...We used a placeholder approach in this study and our preceding analysis of phylogenetic relationships and historical biogeography in Bromeliaceae (Givnish et al., 2011)....

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  • ...CAM should thus be associated with atmospheric Tillandsia that absorb water and nutrients solely via absorptive trichomes, given their exposure, small body size and virtually absent water ious traits in the family Bromeliaceae....

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  • ...Thomas J. Givnish a,*, Michael H.J. Barfuss b, Benjamin Van Ee c, Ricarda Riina d, Katharina Schulte e,f, Ralf Horres g, Philip A. Gonsiska a, Rachel S. Jabaily h, Darren M. Crayn f, J. Andrew C. Smith i, Klaus Winter j, Gregory K. Brown k, Timothy M. Evans l, Bruce K. Holst m, Harry Luther n, Walter Till b, Georg Zizka e, Paul E. Berry o, Kenneth J. Sytsma a a Department of Botany, University of Wisconsin-Madison, Madison, WI 53706, USA b Department of Systematic and Evolutionary Botany, Faculty of Life Sciences, University of Vienna, Vienna A-1030, Austria c School of Natural Sciences, Black Hills State University, Spearfish, SD 57799, USA d Real Jardín Botánico, CSIC, Plaza de Murillo 2, Madrid 28014, Spain e Department of Botany and Molecular Evolution, Research Institute Senckenberg and J.W. Goethe University, Frankfurt am Main D-60325, Germany f Australian Tropical Herbarium, James Cook University, Cairns, QLD 4878, Australia g GenXPro, Frankfurt am Main 60438, Germany h Department of Biology, Rhodes College, Memphis, TN 38112, USA i Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom j Smithsonian Tropical Research Institute, Balboa, Ancon, Republic of Panama k Department of Botany, University of Wyoming, Laramie, WY 82071, USA l Department of Biology, Grand Valley State University, Allendale, MI 49401, USA m Marie Selby Botanical Gardens, Sarasota, FL 34236, USA n Gardens By The Bay, National Parks Board Headquarters, Singapore 259569, Singapore o Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA a r t i c l e i n f o a b s t r a c t Article history: Received 22 May 2013 Revised 18 September 2013 Accepted 11 October 2013 Available online 26 October 2013 Keywords: Biogeography Evolutionary predictions Epiphytes Key innovations Pollination syndromes Species richness We present an integrative model predicting associations among epiphytism, the tank habit, entangling seeds, C3 vs. CAM photosynthesis, avian pollinators, life in fertile, moist montane habitats, and net rates of species diversification in the monocot family Bromeliaceae....

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  • ...…or arid regions and microsites and speciate extensively there (Schimper, 1888; Mez, 1904; Pittendrigh, 1948; McWilliams, 1974; Benzing, 1980, 2000; Givnish et al., 1984, 1997, 2004, 2007, 2010, 2011; Benzing et al., 1985; Gentry and Dodson, 1987; Smith, 1989; Kessler and Krömer, 2000; Crayn…...

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Journal Article•DOI•
Phylogenetic insights into Andean plant diversification

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Federico Luebert1, Federico Luebert2, Maximilian Weigend1•
University of Bonn1, University of Chile2
19 Jun 2014-Frontiers in Ecology and Evolution
TL;DR: In this article, the authors compare available phylogenetic studies and divergence time estimates for plant lineages that may have diversified in response to Andean orogeny, and show that high-elevation lineages originated and diversified during or after the major phases of Andean uplift (mid-Miocene to Pliocene).
Abstract: Andean orogeny is considered as one of the most important events for the developmentof current plant diversity in South America. We compare available phylogenetic studies anddivergence time estimates for plant lineages that may have diversified in response to Andeanorogeny. The influence of the Andes on plant diversification is separated into four major groups:The Andes as source of new high-elevation habitats, as a vicariant barrier, as a North-Southcorridor and as generator of new environmental conditions outside the Andes. Biogeographicalrelationships between the Andes and other regions are also considered. Divergence timeestimates indicate that high-elevation lineages originated and diversified during or after the majorphases of Andean uplift (Mid-Miocene to Pliocene), although there are some exceptions. Asexpected, Andean mid-elevation lineages tend to be older than high-elevation groups. Mostclades with disjunct distribution on both sides of the Andes diverged during Andean uplift.Inner-Andean clades also tend to have divergence time during or after Andean uplift. This isinterpreted as evidence of vicariance. Dispersal along the Andes has been shown to occur ineither direction, mostly dated after the Andean uplift. Divergence time estimates of plant groupsoutside the Andes encompass a wider range of ages, indicating that the Andes may not benecessarily the cause of these diversifications. The Andes are biogeographically related to allneighbouring areas, especially Central America, with floristic interchanges in both directionssince Early Miocene times. Direct biogeographical relationships between the Andes and otherdisjunct regions have also been shown in phylogenetic studies, especially with the easternBrazilian highlands and North America. The history of the Andean flora is complex and plantdiversification has been driven by a variety of processes, including environmental change,adaptation, and biotic interactions

221 citations

Cites background from "Phylogeny, adaptive radiation, and ..."

  • ...The latter is the only dated dispersal scenario available (∼8 Ma; Givnish et al., 2011)....

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  • ...The crown node of the genus Poissonia (Fabaceae) was dated to the Early Miocene (∼ 20 Ma; Pennington et al., 2004; Särkinen et al., 2011)....

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  • ...However, divergence times for this group (∼40 Ma; Becerra et al., 2012) seem to predate Andean uplift....

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  • ...High-Andean species in the genus Lepechinia (Lamiaceae) form a clade of ca. 30 species that may have started their divergence during the Early Pliocene (∼3 Ma; Drew and Sytsma, 2013)....

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  • ...Lycopersicon (∼2 Ma; Särkinen et al., 2013), Vasconcellea (∼10 Ma; Antunes Carvalho and Renner, 2012), Alstroemeria (∼18 Ma; Chacón et al., 2012), Chaetanthera (∼10 Ma; Hershkovitz et al., Frontiers in Ecology and Evolution | Evolutionary and Population Genetics June 2014 | Volume 2 | Article 27 | 10 2006), Schizanthus (∼24 Ma; Särkinen et al., 2013)....

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References
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Journal Article•DOI•
Confidence limits on phylogenies: an approach using the bootstrap.

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Joseph Felsenstein1•
University of Washington1
01 Jul 1985-Evolution
TL;DR: The recently‐developed statistical method known as the “bootstrap” can be used to place confidence intervals on phylogenies and shows significant evidence for a group if it is defined by three or more characters.
Abstract: The recently-developed statistical method known as the "bootstrap" can be used to place confidence intervals on phylogenies. It involves resampling points from one's own data, with replacement, to create a series of bootstrap samples of the same size as the original data. Each of these is analyzed, and the variation among the resulting estimates taken to indicate the size of the error involved in making estimates from the original data. In the case of phylogenies, it is argued that the proper method of resampling is to keep all of the original species while sampling characters with replacement, under the assumption that the characters have been independently drawn by the systematist and have evolved independently. Majority-rule consensus trees can be used to construct a phylogeny showing all of the inferred monophyletic groups that occurred in a majority of the bootstrap samples. If a group shows up 95% of the time or more, the evidence for it is taken to be statistically significant. Existing computer programs can be used to analyze different bootstrap samples by using weights on the characters, the weight of a character being how many times it was drawn in bootstrap sampling. When all characters are perfectly compatible, as envisioned by Hennig, bootstrap sampling becomes unnecessary; the bootstrap method would show significant evidence for a group if it is defined by three or more characters.

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"Phylogeny, adaptive radiation, and ..." refers methods in this paper

  • ...We used bootstrap analysis ( Felsenstein, 1985 ) in the program PAUP* 4.0b10 ( Swofford, 2002 ) to assess the relative support for each node in the strict consensus, using 1000 random resamplings of the data and retaining 200 trees per iteration....

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Journal Article•DOI•
MrBayes 3: Bayesian phylogenetic inference under mixed models

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Fredrik Ronquist1, John P. Huelsenbeck•
Uppsala University1
12 Aug 2003-Bioinformatics
TL;DR: MrBayes 3 performs Bayesian phylogenetic analysis combining information from different data partitions or subsets evolving under different stochastic evolutionary models to analyze heterogeneous data sets and explore a wide variety of structured models mixing partition-unique and shared parameters.
Abstract: Summary: MrBayes 3 performs Bayesian phylogenetic analysis combining information from different data partitions or subsets evolving under different stochastic evolutionary models. This allows the user to analyze heterogeneous data sets consisting of different data types—e.g. morphological, nucleotide, and protein— and to explore a wide variety of structured models mixing partition-unique and shared parameters. The program employs MPI to parallelize Metropolis coupling on Macintosh or UNIX clusters.

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"Phylogeny, adaptive radiation, and ..." refers methods in this paper

  • ...Bayesian inference was performed in the program MrBayes 3.1 ( Ronquist and Huelsenbeck, 2003 ) allowing different models for each region....

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PAUP*: Phylogenetic analysis using parsimony (*and other methods), Version 4.0b10

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Dl Swofford, DL Swofford, D Swofford
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"Phylogeny, adaptive radiation, and ..." refers background or methods in this paper

  • ...Multiple species of Aechmea , Mezobromelia , Navia , Ochagavia , Tillandsia , and Vriesea were sampled due to concerns about the monophyly of those genera ( Crayn et al., 2004 ; Barfuss et al., 2005 ; Schulte et al., 2005 ; Sass and Specht, 2010 )....

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  • ...We used bootstrap analysis ( Felsenstein, 1985 ) in the program PAUP* 4.0b10 ( Swofford, 2002 ) to assess the relative support for each node in the strict consensus, using 1000 random resamplings of the data and retaining 200 trees per iteration....

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Journal Article•DOI•
A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood.

[...]

Stéphane Guindon1, Olivier Gascuel1•
Centre national de la recherche scientifique1
01 Oct 2003-Systematic Biology
TL;DR: This work has used extensive and realistic computer simulations to show that the topological accuracy of this new method is at least as high as that of the existing maximum-likelihood programs and much higher than the performance of distance-based and parsimony approaches.
Abstract: The increase in the number of large data sets and the complexity of current probabilistic sequence evolution models necessitates fast and reliable phylogeny reconstruction methods. We describe a new approach, based on the maximum- likelihood principle, which clearly satisfies these requirements. The core of this method is a simple hill-climbing algorithm that adjusts tree topology and branch lengths simultaneously. This algorithm starts from an initial tree built by a fast distance-based method and modifies this tree to improve its likelihood at each iteration. Due to this simultaneous adjustment of the topology and branch lengths, only a few iterations are sufficient to reach an optimum. We used extensive and realistic computer simulations to show that the topological accuracy of this new method is at least as high as that of the existing maximum-likelihood programs and much higher than the performance of distance-based and parsimony approaches. The reduction of computing time is dramatic in comparison with other maximum-likelihood packages, while the likelihood maximization ability tends to be higher. For example, only 12 min were required on a standard personal computer to analyze a data set consisting of 500 rbcL sequences with 1,428 base pairs from plant plastids, thus reaching a speed of the same order as some popular distance-based and parsimony algorithms. This new method is implemented in the PHYML program, which is freely available on our web page: http://www.lirmm.fr/w3ifa/MAAS/. (Algorithm; computer simulations; maximum likelihood; phylogeny; rbcL; RDPII project.) The size of homologous sequence data sets has in- creased dramatically in recent years, and many of these data sets now involve several hundreds of taxa. More- over, current probabilistic sequence evolution models (Swofford et al., 1996 ; Page and Holmes, 1998 ), notably those including rate variation among sites (Uzzell and Corbin, 1971 ; Jin and Nei, 1990 ; Yang, 1996 ), require an increasing number of calculations. Therefore, the speed of phylogeny reconstruction methods is becoming a sig- nificant requirement and good compromises between speed and accuracy must be found. The maximum likelihood (ML) approach is especially accurate for building molecular phylogenies. Felsenstein (1981) brought this framework to nucleotide-based phy- logenetic inference, and it was later also applied to amino acid sequences (Kishino et al., 1990). Several vari- ants were proposed, most notably the Bayesian meth- ods (Rannala and Yang 1996; and see below), and the discrete Fourier analysis of Hendy et al. (1994), for ex- ample. Numerous computer studies (Huelsenbeck and Hillis, 1993; Kuhner and Felsenstein, 1994; Huelsenbeck, 1995; Rosenberg and Kumar, 2001; Ranwez and Gascuel, 2002) have shown that ML programs can recover the cor- rect tree from simulated data sets more frequently than other methods can. Another important advantage of the ML approach is the ability to compare different trees and evolutionary models within a statistical framework (see Whelan et al., 2001, for a review). However, like all optimality criterion-based phylogenetic reconstruction approaches, ML is hampered by computational difficul- ties, making it impossible to obtain the optimal tree with certainty from even moderate data sets (Swofford et al., 1996). Therefore, all practical methods rely on heuristics that obtain near-optimal trees in reasonable computing time. Moreover, the computation problem is especially difficult with ML, because the tree likelihood not only depends on the tree topology but also on numerical pa- rameters, including branch lengths. Even computing the optimal values of these parameters on a single tree is not an easy task, particularly because of possible local optima (Chor et al., 2000). The usual heuristic method, implemented in the pop- ular PHYLIP (Felsenstein, 1993 ) and PAUP ∗ (Swofford, 1999 ) packages, is based on hill climbing. It combines stepwise insertion of taxa in a growing tree and topolog- ical rearrangement. For each possible insertion position and rearrangement, the branch lengths of the resulting tree are optimized and the tree likelihood is computed. When the rearrangement improves the current tree or when the position insertion is the best among all pos- sible positions, the corresponding tree becomes the new current tree. 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16,261 citations

"Phylogeny, adaptive radiation, and ..." refers methods in this paper

  • ...Maximum-likelihood analyses used the program jModelTest 0.1.1 ( Posada, 2008 ) based on the program Phyml ( Guindon and Gascuel, 2003 ) to select the appropriate model of nucleotide evolution using the Akaike information criterion (AIC) ( Posada and Buckley, 2004 )....

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Journal Article•DOI•
jModelTest: Phylogenetic Model Averaging

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David Posada1•
University of Vigo1
01 Jul 2008-Molecular Biology and Evolution
TL;DR: jModelTest is a new program for the statistical selection of models of nucleotide substitution based on "Phyml" that implements 5 different selection strategies, including "hierarchical and dynamical likelihood ratio tests," the "Akaike information criterion", the "Bayesian information criterion," and a "decision-theoretic performance-based" approach.
Abstract: jModelTest is a new program for the statistical selection of models of nucleotide substitution based on "Phyml" (Guindon and Gascuel 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 52:696-704.). It implements 5 different selection strategies, including "hierarchical and dynamical likelihood ratio tests," the "Akaike information criterion," the "Bayesian information criterion," and a "decision-theoretic performance-based" approach. This program also calculates the relative importance and model-averaged estimates of substitution parameters, including a model-averaged estimate of the phylogeny. jModelTest is written in Java and runs under Mac OSX, Windows, and Unix systems with a Java Runtime Environment installed. The program, including documentation, can be freely downloaded from the software section at http://darwin.uvigo.es.

9,748 citations

"Phylogeny, adaptive radiation, and ..." refers methods in this paper

  • ...Maximum-likelihood analyses used the program jModelTest 0.1.1 ( Posada, 2008 ) based on the program Phyml ( Guindon and Gascuel, 2003 ) to select the appropriate model of nucleotide evolution using the Akaike information criterion (AIC) ( Posada and Buckley, 2004 )....

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