1
|
Earth history events shaped the evolution of uneven biodiversity across tropical moist forests. Proc Natl Acad Sci U S A 2021; 118:2026347118. [PMID: 34599095 PMCID: PMC8501849 DOI: 10.1073/pnas.2026347118] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/28/2021] [Indexed: 02/07/2023] Open
Abstract
Tropical moist forests harbor much of the world’s biodiversity, but this diversity is not evenly distributed globally, with tropical moist forests in the Neotropics and Indomalaya generally exhibiting much greater diversity than in the Afrotropics. Here, we assess the ubiquity of this “pantropical diversity disparity” (PDD) using the present-day distributions of over 150,000 species of plants and animals, and we compare these distributions with a spatial model of diversification combined with reconstructions of plate tectonics, temperature, and aridity. Our study demonstrates that differences in paleoenvironmental dynamics between continents, including mountain building, aridification, and global temperature fluxes, can explain the PDD by shaping spatial and temporal patterns of species origination and extinction, providing a close match to observed distributions of plants and animals. Far from a uniform band, the biodiversity found across Earth’s tropical moist forests varies widely between the high diversity of the Neotropics and Indomalaya and the relatively lower diversity of the Afrotropics. Explanations for this variation across different regions, the “pantropical diversity disparity” (PDD), remain contentious, due to difficulty teasing apart the effects of contemporary climate and paleoenvironmental history. Here, we assess the ubiquity of the PDD in over 150,000 species of terrestrial plants and vertebrates and investigate the relationship between the present-day climate and patterns of species richness. We then investigate the consequences of paleoenvironmental dynamics on the emergence of biodiversity gradients using a spatially explicit model of diversification coupled with paleoenvironmental and plate tectonic reconstructions. Contemporary climate is insufficient in explaining the PDD; instead, a simple model of diversification and temperature niche evolution coupled with paleoaridity constraints is successful in reproducing the variation in species richness and phylogenetic diversity seen repeatedly among plant and animal taxa, suggesting a prevalent role of paleoenvironmental dynamics in combination with niche conservatism. The model indicates that high biodiversity in Neotropical and Indomalayan moist forests is driven by complex macroevolutionary dynamics associated with mountain uplift. In contrast, lower diversity in Afrotropical forests is associated with lower speciation rates and higher extinction rates driven by sustained aridification over the Cenozoic. Our analyses provide a mechanistic understanding of the emergence of uneven diversity in tropical moist forests across 110 Ma of Earth’s history, highlighting the importance of deep-time paleoenvironmental legacies in determining biodiversity patterns.
Collapse
|
2
|
Squaring within the Colless index yields a better balance index. Math Biosci 2020; 331:108503. [PMID: 33253745 DOI: 10.1016/j.mbs.2020.108503] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 10/28/2020] [Accepted: 10/28/2020] [Indexed: 11/24/2022]
Abstract
The Colless index for bifurcating phylogenetic trees, introduced by Colless (1982), is defined as the sum, over all internal nodes v of the tree, of the absolute value of the difference of the sizes of the clades defined by the children of v. It is one of the most popular phylogenetic balance indices, because, in addition to measuring the balance of a tree in a very simple and intuitive way, it turns out to be one of the most powerful and discriminating phylogenetic shape indices. But it has some drawbacks. On the one hand, although its minimum value is reached at the so-called maximally balanced trees, it is almost always reached also at trees that are not maximally balanced. On the other hand, its definition as a sum of absolute values of differences makes it difficult to study analytically its distribution under probabilistic models of bifurcating phylogenetic trees. In this paper we show that if we replace in its definition the absolute values of the differences of clade sizes by the squares of these differences, all these drawbacks are overcome and the resulting index is still more powerful and discriminating than the original Colless index.
Collapse
|
3
|
M Coronado T, Mir A, Rosselló F, Rotger L. On Sackin's original proposal: the variance of the leaves' depths as a phylogenetic balance index. BMC Bioinformatics 2020; 21:154. [PMID: 32326884 PMCID: PMC7181513 DOI: 10.1186/s12859-020-3405-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 02/11/2020] [Indexed: 12/21/2022] Open
Abstract
Background The Sackin indexS of a rooted phylogenetic tree, defined as the sum of its leaves’ depths, is one of the most popular balance indices in phylogenetics, and Sackin’s paper (Syst Zool 21:225–6, 1972) is usually cited as the source for this index. However, what Sackin actually proposed in his paper as a measure of the imbalance of a rooted tree was not the sum of its leaves’ depths, but their “variation”. This proposal was later implemented as the variance of the leaves’ depths by Kirkpatrick and Slatkin in (Evolution 47:1171–81, 1993), where they also posed the problem of finding a closed formula for its expected value under the Yule model. Nowadays, Sackin’s original proposal seems to have passed into oblivion in the phylogenetics literature, replaced by the index bearing his name, which, in fact, was introduced a decade later by Sokal. Results In this paper we study the properties of the variance of the leaves’ depths, V, as a balance index. Firstly, we prove that the rooted trees with n leaves and maximum V value are exactly the combs with n leaves. But although V achieves its minimum value on every space \documentclass[12pt]{minimal}
\usepackage{amsmath}
\usepackage{wasysym}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amsbsy}
\usepackage{mathrsfs}
\usepackage{upgreek}
\setlength{\oddsidemargin}{-69pt}
\begin{document}$\mathcal {BT}_{n}$\end{document}ℬTn of bifurcating rooted phylogenetic trees with n≤183 leaves at the so-called “maximally balanced trees” with n leaves, this property fails for almost every n≥184. We provide then an algorithm that finds the trees in \documentclass[12pt]{minimal}
\usepackage{amsmath}
\usepackage{wasysym}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amsbsy}
\usepackage{mathrsfs}
\usepackage{upgreek}
\setlength{\oddsidemargin}{-69pt}
\begin{document}$\mathcal {BT}_{n}$\end{document}ℬTn with minimum V value in time O(n log(n)). Secondly, we obtain closed formulas for the expected V value of a bifurcating rooted tree with any number n of leaves under the Yule and the uniform models and, as a by-product of the computations leading to these formulas, we also obtain closed formulas for the variance under the uniform model of the Sackin index and the total cophenetic index (Mir et al., Math Biosci 241:125–36, 2013) of a bifurcating rooted tree, as well as of their covariance, thus filling this gap in the literature. Conclusion The phylogenetics community has been wise in preferring the sum S(T) of the leaves’ depths of a phylogenetic tree T over their variance V(T) as a balance index, because the latter does not seem to capture correctly the notion of balance of large bifurcating rooted trees. But it is still a valid and useful shape index.
Collapse
Affiliation(s)
- Tomás M Coronado
- Department of Mathematics and Computer Science, University of the Balearic Islands, Palma, E-07122, Spain.,Balearic Islands Health Research Institute (IdISBa), Palma, E-07010, Spain
| | - Arnau Mir
- Department of Mathematics and Computer Science, University of the Balearic Islands, Palma, E-07122, Spain.,Balearic Islands Health Research Institute (IdISBa), Palma, E-07010, Spain
| | - Francesc Rosselló
- Department of Mathematics and Computer Science, University of the Balearic Islands, Palma, E-07122, Spain. .,Balearic Islands Health Research Institute (IdISBa), Palma, E-07010, Spain.
| | - Lucía Rotger
- Dept. of Mathematics and Computing, University of La Rioja, Logroño, E-26004, Spain
| |
Collapse
|
5
|
Rivero-Guerra AO. Diversidad y distribución de los endemismos de Asteraceae (Compositae) en la Flora del Ecuador. COLLECTANEA BOTANICA 2020. [DOI: 10.3989/collectbot.2020.v39.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
La familia Asteraceae está representada en la Flora de Ecuador por un total de 310 táxones endémicos. Están agrupadas en 4 subfamilias (Asteroideae, Barnadesioideae, Cichorioideae y Mutisioideae), 16 tribus y 89 géneros. Doscientas setenta y dos táxones (87,74%) restringen su hábitat a la región andina. Los niveles más altos de endemismos están asociados a los Andes, mayoritariamente desde el bosque andino alto hasta el páramo, y a las Islas Galápagos. Los géneros con mayor riqueza de endemismos son Mikania (26), Pentacalia (23), y Gynoxys (20). Tres géneros monotípicos son endémicos: Cyathomone, Idiopappus y Trigonopterum. Los géneros Darwiniothamnus, Kingianthus, Lecocarpus, y Scalesia también son endémicos. La diversidad de la familia se incrementa desde los 2000 m a 3000 m, alcanzando su mayor riqueza entre los 2900-3000 m, con dominancia de las plantas arbustivas (195 especies, 1 subespecie, 2 variedades) y herbáceas (97 especies). Ciento veinteseis especies tienen categoría de vulnerable, 90 están en peligro de extinción y 24 están en estado crítico de amenaza. Las temperaturas y precipitaciones medias anuales varían significativamente entre los sectores biogeográficos.
Collapse
|
6
|
Pontarp M, Bunnefeld L, Cabral JS, Etienne RS, Fritz SA, Gillespie R, Graham CH, Hagen O, Hartig F, Huang S, Jansson R, Maliet O, Münkemüller T, Pellissier L, Rangel TF, Storch D, Wiegand T, Hurlbert AH. The Latitudinal Diversity Gradient: Novel Understanding through Mechanistic Eco-evolutionary Models. Trends Ecol Evol 2018; 34:211-223. [PMID: 30591209 DOI: 10.1016/j.tree.2018.11.009] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 11/13/2018] [Accepted: 11/22/2018] [Indexed: 11/19/2022]
Abstract
The latitudinal diversity gradient (LDG) is one of the most widely studied patterns in ecology, yet no consensus has been reached about its underlying causes. We argue that the reasons for this are the verbal nature of existing hypotheses, the failure to mechanistically link interacting ecological and evolutionary processes to the LDG, and the fact that empirical patterns are often consistent with multiple explanations. To address this issue, we synthesize current LDG hypotheses, uncovering their eco-evolutionary mechanisms, hidden assumptions, and commonalities. Furthermore, we propose mechanistic eco-evolutionary modeling and an inferential approach that makes use of geographic, phylogenetic, and trait-based patterns to assess the relative importance of different processes for generating the LDG.
Collapse
Affiliation(s)
- Mikael Pontarp
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland.
| | - Lynsey Bunnefeld
- Biological & Environmental Sciences, University of Stirling, Stirling FK9 4LA, Scotland
| | - Juliano Sarmento Cabral
- Ecosystem Modeling, Center for Computational and Theoretical Biology (CCTB), University of Würzburg, Emil-Fischer-Str. 32, 97074 Würzburg, Germany
| | - Rampal S Etienne
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Box 11103, 9700 CC Groningen, The Netherlands
| | - Susanne A Fritz
- Senckenberg Biodiversity and Climate Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, D-60325 Frankfurt, Germany; Institute of Ecology, Evolution and Diversity, Goethe-University, D-60438 Frankfurt, Germany
| | - Rosemary Gillespie
- Environmental Science, 130 Mulford Hall, University of California, Berkeley, CA 94720, USA
| | | | - Oskar Hagen
- Swiss Federal Research Institute WSL, CH-8903 Birmensdorf, Switzerland; Landscape Ecology, Institute of Terrestrial Ecosystems, ETH Zürich, CH-8092 Zürich, Switzerland
| | - Florian Hartig
- Theoretical Ecology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Shan Huang
- Senckenberg Biodiversity Research Centre, Senckenberganlage 25, 60327, Frankfurt am Main, Germany
| | - Roland Jansson
- Department of Ecology and Environmental Science, Umeå University, 901 87 Umeå, Sweden
| | - Odile Maliet
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, 75005 Paris, France
| | - Tamara Münkemüller
- Univ. Grenoble Alpes, CNRS, Univ. Savoie Mont Blanc, CNRS, LECA, Laboratoire d'ÉcologieAlpine, F-38000 Grenoble, France
| | - Loïc Pellissier
- Swiss Federal Research Institute WSL, CH-8903 Birmensdorf, Switzerland; Landscape Ecology, Institute of Terrestrial Ecosystems, ETH Zürich, CH-8092 Zürich, Switzerland
| | - Thiago F Rangel
- Department of Ecology, Federal University of Goiás, Campus Samambaia, Goiânia GO, 74690-900, Brazil
| | - David Storch
- Center for Theoretical Study, Charles University and Czech Academy of Sciences, Jilská 1, 110 00 Praha 1, Czech Republic; Department of Ecology, Faculty of Science, Charles University, Viničná 7, 128 44 Praha 2, Czech Republic
| | - Thorsten Wiegand
- Department of Ecological Modeling, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318 Leipzig, Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Allen H Hurlbert
- Department of Biology and Curriculum in Environment and Ecology, University of North Carolina, Chapel Hill, NC 27599, USA
| |
Collapse
|