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Tian Q, Stull GW, Kellermann J, Medan D, Nge FJ, Liu SY, Kates HR, Soltis DE, Soltis PS, Guralnick RP, Folk RA, Onstein RE, Yi TS. Rapid in situ diversification rates in Rhamnaceae explain the parallel evolution of high diversity in temperate biomes from global to local scales. THE NEW PHYTOLOGIST 2024; 241:1851-1865. [PMID: 38229185 DOI: 10.1111/nph.19504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 11/20/2023] [Indexed: 01/18/2024]
Abstract
The macroevolutionary processes that have shaped biodiversity across the temperate realm remain poorly understood and may have resulted from evolutionary dynamics related to diversification rates, dispersal rates, and colonization times, closely coupled with Cenozoic climate change. We integrated phylogenomic, environmental ordination, and macroevolutionary analyses for the cosmopolitan angiosperm family Rhamnaceae to disentangle the evolutionary processes that have contributed to high species diversity within and across temperate biomes. Our results show independent colonization of environmentally similar but geographically separated temperate regions mainly during the Oligocene, consistent with the global expansion of temperate biomes. High global, regional, and local temperate diversity was the result of high in situ diversification rates, rather than high immigration rates or accumulation time, except for Southern China, which was colonized much earlier than the other regions. The relatively common lineage dispersals out of temperate hotspots highlight strong source-sink dynamics across the cosmopolitan distribution of Rhamnaceae. The proliferation of temperate environments since the Oligocene may have provided the ecological opportunity for rapid in situ diversification of Rhamnaceae across the temperate realm. Our study illustrates the importance of high in situ diversification rates for the establishment of modern temperate biomes and biodiversity hotspots across spatial scales.
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Affiliation(s)
- Qin Tian
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 101408, China
- Key Laboratory of Plant Diversity and Specialty Crops, Chinese Academy of Sciences, Beijing, 100093, China
- Naturalis Biodiversity Center, Darwinweg 2, 2333CR, Leiden, the Netherlands
| | - Gregory W Stull
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Jürgen Kellermann
- State Herbarium of South Australia, Botanic Gardens and State Herbarium, Hackney Road, Adelaide, SA, 5000, Australia
- School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Diego Medan
- Cátedra de Botánica General, Facultad de Agronomía, Universidad de Buenos Aires, Ave San Martín 4453, C1417DSE, Buenos Aires, Argentina
| | - Francis J Nge
- State Herbarium of South Australia, Botanic Gardens and State Herbarium, Hackney Road, Adelaide, SA, 5000, Australia
- School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia
- IRD - Institut de Recherche pour le Développement, Ave Agropolis BP 64501, Montpellier, 34394, France
| | - Shui-Yin Liu
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 101408, China
- Key Laboratory of Plant Diversity and Specialty Crops, Chinese Academy of Sciences, Beijing, 100093, China
| | - Heather R Kates
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Robert P Guralnick
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Ryan A Folk
- Department of Biological Sciences, Mississippi State University, Mississippi, MS, 39762, USA
| | - Renske E Onstein
- Naturalis Biodiversity Center, Darwinweg 2, 2333CR, Leiden, the Netherlands
- Evolution and Adaptation, German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, Leipzig, 04103, Germany
- Leipzig University, Leipzig, 04013, Germany
| | - Ting-Shuang Yi
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 101408, China
- Key Laboratory of Plant Diversity and Specialty Crops, Chinese Academy of Sciences, Beijing, 100093, China
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2
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Boucher FC, Quatela AS, Ellis AG, Verboom GA. Diversification rate vs. diversification density: Decoupled consequences of plant height for diversification of Alooideae in time and space. PLoS One 2020; 15:e0233597. [PMID: 32453786 PMCID: PMC7250425 DOI: 10.1371/journal.pone.0233597] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 05/10/2020] [Indexed: 01/20/2023] Open
Abstract
While biodiversity hotspots are typically identified on the basis of species number per unit area, their exceptional richness is often attributed, either implicitly or explicitly, to high diversification rates. High species concentrations, however, need not reflect rapid diversification, with the diversity of some hotspots accumulating at modest rates over long timespans. Here we explore the relationship between diversification in time vs. diversification in space and develop the concept of diversification density to describe the spatial scale of species accumulation in a clade. We investigate how plant height is associated with both aspects of diversification in Alooideae, a large plant subfamily with its center of diversity in the Greater Cape Floristic Region. We first reconstruct a time-calibrated phylogeny for Alooideae and demonstrate an evolutionary tendency towards reduced plant height. While plant height does not correlate with diversification rate across Alooideae it does so with diversification per unit space: clades of small plants tend to have the highest diversification densities. Furthermore, we find that diversification in time vs. space are uncorrelated. Our results show that diversification rate and density can be decoupled, and suggest that while some biodiversity hotspots might have been generated by high diversification rates, others are the product of high diversification density.
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Affiliation(s)
- Florian C Boucher
- Department of Botany and Zoology, University of Stellenbosch, Matieland, South Africa.,Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - Anne-Sophie Quatela
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
| | - Allan G Ellis
- Department of Botany and Zoology, University of Stellenbosch, Matieland, South Africa
| | - G Anthony Verboom
- Department of Biological Sciences, University of Cape Town, Rondebosch, South Africa
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3
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Harris LW, Davies TJ. A Complete Fossil-Calibrated Phylogeny of Seed Plant Families as a Tool for Comparative Analyses: Testing the 'Time for Speciation' Hypothesis. PLoS One 2016; 11:e0162907. [PMID: 27706173 PMCID: PMC5051821 DOI: 10.1371/journal.pone.0162907] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 08/30/2016] [Indexed: 01/17/2023] Open
Abstract
Explaining the uneven distribution of species richness across the branches of the tree of life has been a major challenge for evolutionary biologists. Advances in phylogenetic reconstruction, allowing the generation of large, well-sampled, phylogenetic trees have provided an opportunity to contrast competing hypotheses. Here, we present a new time-calibrated phylogeny of seed plant families using Bayesian methods and 26 fossil calibrations. While there are various published phylogenetic trees for plants which have a greater density of species sampling, we are still a long way from generating a complete phylogeny for all ~300,000+ plants. Our phylogeny samples all seed plant families and is a useful tool for comparative analyses. We use this new phylogenetic hypothesis to contrast two alternative explanations for differences in species richness among higher taxa: time for speciation versus ecological limits. We calculated net diversification rate for each clade in the phylogeny and assessed the relationship between clade age and species richness. We then fit models of speciation and extinction to individual branches in the tree to identify major rate-shifts. Our data suggest that the majority of lineages are diversifying very slowly while a few lineages, distributed throughout the tree, are diversifying rapidly. Diversification is unrelated to clade age, no matter the age range of the clades being examined, contrary to both the assumption of an unbounded lineage increase through time, and the paradigm of fixed ecological limits. These findings are consistent with the idea that ecology plays a role in diversification, but rather than imposing a fixed limit, it may have variable effects on per lineage diversification rates through time.
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Affiliation(s)
- Liam W. Harris
- Department of Biology, McGill University, 1205 Docteur-Penfield Avenue, Montreal, Quebec, Canada, H3A 1B1
| | - T. Jonathan Davies
- Department of Biology, McGill University, 1205 Docteur-Penfield Avenue, Montreal, Quebec, Canada, H3A 1B1
- African Centre for DNA Barcoding, University of Johannesburg, PO Box 524, Auckland Park, 2006, Johannesburg, South Africa
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4
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Daru BH, van der Bank M, Davies TJ. Spatial incongruence among hotspots and complementary areas of tree diversity in southern Africa. DIVERS DISTRIB 2014. [DOI: 10.1111/ddi.12290] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Affiliation(s)
- Barnabas H. Daru
- African Centre for DNA Barcoding; University of Johannesburg; APK Campus, PO Box 524 Auckland Park 2006 Johannesburg South Africa
| | - Michelle van der Bank
- African Centre for DNA Barcoding; University of Johannesburg; APK Campus, PO Box 524 Auckland Park 2006 Johannesburg South Africa
| | - T. Jonathan Davies
- African Centre for DNA Barcoding; University of Johannesburg; APK Campus, PO Box 524 Auckland Park 2006 Johannesburg South Africa
- Department of Biology; McGill University; 1205 Avenue Docteur Penfield Montreal QC Canada
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5
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Affiliation(s)
- Malin Strand
- Swedish Species Information Centre - Tjärnö; The Sven Lovéns Centre for Marine Sciences; SE 452 96 Strömstad Sweden
| | - Marina Panova
- Department of Biology and Environmental Sciences - Tjärnö; University of Gothenburg; SE 452 96 Strömstad Sweden
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Augusto L, Davies TJ, Delzon S, De Schrijver A. The enigma of the rise of angiosperms: can we untie the knot? Ecol Lett 2014; 17:1326-38. [PMID: 24975818 DOI: 10.1111/ele.12323] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 04/02/2014] [Accepted: 06/10/2014] [Indexed: 11/29/2022]
Abstract
Multiple hypotheses have been put forward to explain the rise of angiosperms to ecological dominance following the Cretaceous. A unified scheme incorporating all these theories appears to be an inextricable knot of relationships, processes and plant traits. Here, we revisit these hypotheses, categorising them within frameworks based on plant carbon economy, resistance to climatic stresses, nutrient economy, biotic interactions and diversification. We maintain that the enigma remains unresolved partly because our current state of knowledge is a result of the fragmentary nature of palaeodata. This lack of palaeodata limits our ability to draw firm conclusions. Nonetheless, based on consistent results, some inferences may be drawn. Our results indicate that a complex multidriver hypothesis may be more suitable than any single-driver theory. We contend that plant carbon economy and diversification may have played an important role during the early stages of gymnosperms replacement by angiosperms in fertile tropical sites. Plant tolerance to climatic stresses, plant nutrition, biotic interactions and diversification may have played a role in later stages of angiosperm expansion within temperate and harsh environments. The angiosperm knot remains partly tied, but to unravel it entirely will only be feasible if new discoveries are made by scientific communities.
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Affiliation(s)
- L Augusto
- INRA, Bordeaux Sciences Agro, UMR 1391 ISPA, Villenave d'Ornon, 33882, France
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7
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Davies TJ, Buckley LB. Phylogenetic diversity as a window into the evolutionary and biogeographic histories of present-day richness gradients for mammals. Philos Trans R Soc Lond B Biol Sci 2011; 366:2414-25. [PMID: 21768156 PMCID: PMC3130431 DOI: 10.1098/rstb.2011.0058] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Phylogenetic diversity (PD) captures the shared ancestry of species, and is increasingly being recognized as a valuable conservation currency. Regionally, PD frequently covaries closely with species richness; however, variation in speciation and extinction rates and/or the biogeographic history of lineages can result in significant deviation. Locally, these differences may be pronounced. Rapid recent speciation or high temporal turnover of lineages can result in low PD but high richness. In contrast, rare dispersal events, for example, between biomes, can elevate PD but have only small impact on richness. To date, environmental predictors of species richness have been well studied but global models explaining variation in PD are lacking. Here, we contrast the global distribution of PD versus species richness for terrestrial mammals. We show that an environmental model of lineage diversification can predict well the discrepancy in the distribution of these two variables in some places, for example, South America and Africa but not others, such as Southeast Asia. When we have information on multiple diversity indices, conservation efforts directed towards maximizing one currency or another (e.g. species richness versus PD) should also consider the underlying processes that have shaped their distributions.
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Affiliation(s)
- T Jonathan Davies
- Department of Biology, McGill University, Montreal, Quebec, Canada H3A 1B1.
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8
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Herrada A, Eguíluz VM, Hernández-García E, Duarte CM. Scaling properties of protein family phylogenies. BMC Evol Biol 2011; 11:155. [PMID: 21645345 PMCID: PMC3277297 DOI: 10.1186/1471-2148-11-155] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Accepted: 06/06/2011] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND One of the classical questions in evolutionary biology is how evolutionary processes are coupled at the gene and species level. With this motivation, we compare the topological properties (mainly the depth scaling, as a characterization of balance) of a large set of protein phylogenies with those of a set of species phylogenies. RESULTS The comparative analysis between protein and species phylogenies shows that both sets of phylogenies share a remarkably similar scaling behavior, suggesting the universality of branching rules and of the evolutionary processes that drive biological diversification from gene to species level. In order to explain such generality, we propose a simple model which allows us to estimate the proportion of evolvability/robustness needed to approximate the scaling behavior observed in the phylogenies, highlighting the relevance of the robustness of a biological system (species or protein) in the scaling properties of the phylogenetic trees. CONCLUSIONS The invariance of the scaling properties at levels spanning from genes to species suggests that rules that govern the incapability of a biological system to diversify are equally relevant both at the gene and at the species level.
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Affiliation(s)
- Alejandro Herrada
- Instituto de Física Interdisciplinar y Sistemas Complejos, IFISC (CSIC-UIB), Campus Universitat de les Illes Balears, E-07122 Palma de Mallorca, Spain
| | - Víctor M Eguíluz
- Instituto de Física Interdisciplinar y Sistemas Complejos, IFISC (CSIC-UIB), Campus Universitat de les Illes Balears, E-07122 Palma de Mallorca, Spain
| | - Emilio Hernández-García
- Instituto de Física Interdisciplinar y Sistemas Complejos, IFISC (CSIC-UIB), Campus Universitat de les Illes Balears, E-07122 Palma de Mallorca, Spain
| | - Carlos M Duarte
- Instituto Mediterráneo de Estudios Avanzados, IMEDEA (CSIC-UIB), C/Miquel Marqués 21, E-07190 Esporles, Spain
- Oceans Institute, University of Western Australia, 35 Stirling Highway, Crawley 6009, Australia
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9
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Davies TJ, Smith GF, Bellstedt DU, Boatwright JS, Bytebier B, Cowling RM, Forest F, Harmon LJ, Muasya AM, Schrire BD, Steenkamp Y, van der Bank M, Savolainen V. Extinction risk and diversification are linked in a plant biodiversity hotspot. PLoS Biol 2011; 9:e1000620. [PMID: 21629678 PMCID: PMC3101198 DOI: 10.1371/journal.pbio.1000620] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2010] [Accepted: 04/14/2011] [Indexed: 11/18/2022] Open
Abstract
It is widely recognized that we are entering an extinction event on a scale approaching the mass extinctions seen in the fossil record. Present-day rates of extinction are estimated to be several orders of magnitude greater than background rates and are projected to increase further if current trends continue. In vertebrates, species traits, such as body size, fecundity, and geographic range, are important predictors of vulnerability. Although plants are the basis for life on Earth, our knowledge of plant extinctions and vulnerabilities is lagging. Here, we disentangle the underlying drivers of extinction risk in plants, focusing on the Cape of South Africa, a global biodiversity hotspot. By comparing Red List data for the British and South African floras, we demonstrate that the taxonomic distribution of extinction risk differs significantly between regions, inconsistent with a simple, trait-based model of extinction. Using a comprehensive phylogenetic tree for the Cape, we reveal a phylogenetic signal in the distribution of plant extinction risks but show that the most threatened species cluster within short branches at the tips of the phylogeny--opposite to trends in mammals. From analyzing the distribution of threatened species across 11 exemplar clades, we suggest that mode of speciation best explains the unusual phylogenetic structure of extinction risks in plants of the Cape. Our results demonstrate that explanations for elevated extinction risk in plants of the Cape flora differ dramatically from those recognized for vertebrates. In the Cape, extinction risk is higher for young and fast-evolving plant lineages and cannot be explained by correlations with simple biological traits. Critically, we find that the most vulnerable plant species are nonetheless marching towards extinction at a more rapid pace but, surprisingly, independently from anthropogenic effects. Our results have important implications for conservation priorities and cast doubts on the utility of current Red List criteria for plants in regions such as the Cape, where speciation has been rapid, if our aim is to maximize the preservation of the tree-of-life.
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Affiliation(s)
- T Jonathan Davies
- National Center for Ecological Analysis and Synthesis, University of California, Santa Barbara, California, United States of America.
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10
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Schnitzler J, Barraclough TG, Boatwright JS, Goldblatt P, Manning JC, Powell MP, Rebelo T, Savolainen V. Causes of Plant Diversification in the Cape Biodiversity Hotspot of South Africa. Syst Biol 2011; 60:343-57. [DOI: 10.1093/sysbio/syr006] [Citation(s) in RCA: 163] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Jan Schnitzler
- Division of Biology, Imperial College London, Silwood Park Campus, Ascot, Berkshire SL5 7PY, UK
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK
| | - Timothy G. Barraclough
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK
- Division of Biology and NERC Centre for Population Biology, Imperial College London, Silwood Park Campus, Ascot, Berkshire SL5 7PY, UK
| | - James S. Boatwright
- South African National Biodiversity Institute, Kirstenbosch, Private Bag X7, Claremont 7735, Cape Town, South Africa
- Department of Botany and Plant Biotechnology, University of Johannesburg, P.O. Box 524, Auckland Park, Johannesburg, South Africa
| | - Peter Goldblatt
- Missouri Botanical Garden, PO Box 299, St Louis, MO 63166-0299, USA
| | - John C. Manning
- South African National Biodiversity Institute, Kirstenbosch, Private Bag X7, Claremont 7735, Cape Town, South Africa
| | - Martyn P. Powell
- Division of Biology, Imperial College London, Silwood Park Campus, Ascot, Berkshire SL5 7PY, UK
| | - Tony Rebelo
- South African National Biodiversity Institute, Kirstenbosch, Private Bag X7, Claremont 7735, Cape Town, South Africa
| | - Vincent Savolainen
- Division of Biology, Imperial College London, Silwood Park Campus, Ascot, Berkshire SL5 7PY, UK
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK
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11
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Affiliation(s)
- Daniel L. Rabosky
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, 4161 Valley Life Sciences Building, Berkeley, CA 94720, USA
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12
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Barraclough TG. Evolving entities: towards a unified framework for understanding diversity at the species and higher levels. Philos Trans R Soc Lond B Biol Sci 2010; 365:1801-13. [PMID: 20439282 PMCID: PMC2871889 DOI: 10.1098/rstb.2009.0276] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Current approaches to studying the evolution of biodiversity differ in their treatment of species and higher level diversity patterns. Species are regarded as the fundamental evolutionarily significant units of biodiversity, both in theory and in practice, and extensive theory explains how they originate and evolve. However, most species are still delimited using qualitative methods that only relate indirectly to the underlying theory. In contrast, higher level patterns of diversity have been subjected to rigorous quantitative study (using phylogenetics), but theory that adequately explains the observed patterns has been lacking. Most evolutionary analyses of higher level diversity patterns have considered non-equilibrium explanations based on rates of diversification (i.e. exponentially growing clades), rather than equilibrium explanations normally used at the species level and below (i.e. constant population sizes). This paper argues that species level and higher level patterns of diversity can be considered within a common framework, based on equilibrium explanations. It shows how forces normally considered in the context of speciation, namely divergent selection and geographical isolation, can generate evolutionarily significant units of diversity above the level of reproductively isolated species. Prospects for the framework to answer some unresolved questions about higher level diversity patterns are discussed.
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Affiliation(s)
- Timothy G Barraclough
- Division of Biology and NERC Centre for Population Biology, Imperial College London, Silwood Park Campus, Ascot, Berkshire SL5 7PY, UK.
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13
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Valente LM, Reeves G, Schnitzler J, Mason IP, Fay MF, Rebelo TG, Chase MW, Barraclough TG. DIVERSIFICATION OF THE AFRICAN GENUSPROTEA(PROTEACEAE) IN THE CAPE BIODIVERSITY HOTSPOT AND BEYOND: EQUAL RATES IN DIFFERENT BIOMES. Evolution 2010; 64:745-60. [DOI: 10.1111/j.1558-5646.2009.00856.x] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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14
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Rabosky DL, McCune AR. Reinventing species selection with molecular phylogenies. Trends Ecol Evol 2009; 25:68-74. [PMID: 19740566 DOI: 10.1016/j.tree.2009.07.002] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2009] [Revised: 07/08/2009] [Accepted: 07/08/2009] [Indexed: 11/26/2022]
Abstract
Species selection as a potential driver of macroevolutionary trends has been relegated to a largely philosophical position in modern evolutionary biology. Fundamentally, species selection is the outcome of heritable differences in speciation and extinction rates among lineages when the causal basis of those rate differences can be decoupled from genotypic (within-population) fitnesses. Here, we discuss the rapidly growing literature on variation in species diversification rates as inferred from molecular phylogenies. We argue that modern studies of diversification rates demonstrate that species selection is an important process influencing both the evolution of biological diversity and distributions of phenotypic traits within higher taxa. Explicit recognition of multi-level selection refocuses our attention on the mechanisms by which traits influence speciation and extinction rates.
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Affiliation(s)
- Daniel L Rabosky
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA.
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15
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Rabosky DL. Ecological limits and diversification rate: alternative paradigms to explain the variation in species richness among clades and regions. Ecol Lett 2009; 12:735-43. [DOI: 10.1111/j.1461-0248.2009.01333.x] [Citation(s) in RCA: 367] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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16
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17
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Explaining the uniqueness of the Cape flora: Incorporating geomorphic evolution as a factor for explaining its diversification. Mol Phylogenet Evol 2009; 51:64-74. [DOI: 10.1016/j.ympev.2008.05.034] [Citation(s) in RCA: 150] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2007] [Revised: 04/06/2008] [Accepted: 05/22/2008] [Indexed: 11/17/2022]
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18
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HEADS MICHAEL. Globally basal centres of endemism: the Tasman-Coral Sea region (south-west Pacific), Latin America and Madagascar/South Africa. Biol J Linn Soc Lond 2008. [DOI: 10.1111/j.1095-8312.2008.01118.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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19
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Rabosky DL, Donnellan SC, Talaba AL, Lovette IJ. Exceptional among-lineage variation in diversification rates during the radiation of Australia's most diverse vertebrate clade. Proc Biol Sci 2008; 274:2915-23. [PMID: 17878143 PMCID: PMC2291154 DOI: 10.1098/rspb.2007.0924] [Citation(s) in RCA: 188] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The disparity in species richness among groups of organisms is one of the most pervasive features of life on earth. A number of studies have addressed this pattern across higher taxa (e.g. 'beetles'), but we know much less about the generality and causal basis of the variation in diversity within evolutionary radiations at lower taxonomic scales. Here, we address the causes of variation in species richness among major lineages of Australia's most diverse vertebrate radiation, a clade of at least 232 species of scincid lizards. We use new mitochondrial and nuclear intron DNA sequences to test the extent of diversification rate variation in this group. We present an improved likelihood-based method for estimating per-lineage diversification rates from combined phylogenetic and taxonomic (species richness) data, and use the method in a hypothesis-testing framework to localize diversification rate shifts on phylogenetic trees. We soundly reject homogeneity of diversification rates among members of this radiation, and find evidence for a dramatic rate increase in the common ancestor of the genera Ctenotus and Lerista. Our results suggest that the evolution of traits associated with climate tolerance may have had a role in shaping patterns of diversity in this group.
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Affiliation(s)
- Daniel L Rabosky
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853-2701, USA.
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20
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Day JJ, Cotton JA, Barraclough TG. Tempo and mode of diversification of lake Tanganyika cichlid fishes. PLoS One 2008; 3:e1730. [PMID: 18320049 PMCID: PMC2248707 DOI: 10.1371/journal.pone.0001730] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2007] [Accepted: 02/05/2008] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Understanding the causes of disparities in species diversity across taxonomic groups and regions is a fundamental aim in evolutionary biology. Addressing these questions is difficult because of the need for densely sampled phylogenies and suitable empirical systems. METHODOLOGY/PRINCIPAL FINDINGS Here we investigate the cichlid fish radiation of Lake Tanganyika and show that per lineage diversification rates have been more than six times slower than in the species flocks of Lakes Victoria and Malawi. The result holds even at peak periods of diversification in Lake Tanganyika, ruling out the age of the lake as an explanation for slow average rates, and is robust to uncertainties over the calibration of cichlid radiations in geological time. Moreover, Lake Tanganyika lineages, irrespective of different biological characteristics (e.g. sexually dichromatic versus sexually monochromatic clades), have diversified at similar rates, falling within typical estimates across a range of plant and animal clades. For example, the mostly sexually dichromatic haplochromines, which have speciated explosively in Lakes Victoria and Malawi, have displayed modest rates in Lake Tanganyika (where they are called Tropheini). CONCLUSION/SIGNIFICANCE Our results show that either the Lake Tanganyika environment is less conducive for cichlid speciation or the remarkable diversifying abilities of the haplochromines were inhibited by the prior occupancy of older radiations. Although the results indicate a dominant role for the environment in shaping cichlid diversification, differences in the timing of diversification among the Tanganyikan tribes indicate that biological differences were still important for the dynamics of species build-up in the lake. While we cannot resolve the timing of the radiation relative to the origin of the lake, because of the lack of robust geological date calibrations for cichlids, our results are consistent with a scenario that the different clades reflect independent adaptive radiations into different broad niches in the lake.
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Affiliation(s)
- Julia J Day
- Department of Biology, University College London, London, United Kingdom.
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Jansson R, Davies TJ. Global variation in diversification rates of flowering plants: energy vs. climate change. Ecol Lett 2007; 11:173-83. [DOI: 10.1111/j.1461-0248.2007.01138.x] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Qian H, White PS, Song JS. EFFECTS OF REGIONAL VS. ECOLOGICAL FACTORS ON PLANT SPECIES RICHNESS: AN INTERCONTINENTAL ANALYSIS. Ecology 2007; 88:1440-53. [PMID: 17601137 DOI: 10.1890/06-0916] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Conclusions from past studies on the roles that historical and regional factors and contemporary and ecological factors have played in regulating large-scale patterns of species richness have been controversial. Conflicting past results were likely affected by differences in the range of environments analyzed and the scales of observation. Eastern North America and eastern Asia are ideal regions for examining the relative effects of historical and regional factors and contemporary and ecological factors on large-scale patterns of plant species richness because these two regions are closely matched in terms of climate and because their floras originated from the same paleoflora but have experienced different histories of development since the late Paleogene when climate cooling caused their separation. We report on a comprehensive data set of 471 floras ranging from 10 km2 to 4.7 x 10(6) km2 and spanning a wide range of climate and latitude (from 21 degrees to 55 degrees N) to examine whether the contribution of region relative to climate persists from small to large floras and increases from cooler to warmer climates. We found that eastern Asia is richer than eastern North America when sample area, maximum elevation, and climate are accounted for, that this difference diminishes toward higher latitudes, and that elevation plays a much stronger role in eastern Asia than in eastern North America. Our analysis reconciles contemporary/ecological and historical/regional explanations for species richness variation and helps explain why different conclusions have been reached by different authors working in the same geographical areas: the strength of the region effect itself varies with location and range of climatic conditions of the observations.
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Affiliation(s)
- Hong Qian
- Research and Collections Center, Illinois State Museum, 1011 East Ash Street, Springfield, Illinois 62703, USA.
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Heard SB, Cox GH. The Shapes of Phylogenetic Trees of Clades, Faunas, and Local Assemblages: Exploring Spatial Pattern in Differential Diversification. Am Nat 2007; 169:E107-18. [PMID: 17427125 DOI: 10.1086/512690] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2006] [Accepted: 12/13/2006] [Indexed: 11/03/2022]
Abstract
Life on Earth is characterized by strong diversity skewness: related lineages typically show pronounced variation in diversification success, and clades contain hyperdiverse and depauperate subclades. Previous studies have documented diversity skewness only for entire (global) clades. We demonstrate methods for measurement and significance testing of diversity skewness of local assemblages and regional biotas; we illustrate this with an analysis of geographic structure in diversity skewness of primate assemblages. For primates, continental faunas differ in diversity skewness from expectations based on the global phylogeny: South American faunas have significantly low skewness and African faunas have significantly high skewness. However, no local assemblage has diversity skewness different from that expected based on sampling the continental fauna. We also document a latitudinal gradient in diversity skewness for the African assemblages and test for (but do not find) associations of skewness with longitude, local species richness, and net primary productivity. Our data suggest that continental-scale biogeographic events rather than local-scale processes have shaped diversity skewness in modern primate faunas.
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Affiliation(s)
- Stephen B Heard
- Department of Biology, University of New Brunswick, Fredericton, New Brunswick E3B 6E1, Canada.
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Smith SA, de Oca ANM, Reeder TW, Wiens JJ. A PHYLOGENETIC PERSPECTIVE ON ELEVATIONAL SPECIES RICHNESS PATTERNS IN MIDDLE AMERICAN TREEFROGS: WHY SO FEW SPECIES IN LOWLAND TROPICAL RAINFORESTS? Evolution 2007; 61:1188-207. [PMID: 17492971 DOI: 10.1111/j.1558-5646.2007.00085.x] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Differences in species richness at different elevations are widespread and important for conservation, but the causes of these patterns remain poorly understood. Here, we use a phylogenetic perspective to address the evolutionary and biogeographic processes that underlie elevational diversity patterns within a region. We focus on a diverse but well-studied fauna of tropical amphibians, the hylid frogs of Middle America. Middle American treefrogs show a "hump-shaped" pattern of species richness (common in many organisms and regions), with the highest regional diversity at intermediate elevations. We reconstructed phylogenetic relationships among 138 species by combining new and published sequence data from 10 genes and then used this phylogeny to infer evolutionary rates and patterns. The high species richness of intermediate elevations seems to result from two factors. First, a tendency for montane clades to have higher rates of diversification. Second, the early colonization of montane regions, leaving less time for speciation to build up species richness in lowland regions (including tropical rainforests) that have been colonized more recently. This "time-for-speciation" effect may explain many diversity patterns and has important implications for conservation. The results also imply that local-scale environmental factors alone may be insufficient to explain the high species richness of lowland tropical rainforests, and that diversification rates are lower in earth's most species-rich biome.
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Affiliation(s)
- Sarah A Smith
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York 11794-5245, USA.
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Clarke A, Gaston KJ. Climate, energy and diversity. Proc Biol Sci 2006; 273:2257-66. [PMID: 16928626 PMCID: PMC1636092 DOI: 10.1098/rspb.2006.3545] [Citation(s) in RCA: 163] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2005] [Accepted: 03/08/2006] [Indexed: 11/12/2022] Open
Abstract
In recent years, a number of species-energy hypotheses have been developed to explain global patterns in plant and animal diversity. These hypotheses frequently fail to distinguish between fundamentally different forms of energy which influence diversity in dissimilar ways. Photosynthetically active radiation (PAR) can be utilized only by plants, though their abundance and growth rate is also greatly influenced by water. The Gibbs free energy (chemical energy) retained in the reduced organic compounds of tissue can be utilized by all heterotrophic organisms. Neither PAR nor chemical energy influences diversity directly. Both, however, influence biomass and/or abundance; diversity may then increase as a result of secondary population dynamic or evolutionary processes. Temperature is not a form of energy, though it is often used loosely by ecologists as a proxy for energy; it does, however, influence the rate of utilization of chemical energy by organisms. It may also influence diversity by allowing a greater range of energetic lifestyles at warmer temperatures (the metabolic niche hypothesis). We conclude that there is no single species/energy mechanism; fundamentally different processes link energy to abundance in plants and animals, and diversity is affected secondarily. If we are to make progress in elucidating these mechanisms, it is important to distinguish climatic effects on species' distribution and abundance from processes linking energy supply to plant and animal diversity.
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Affiliation(s)
- Andrew Clarke
- Biological Sciences, British Antarctic Survey, NERC, Cambridge, UK.
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Vamosi JC, Knight TM, Steets JA, Mazer SJ, Burd M, Ashman TL. Pollination decays in biodiversity hotspots. Proc Natl Acad Sci U S A 2006; 103:956-61. [PMID: 16418284 PMCID: PMC1347978 DOI: 10.1073/pnas.0507165103] [Citation(s) in RCA: 135] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2005] [Indexed: 11/18/2022] Open
Abstract
As pollinators decline globally, competition for their services is expected to intensify, and this antagonism may be most severe where the number of plant species is the greatest. Using meta-analysis and comparative phylogenetic analysis, we provide a global-scale test of whether reproduction becomes more limited by pollen receipt (pollen limitation) as the number of coexisting plant species increases. As predicted, we find a significant positive relationship between pollen limitation and species richness. In addition, this pattern is particularly strong for species that are obligately outcrossing and for trees relative to herbs or shrubs. We suggest that plants occurring in species-rich communities may be more prone to pollen limitation because of interspecific competition for pollinators. As a consequence, plants in biodiversity hotspots may have a higher risk of extinction and/or experience increased selection pressure to specialize on certain pollinators or diversify into different phenological niches. The combination of higher pollen limitation and habitat destruction represents a dual risk to tropical plant species that has not been previously identified.
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Affiliation(s)
- Jana C Vamosi
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB, Canada T2N 1N4.
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Linder HP. Evolution of diversity: the Cape flora. TRENDS IN PLANT SCIENCE 2005; 10:536-41. [PMID: 16213780 DOI: 10.1016/j.tplants.2005.09.006] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2005] [Revised: 08/09/2005] [Accepted: 09/22/2005] [Indexed: 05/04/2023]
Abstract
Although the environmental correlates of plant species richness have long received attention, research into the genesis of this diversity is in its infancy. The recent development of molecular dating methods and the inference of robust phylogenetic hypotheses have made it possible to investigate this problem. I use the Cape flora as a model to show that much modern diversity could be the result of recruiting diverse lineages over the entire Cenozoic into this flora, followed by in situ diversification (thus increasing species richness) of at least some of these lineages over a long period in an environmentally heterogeneous area.
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Affiliation(s)
- H Peter Linder
- Institute for Systematic Botany, University of Zurich, Zollikerstrasse 107, Zurich CH-8008, Switzerland.
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