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Boussange V, Pellissier L. Eco-evolutionary model on spatial graphs reveals how habitat structure affects phenotypic differentiation. Commun Biol 2022; 5:668. [PMID: 35794362 PMCID: PMC9259634 DOI: 10.1038/s42003-022-03595-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 06/16/2022] [Indexed: 11/20/2022] Open
Abstract
Differentiation mechanisms are influenced by the properties of the landscape over which individuals interact, disperse and evolve. Here, we investigate how habitat connectivity and habitat heterogeneity affect phenotypic differentiation by formulating a stochastic eco-evolutionary model where individuals are structured over a spatial graph. We combine analytical insights into the eco-evolutionary dynamics with numerical simulations to understand how the graph topology and the spatial distribution of habitat types affect differentiation. We show that not only low connectivity but also heterogeneity in connectivity promotes neutral differentiation, due to increased competition in highly connected vertices. Habitat assortativity, a measure of habitat spatial auto-correlation in graphs, additionally drives differentiation under habitat-dependent selection. While assortative graphs systematically amplify adaptive differentiation, they can foster or depress neutral differentiation depending on the migration regime. By formalising the eco-evolutionary and spatial dynamics of biological populations on graphs, our study establishes fundamental links between landscape features and phenotypic differentiation.
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Affiliation(s)
- Victor Boussange
- Swiss Federal Research Institute WSL, CH-8903, Birmensdorf, Switzerland.
- Landscape Ecology, Institute of Terrestrial Ecosystems, Department of Environmental Systems Science, ETH Zürich, CH-8092, Zürich, Switzerland.
| | - Loïc Pellissier
- Swiss Federal Research Institute WSL, CH-8903, Birmensdorf, Switzerland.
- Landscape Ecology, Institute of Terrestrial Ecosystems, Department of Environmental Systems Science, ETH Zürich, CH-8092, Zürich, Switzerland.
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2
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Smyčka J, Roquet C, Boleda M, Alberti A, Boyer F, Douzet R, Perrier C, Rome M, Valay JG, Denoeud F, Šemberová K, Zimmermann NE, Thuiller W, Wincker P, Alsos IG, Coissac E, Lavergne S. Tempo and drivers of plant diversification in the European mountain system. Nat Commun 2022; 13:2750. [PMID: 35585056 PMCID: PMC9117672 DOI: 10.1038/s41467-022-30394-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 04/26/2022] [Indexed: 12/03/2022] Open
Abstract
There is still limited consensus on the evolutionary history of species-rich temperate alpine floras due to a lack of comparable and high-quality phylogenetic data covering multiple plant lineages. Here we reconstructed when and how European alpine plant lineages diversified, i.e., the tempo and drivers of speciation events. We performed full-plastome phylogenomics and used multi-clade comparative models applied to six representative angiosperm lineages that have diversified in European mountains (212 sampled species, 251 ingroup species total). Diversification rates remained surprisingly steady for most clades, even during the Pleistocene, with speciation events being mostly driven by geographic divergence and bedrock shifts. Interestingly, we inferred asymmetrical historical migration rates from siliceous to calcareous bedrocks, and from higher to lower elevations, likely due to repeated shrinkage and expansion of high elevation habitats during the Pleistocene. This may have buffered climate-related extinctions, but prevented speciation along elevation gradients as often documented for tropical alpine floras. Here, the authors use full-plastome phylogenomics and multiclade comparative models to reconstruct the tempo and drivers of six European Alpine angiosperm lineages before and during the Pleistocene. They find that geographic divergence and bedrock shifts drive speciation events, while diversification rates remained steady.
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Affiliation(s)
- Jan Smyčka
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, FR-38000, Grenoble, France. .,Center for Theoretical Study, Charles University and the Academy of Sciences of the Czech Republic, CZ-11000, Prague, Czech Republic. .,Department of Botany, Faculty of Science, Charles University, CZ-12801, Prague, Czech Republic.
| | - Cristina Roquet
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, FR-38000, Grenoble, France.,Systematics and Evolution of Vascular Plants (UAB) - Associated Unit to CSIC, Departament de Biologia Animal, Biologia Vegetal i Ecologia, Facultat de Biociències, Universitat Autònoma de Barcelona, ES-08193, Bellaterra, Spain
| | - Martí Boleda
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, FR-38000, Grenoble, France
| | - Adriana Alberti
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, FR-91057, Evry, France.,Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), FR-91190, Gif-sur-Yvette, France
| | - Frédéric Boyer
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, FR-38000, Grenoble, France
| | - Rolland Douzet
- CNRS, Lautaret, Jardin du Lautaret, Université Grenoble Alpes, FR-38000, Grenoble, France
| | - Christophe Perrier
- CNRS, Lautaret, Jardin du Lautaret, Université Grenoble Alpes, FR-38000, Grenoble, France
| | - Maxime Rome
- CNRS, Lautaret, Jardin du Lautaret, Université Grenoble Alpes, FR-38000, Grenoble, France
| | - Jean-Gabriel Valay
- CNRS, Lautaret, Jardin du Lautaret, Université Grenoble Alpes, FR-38000, Grenoble, France
| | - France Denoeud
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, FR-91057, Evry, France
| | - Kristýna Šemberová
- Department of Botany, Faculty of Science, Charles University, CZ-12801, Prague, Czech Republic.,Czech Academy of Sciences, Institute of Botany, CZ-25243, Průhonice, Czech Republic
| | | | - Wilfried Thuiller
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, FR-38000, Grenoble, France
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, FR-91057, Evry, France
| | - Inger G Alsos
- UiT - The Arctic University of Norway, The Arctic University Museum of Norway, N-9037, Tromsø, Norway
| | - Eric Coissac
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, FR-38000, Grenoble, France
| | | | - Sébastien Lavergne
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, FR-38000, Grenoble, France
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3
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Fielding AP, Pantel JH. Eco-Evolutionary Feedbacks and the Maintenance of Metacommunity Diversity in a Changing Environment. Genes (Basel) 2020; 11:E1433. [PMID: 33260620 PMCID: PMC7761218 DOI: 10.3390/genes11121433] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 11/23/2020] [Accepted: 11/26/2020] [Indexed: 11/16/2022] Open
Abstract
The presence and strength of resource competition can influence how organisms adaptively respond to environmental change. Selection may thus reflect a balance between two forces, adaptation to an environmental optimum and evolution to avoid strong competition. While this phenomenon has previously been explored in the context of single communities, its implications for eco-evolutionary dynamics at the metacommunity scale are largely unknown. We developed a simulation model for the evolution of a quantitative trait that influences both an organism's carrying capacity and its intra- and interspecific competitive ability. In the model, multiple species inhabit a three-patch landscape, and we investigated the effect of varying the connectivity level among patches, the presence and pace of directional environmental change, and the strength of competition between the species. Our model produced some patterns previously observed in evolving metacommunity models, such as species sorting and community monopolization. However, we found that species sorting was diminished even at low rates of dispersal and was influenced by competition strength, and that monopolization was observed only when environmental change was very rapid. We also detected an eco-evolutionary feedback loop between local phenotypic evolution at one site and competition at another site, which maintains species diversity in some conditions. The existence of a feedback loop maintained by dispersal indicates that eco-evolutionary dynamics in communities operate at a landscape scale.
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Affiliation(s)
- Aidan P. Fielding
- Department of Biology, The College of William and Mary, P.O. Box 8795, Williamsburg, VA 23187-8795, USA;
| | - Jelena H. Pantel
- Department of Biology, The College of William and Mary, P.O. Box 8795, Williamsburg, VA 23187-8795, USA;
- Department of Computer Science, Mathematics, and Environmental Science, The American University of Paris, 6 rue du Colonel Combes, 75007 Paris, France
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4
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Naciri Y, Linder HP. The genetics of evolutionary radiations. Biol Rev Camb Philos Soc 2020; 95:1055-1072. [PMID: 32233014 DOI: 10.1111/brv.12598] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 03/12/2020] [Accepted: 03/17/2020] [Indexed: 02/06/2023]
Abstract
With the realization that much of the biological diversity on Earth has been generated by discrete evolutionary radiations, there has been a rapid increase in research into the biotic (key innovations) and abiotic (key environments) circumstances in which such radiations took place. Here we focus on the potential importance of population genetic structure and trait genetic architecture in explaining radiations. We propose a verbal model describing the stages of an evolutionary radiation: first invading a suitable adaptive zone and expanding both spatially and ecologically through this zone; secondly, diverging genetically into numerous distinct populations; and, finally, speciating. There are numerous examples of the first stage; the difficulty, however, is explaining how genetic diversification can take place from the establishment of a, presumably, genetically depauperate population in a new adaptive zone. We explore the potential roles of epigenetics and transposable elements (TEs), of neutral process such as genetic drift in combination with trait genetic architecture, of gene flow limitation through isolation by distance (IBD), isolation by ecology and isolation by colonization, the possible role of intra-specific competition, and that of admixture and hybridization in increasing the genetic diversity of the founding populations. We show that many of the predictions of this model are corroborated. Most radiations occur in complex adaptive zones, which facilitate the establishment of many small populations exposed to genetic drift and divergent selection. We also show that many radiations (especially those resulting from long-distance dispersal) were established by polyploid lineages, and that many radiating lineages have small genome sizes. However, there are several other predictions which are not (yet) possible to test: that epigenetics has played a role in radiations, that radiations occur more frequently in clades with small gene flow distances, or that the ancestors of radiations had large fundamental niches. At least some of these may be testable in the future as more genome and epigenome data become available. The implication of this model is that many radiations may be hard polytomies because the genetic divergence leading to speciation happens within a very short time, and that the divergence history may be further obscured by hybridization. Furthermore, it suggests that only lineages with the appropriate genetic architecture will be able to radiate, and that such a radiation will happen in a meta-population environment. Understanding the genetic architecture of a lineage may be an essential part of accounting for why some lineages radiate, and some do not.
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Affiliation(s)
- Yamama Naciri
- Plant Systematics and Biodiversity Laboratory, Department of Botany and Plant biology of the University of Geneva, 1 Chemin de l'Impératrice, CH-1292, Chambésy, Geneva, Switzerland
| | - H Peter Linder
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, CH-8008, Zurich, Switzerland
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5
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Aubier TG, Elias M. Positive and negative interactions jointly determine the structure of Müllerian mimetic communities. OIKOS 2020. [DOI: 10.1111/oik.06789] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Thomas G. Aubier
- Centre d'Ecologie Fonctionnelle et Evolutive, CEFE – UMR 5175 – CNRS, Univ. de Montpellier, EPHE, Univ. Paul Valéry 1919 route de Mende FR‐34293 Montpellier 5 France
- Dept of Evolutionary Biology and Environmental Studies, Univ. of Zurich Zurich Switzerland
| | - Marianne Elias
- Inst. de Systématique, Evolution, Biodiversité, ISYEB ‐ UMR 7205 ‐ Mus. Natl d'Hist. Nat., CNRS, Sorbonne Univ., EPHE, Univ. des Antilles Paris France
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6
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Doenz CJ, Krähenbühl AK, Walker J, Seehausen O, Brodersen J. Ecological opportunity shapes a large Arctic charr species radiation. Proc Biol Sci 2019; 286:20191992. [PMID: 31640512 DOI: 10.1098/rspb.2019.1992] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Ecological opportunity is considered a crucial factor for adaptive radiation. Here, we combine genetic, morphological and ecological data to assess species and ecomorphological diversity of Artic charr in six lakes of a catchment in southernmost Greenland, where only charr and stickleback occur. Because the diversity of habitats and resources increases with lake size, we predict a positive association between lake size and the extent of ecomorphological diversity. The largest lake of the catchment harbours the largest Arctic charr assemblage known today. It consists of six genetically differentiated species belonging to five ecomorphs (anadromous, littoral benthic, profundal dwarf, planktivorous, piscivorous), of which the latter comprises two ecomorphologically extremely similar species. Lakes of intermediate size contain two ecomorphologically and genetically distinct species. Small lakes harbour one genetically homogeneous, yet sometimes ecomorphologically variable population. Supporting our prediction, lake size is positively correlated with the extent of ecomorphological specialization towards profundal, pelagic and piscivorous lifestyle. Furthermore, assemblage-wide morphospace increases sharply when more than one genetic cluster is present. Our data suggest that ecological opportunity and speciation jointly determine phenotypic expansion in this charr radiation.
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Affiliation(s)
- Carmela J Doenz
- Department of Fish Ecology and Evolution, EAWAG, Center for Ecology, Evolution and Biogeochemistry, 6047 Kastanienbaum, Switzerland.,Department of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Andrin K Krähenbühl
- Department of Fish Ecology and Evolution, EAWAG, Center for Ecology, Evolution and Biogeochemistry, 6047 Kastanienbaum, Switzerland.,Department of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Jonas Walker
- Department of Fish Ecology and Evolution, EAWAG, Center for Ecology, Evolution and Biogeochemistry, 6047 Kastanienbaum, Switzerland.,Department of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Ole Seehausen
- Department of Fish Ecology and Evolution, EAWAG, Center for Ecology, Evolution and Biogeochemistry, 6047 Kastanienbaum, Switzerland.,Department of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Jakob Brodersen
- Department of Fish Ecology and Evolution, EAWAG, Center for Ecology, Evolution and Biogeochemistry, 6047 Kastanienbaum, Switzerland.,Department of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
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7
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Barrabé L, Lavergne S, Karnadi-Abdelkader G, Drew BT, Birnbaum P, Gâteblé G. Changing Ecological Opportunities Facilitated the Explosive Diversification of New Caledonian Oxera (Lamiaceae). Syst Biol 2019; 68:460-481. [PMID: 30365031 PMCID: PMC6472440 DOI: 10.1093/sysbio/syy070] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 10/04/2018] [Accepted: 10/23/2018] [Indexed: 11/28/2022] Open
Abstract
Phylogenies recurrently demonstrate that oceanic island systems have been home to rapid clade diversification and adaptive radiations. The existence of adaptive radiations posits a central role of natural selection causing ecological divergence and speciation, and some plant radiations have been highlighted as paradigmatic examples of such radiations. However, neutral processes may also drive speciation during clade radiations, with ecological divergence occurring following speciation. Here, we document an exceptionally rapid and unique radiation of Lamiaceae within the New Caledonian biodiversity hotspot. Specifically, we investigated various biological, ecological, and geographical drivers of species diversification within the genus Oxera. We found that Oxera underwent an initial process of rapid cladogenesis likely triggered by a dramatic period of aridity during the early Pliocene. This early diversification of Oxera was associated with an important phase of ecological diversification triggered by significant shifts of pollination syndromes, dispersal modes, and life forms. Finally, recent diversification of Oxera appears to have been further driven by the interplay of allopatry and habitat shifts likely related to climatic oscillations. This suggests that Oxera could be regarded as an adaptive radiation at an early evolutionary stage that has been obscured by more recent joint habitat diversification and neutral geographical processes. Diversification within Oxera has perhaps been triggered by varied ecological and biological drivers acting in a leapfrog pattern, but geographic processes may have been an equally important driver. We suspect that strictly adaptive radiations may be rare in plants and that most events of rapid clade diversification may have involved a mixture of geographical and ecological divergence.
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Affiliation(s)
- Laure Barrabé
- Institut Agronomique néo-Calédonien (IAC), Equipes ARBOREAL and SOLVEG, BP 711, Mont-Dore 98810, New Caledonia.,Endemia, Plant Red List Authority, 7 rue Pierre Artigue, Nouméa 98800, New Caledonia
| | - Sébastien Lavergne
- Laboratoire d'Ecologie Alpine, CNRS - Université Grenoble Alpes, UMR 5553, Grenoble F-38000, France
| | - Giliane Karnadi-Abdelkader
- Institut Agronomique néo-Calédonien (IAC), Equipes ARBOREAL and SOLVEG, BP 711, Mont-Dore 98810, New Caledonia
| | - Bryan T Drew
- Department of Biology, University of Nebraska-Kearney, Kearney, NE 68849, USA
| | - Philippe Birnbaum
- Institut Agronomique néo-Calédonien (IAC), Equipes ARBOREAL and SOLVEG, BP 711, Mont-Dore 98810, New Caledonia.,UMR AMAP, Université de Montpellier, CIRAD, CNRS, INRA, IRD, Montpellier 34398, France
| | - Gildas Gâteblé
- Institut Agronomique néo-Calédonien (IAC), Equipes ARBOREAL and SOLVEG, BP 711, Mont-Dore 98810, New Caledonia
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8
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Gu QH, Husemann M, Wu HH, Dong J, Zhou CJ, Wang XF, Gao YN, Zhang M, Zhu GR, Nie GX. Phylogeography of Bellamya (Mollusca: Gastropoda: Viviparidae) snails on different continents: contrasting patterns of diversification in China and East Africa. BMC Evol Biol 2019; 19:82. [PMID: 30898091 PMCID: PMC6429760 DOI: 10.1186/s12862-019-1397-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Accepted: 02/22/2019] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Species diversity is determined by both local environmental conditions that control differentiation and extinction and the outcome of large-scale processes that affect migration. The latter primarily comprises climatic change and dynamic landscape alteration. In the past few million years, both Southeast Asia and Eastern Africa experienced drastic climatic and geological oscillations: in Southeast Asia, especially in China, the Tibetan Plateau significantly rose up, and the flow of the Yangtze River was reversed. In East Africa, lakes and rivers experienced frequent range expansions and regressions due to the African mega-droughts. To test how such climatic and geological histories of both regions relate to their respective regional species and genetic diversity, a large scale comparative phylogeographic study is essential. Bellamya, a species rich freshwater snail genus that is widely distributed across China and East Africa, represents a suitable model system to address this question. We sequenced mitochondrial and nuclear DNA for members of the genus from China and used published sequences from Africa and some other locations in Asia to investigate their phylogeny and distribution of genetic diversity. RESULTS Our phylogenetic analysis revealed two monophyletic groups, one in China and one in East Africa. Within the Chinese group, Bellamya species show little genetic differentiation. In contrast, we observe fairly deep divergence among the East African lakes with almost every lake possessing its unique clade. Our results show that strong divergence does not necessarily depend on intrinsic characteristics of a species, but rather is related to the landscape dynamics of a region. CONCLUSION Our phylogenetic results suggest that the Bellamya in China and East Africa are independent phylogenetic clades with different evolutionary trajectories. The different climate and geological histories likely contributed to the diverging evolutionary patterns. Repeated range expansions and regressions of lakes likely contributed to the great divergence of Bellamya in East Africa, while reversal of the river courses and intermingling of different lineages had an opposite effect on Bellamya diversification in China.
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Affiliation(s)
- Qian H. Gu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, No. 36 Lushan Road, Changsha City, 410081 Hunan People’s Republic of China
| | - Martin Husemann
- Centrum für Naturkunde, Universität Hamburg, 20146 Hamburg, Germany
| | - Hui H. Wu
- College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, 453007 Henan People’s Republic of China
| | - Jing Dong
- College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, 453007 Henan People’s Republic of China
| | - Chuan J. Zhou
- College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, 453007 Henan People’s Republic of China
| | - Xian F. Wang
- College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, 453007 Henan People’s Republic of China
| | - Yun N. Gao
- College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, 453007 Henan People’s Republic of China
| | - Man Zhang
- College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, 453007 Henan People’s Republic of China
| | - Guo R. Zhu
- College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, 453007 Henan People’s Republic of China
| | - Guo X. Nie
- College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, 453007 Henan People’s Republic of China
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9
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Ávila SP, Melo C, Berning B, Sá N, Quartau R, Rijsdijk KF, Ramalho RS, Cordeiro R, De Sá NC, Pimentel A, Baptista L, Medeiros A, Gil A, Johnson ME. Towards a 'Sea-Level Sensitive' dynamic model: impact of island ontogeny and glacio-eustasy on global patterns of marine island biogeography. Biol Rev Camb Philos Soc 2019; 94:1116-1142. [PMID: 30609249 DOI: 10.1111/brv.12492] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 11/29/2018] [Accepted: 12/03/2018] [Indexed: 01/04/2023]
Abstract
A synthetic model is presented to enlarge the evolutionary framework of the General Dynamic Model (GDM) and the Glacial Sensitive Model (GSM) of oceanic island biogeography from the terrestrial to the marine realm. The proposed 'Sea-Level Sensitive' dynamic model (SLS) of marine island biogeography integrates historical and ecological biogeography with patterns of glacio-eustasy, merging concepts from areas as diverse as taxonomy, biogeography, marine biology, volcanology, sedimentology, stratigraphy, palaeontology, geochronology and geomorphology. Fundamental to the SLS model is the dynamic variation of the littoral area of volcanic oceanic islands (defined as the area between the intertidal and the 50-m isobath) in response to sea-level oscillations driven by glacial-interglacial cycles. The following questions are considered by means of this revision: (i) what was the impact of (global) glacio-eustatic sea-level oscillations, particularly those of the Pleistocene glacial-interglacial episodes, on the littoral marine fauna and flora of volcanic oceanic islands? (ii) What are the main factors that explain the present littoral marine biodiversity on volcanic oceanic islands? (iii) How can differences in historical and ecological biogeography be reconciled, from a marine point of view? These questions are addressed by compiling the bathymetry of 11 Atlantic archipelagos/islands to obtain quantitative data regarding changes in the littoral area based on Pleistocene sea-level oscillations, from 150 thousand years ago (ka) to the present. Within the framework of a model sensitive to changing sea levels, we discuss the principal factors affecting the geographical range of marine species; the relationships between modes of larval development, dispersal strategies and geographical range; the relationships between times of speciation, modes of larval development, ecological zonation and geographical range; the influence of sea-surface temperatures and latitude on littoral marine species diversity; the effect of eustatic sea-level changes and their impact on the littoral marine biota; island marine species-area relationships; and finally, the physical effects of island ontogeny and its associated submarine topography and marine substrate on littoral biota. Based on the SLS dynamic model, we offer a number of predictions for tropical, subtropical and temperate volcanic oceanic islands on how rates of immigration, colonization, in-situ speciation, local disappearance, and extinction interact and affect the marine biodiversity around islands during glacials and interglacials, thus allowing future testing of the theory.
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Affiliation(s)
- Sérgio P Ávila
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Pólo dos Açores, Ponta Delgada 9501-801, Portugal.,Departamento de Biologia, Faculdade de Ciências e Tecnologia da Universidade dos Açores, Ponta Delgada 9501-801, Portugal.,MPB-Marine PalaeoBiogeography Working Group of the University of the Azores, Rua da Mãe de Deus, Ponta Delgada 9501-801, Portugal
| | - Carlos Melo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Pólo dos Açores, Ponta Delgada 9501-801, Portugal.,MPB-Marine PalaeoBiogeography Working Group of the University of the Azores, Rua da Mãe de Deus, Ponta Delgada 9501-801, Portugal.,Departamento de Geologia, Faculdade de Ciências, Universidade de Lisboa, Lisbon 1749-016, Portugal
| | - Björn Berning
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Pólo dos Açores, Ponta Delgada 9501-801, Portugal.,Oberösterreichisches Landesmuseum, Geowissenschaftliche Sammlungen, Leonding 4060, Austria
| | - Nuno Sá
- Departamento de Ciências Tecnológicas e do Desenvolvimento, Faculdade de Ciências da Universidade dos Açores, Ponta Delgada 9501-801, Portugal
| | - Rui Quartau
- Instituto Dom Luiz, Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal.,Divisão de Geologia Marinha, Instituto Hidrográfico, Lisboa, Portugal
| | - Kenneth F Rijsdijk
- Theoretical and Computational Ecology, Institute for Biodiversity and Ecosystem, University of Amsterdam, Amsterdam 1098, The Netherlands
| | - Ricardo S Ramalho
- Departamento de Geologia, Faculdade de Ciências, Universidade de Lisboa, Lisbon 1749-016, Portugal.,Instituto Dom Luiz, Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal.,School of Earth Sciences, University of Bristol, Bristol, BS8 1RJ, U.K
| | - Ricardo Cordeiro
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Pólo dos Açores, Ponta Delgada 9501-801, Portugal.,Departamento de Biologia, Faculdade de Ciências e Tecnologia da Universidade dos Açores, Ponta Delgada 9501-801, Portugal.,MPB-Marine PalaeoBiogeography Working Group of the University of the Azores, Rua da Mãe de Deus, Ponta Delgada 9501-801, Portugal
| | - Nuno C De Sá
- Institute of Environmental Sciences, Leiden University, Leiden, 2300, The Netherlands
| | - Adriano Pimentel
- Centro de Informação e Vigilância Sismovulcânica dos Açores, Rua Mãe de Deus, Ponta Delgada, 9501-801, Portugal.,Instituto de Investigação em Vulcanologia e Avaliação de Riscos, University of the Azores, Ponta Delgada, 9501-801, Portugal
| | - Lara Baptista
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Pólo dos Açores, Ponta Delgada 9501-801, Portugal.,MPB-Marine PalaeoBiogeography Working Group of the University of the Azores, Rua da Mãe de Deus, Ponta Delgada 9501-801, Portugal
| | - António Medeiros
- Departamento de Biologia, Faculdade de Ciências e Tecnologia da Universidade dos Açores, Ponta Delgada 9501-801, Portugal
| | - Artur Gil
- Departamento de Biologia, Faculdade de Ciências e Tecnologia da Universidade dos Açores, Ponta Delgada 9501-801, Portugal.,Ce3C - Centre for Ecology, Evolution and Environmental Changes, Azorean Biodiversity Group, University of the Azores, Ponta Delgada, 9501-801, Portugal
| | - Markes E Johnson
- Department of Geosciences, Williams College, Williamstown, MA 01267, U.S.A
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10
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Govaert L, Fronhofer EA, Lion S, Eizaguirre C, Bonte D, Egas M, Hendry AP, De Brito Martins A, Melián CJ, Raeymaekers JAM, Ratikainen II, Saether B, Schweitzer JA, Matthews B. Eco‐evolutionary feedbacks—Theoretical models and perspectives. Funct Ecol 2018. [DOI: 10.1111/1365-2435.13241] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Lynn Govaert
- Laboratory of Aquatic Ecology, Evolution and Conservation KU Leuven Leuven Belgium
- Department of Aquatic Ecology Eawag: Swiss Federal Institute of Aquatic Science and Technology Dübendorf Switzerland
- Department of Evolutionary Biology and Environmental Studies University of Zurich Zürich Switzerland
| | | | - Sébastien Lion
- Centre d'Ecologie Fonctionnelle et Evolutive CNRS, IRD, EPHE Université de Montpellier Montpellier France
| | | | - Dries Bonte
- Department of Biology Ghent University Ghent Belgium
| | - Martijn Egas
- Institute for Biodiversity and Ecosystem Dynamics University of Amsterdam Amsterdam The Netherlands
| | - Andrew P. Hendry
- Redpath Museum and Department of Biology McGill University Montreal Quebec Canada
| | - Ayana De Brito Martins
- Fish Ecology and Evolution DepartmentCenter for Ecology, Evolution and BiogeochemistryEawag: Swiss Federal Institute of Aquatic Science and Technology Dübendorf Switzerland
| | - Carlos J. Melián
- Fish Ecology and Evolution DepartmentCenter for Ecology, Evolution and BiogeochemistryEawag: Swiss Federal Institute of Aquatic Science and Technology Dübendorf Switzerland
| | | | - Irja I. Ratikainen
- Department of Biology Centre for Biodiversity Dynamics Norwegian University of Science and Technology Trondheim Norway
- Institute of Biodiversity, Animal Health and Comparative Medicine University of Glasgow Glasgow UK
| | - Bernt‐Erik Saether
- Department of Biology Centre for Biodiversity Dynamics Norwegian University of Science and Technology Trondheim Norway
| | - Jennifer A. Schweitzer
- Department of Ecology and Evolutionary Biology University of Tennessee Knoxville Tennessee
| | - Blake Matthews
- Department of Aquatic Ecology Eawag: Swiss Federal Institute of Aquatic Science and Technology Dübendorf Switzerland
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11
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Antonelli A, Ariza M, Albert J, Andermann T, Azevedo J, Bacon C, Faurby S, Guedes T, Hoorn C, Lohmann LG, Matos-Maraví P, Ritter CD, Sanmartín I, Silvestro D, Tejedor M, ter Steege H, Tuomisto H, Werneck FP, Zizka A, Edwards SV. Conceptual and empirical advances in Neotropical biodiversity research. PeerJ 2018; 6:e5644. [PMID: 30310740 PMCID: PMC6174874 DOI: 10.7717/peerj.5644] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 08/27/2018] [Indexed: 01/23/2023] Open
Abstract
The unparalleled biodiversity found in the American tropics (the Neotropics) has attracted the attention of naturalists for centuries. Despite major advances in recent years in our understanding of the origin and diversification of many Neotropical taxa and biotic regions, many questions remain to be answered. Additional biological and geological data are still needed, as well as methodological advances that are capable of bridging these research fields. In this review, aimed primarily at advanced students and early-career scientists, we introduce the concept of "trans-disciplinary biogeography," which refers to the integration of data from multiple areas of research in biology (e.g., community ecology, phylogeography, systematics, historical biogeography) and Earth and the physical sciences (e.g., geology, climatology, palaeontology), as a means to reconstruct the giant puzzle of Neotropical biodiversity and evolution in space and time. We caution against extrapolating results derived from the study of one or a few taxa to convey general scenarios of Neotropical evolution and landscape formation. We urge more coordination and integration of data and ideas among disciplines, transcending their traditional boundaries, as a basis for advancing tomorrow's ground-breaking research. Our review highlights the great opportunities for studying the Neotropical biota to understand the evolution of life.
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Affiliation(s)
- Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Gothenburg Botanical Garden, Gothenburg, Sweden
- Department of Organismic Biology and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - María Ariza
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Laboratory Ecologie et Biologie des Interactions, Team “Ecologie, Evolution, Symbiose”, Université de Poitiers, Poitiers, France
| | - James Albert
- Department of Biology, University of Louisiana at Lafayette, Lafayette, LA, USA
| | - Tobias Andermann
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Josué Azevedo
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Christine Bacon
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Søren Faurby
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Thais Guedes
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Federal University of São Paulo, Diadema, Brazil
- Museum of Zoology, University of São Paulo, São Paulo, Brazil
| | - Carina Hoorn
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
- Universidad Regional Amazonica IKIAM, Napo, Ecuador
| | - Lúcia G. Lohmann
- Instituto de Biociências, Departamento de Botânica, Universidade de São Paulo, São Paulo, Brazil
- Integrative Biology, University of California, Berkeley, CA, USA
| | - Pável Matos-Maraví
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Camila D. Ritter
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | | | - Daniele Silvestro
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Marcelo Tejedor
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Instituto Patagónico de Geología y Paleontología, Puerto Madryn, Guatemala
| | - Hans ter Steege
- Naturalis Biodiversity Center, Leiden, Netherlands
- Systems Ecology, Free University, Amsterdam, Netherlands
| | - Hanna Tuomisto
- Department of Biology, University of Turku, Turku, Finland
| | | | - Alexander Zizka
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Scott V. Edwards
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Department of Organismic Biology and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
- Gothenburg Centre for Advanced Studies in Science and Technology, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden
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12
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Clade diversification dynamics and the biotic and abiotic controls of speciation and extinction rates. Nat Commun 2018; 9:3013. [PMID: 30068945 PMCID: PMC6070539 DOI: 10.1038/s41467-018-05419-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 06/21/2018] [Indexed: 11/23/2022] Open
Abstract
How ecological interactions, genetic processes, and environmental variability jointly shape the evolution of species diversity remains a challenging problem in biology. We developed an individual-based model of clade diversification to predict macroevolutionary dynamics when resource competition, genetic differentiation, and landscape fluctuations interact. Diversification begins with a phase of geographic adaptive radiation. Extinction rates rise sharply at the onset of the next phase. In this phase of niche self-structuring, speciation and extinction processes, albeit driven by biotic mechanisms (competition and hybridization), have essentially constant rates, determined primarily by the abiotic pace of landscape dynamics. The final phase of diversification begins when intense competition prevents dispersing individuals from establishing new populations. Species’ ranges shrink, causing negative diversity-dependence of speciation rates. These results show how ecological and microevolutionary processes shape macroevolutionary dynamics and rates; they caution against the notion of ecological limits to diversity, and suggest new directions for the phylogenetic analysis of diversification. The history and patterns of species diversity are shaped by a variety of ecological and evolutionary factors. Here, the authors develop a computational model to predict clade diversification dynamics and rates of speciation and extinction under the influences of resource competition, genetic differentiation, and random landscape fluctuation.
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13
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Diversification rates indicate an early role of adaptive radiations at the origin of modern echinoid fauna. PLoS One 2018; 13:e0194575. [PMID: 29566024 PMCID: PMC5864014 DOI: 10.1371/journal.pone.0194575] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 03/06/2018] [Indexed: 11/25/2022] Open
Abstract
Evolutionary radiations are fascinating phenomena corresponding to a dramatic diversification of taxa and a burst of cladogenesis over short periods of time. Most evolutionary radiations have long been regarded as adaptive but this has seldom been demonstrated with large-scale comparative datasets including fossil data. Originating in the Early Jurassic, irregular echinoids are emblematic of the spectacular diversification of mobile marine faunas during the Mesozoic Marine Revolution. They diversified as they colonized various habitats, and now constitute the main component of echinoid fauna in modern seas. The evolutionary radiation of irregular echinoids has long been considered as adaptive but this hypothesis has never been tested. In the present work we analyze the evolution of echinoid species richness and morphological disparity over 37 million years based on an extensive fossil dataset. Our results demonstrate that morphological and functional diversifications in certain clades of irregular echinoids were exceptionally high compared to other clades and that they were associated with the evolution of new modes of life and so can be defined as adaptive radiations. The role played by ecological opportunities in the diversification of these clades was critical, with the evolution of the infaunal mode of life promoting the adaptive radiation of irregular echinoids.
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14
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Abstract
Background Much evolutionary theory predicts that diversity arises via both adaptive radiation (diversification driven by selection against niche-overlap within communities) and divergence of geographically isolated populations. We focus on tropical fruit flies (Blepharoneura, Tephritidae) that reveal unexpected patterns of niche-overlap within local communities. Throughout the Neotropics, multiple sympatric non-interbreeding populations often share the same highly specialized patterns of host use (e.g., flies are specialists on flowers of a single gender of a single species of host plants). Lineage through time (LTT) plots can help distinguish patterns of diversification consistent with ecologically limited adaptive radiation from those predicted by ecologically neutral theories. Here, we use a time-calibrated phylogeny of Blepharoneura to test the hypothesis that patterns of Blepharoneura diversification are consistent with an “ecologically neutral” model of diversification that predicts that diversification is primarily a function of time and space. Results The Blepharoneura phylogeny showed more cladogenic divergence associated with geography than with shifts in host-use. Shifts in host-use were associated with ~ 20% of recent splits (< 3 Ma), but > 60% of older splits (> 3 Ma). In the overall tree, gamma statistic and maximum likelihood model fitting showed no evidence of diversification rate changes though there was a weak signature of slowing diversification rate in one of the component clades. Conclusions Overall patterns of Blepharoneura diversity are inconsistent with a traditional explanation of adaptive radiation involving decreases in diversification rates associated with niche-overlap. Sister lineages usually use the same host-species and host-parts, and multiple non-interbreeding sympatric populations regularly co-occur on the same hosts. We suggest that most lineage origins (phylogenetic splits) occur in allopatry, usually without shifts in host-use, and that subsequent dispersal results in assembly of communities composed of multiple sympatric non-interbreeding populations of flies that share the same hosts. Electronic supplementary material The online version of this article (10.1186/s12862-018-1146-9) contains supplementary material, which is available to authorized users.
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15
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Biodiversity Dynamics on Islands: Explicitly Accounting for Causality in Mechanistic Models. DIVERSITY-BASEL 2017. [DOI: 10.3390/d9030030] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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16
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Alcala N, Jensen JD, Telenti A, Vuilleumier S. The Genomic Signature of Population Reconnection Following Isolation: From Theory to HIV. G3 (BETHESDA, MD.) 2015; 6:107-20. [PMID: 26546308 PMCID: PMC4704709 DOI: 10.1534/g3.115.024208] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Accepted: 11/02/2015] [Indexed: 01/19/2023]
Abstract
Ease of worldwide travel provides increased opportunities for organisms not only to colonize new environments but also to encounter related but diverged populations. Such events of reconnection and secondary contact of previously isolated populations are widely observed at different time scales. For example, during the quaternary glaciation, sea water level fluctuations caused temporal isolation of populations, often to be followed by secondary contact. At shorter time scales, population isolation and reconnection of viruses are commonly observed, and such events are often associated with epidemics and pandemics. Here, using coalescent theory and simulations, we describe the temporal impact of population reconnection after isolation on nucleotide differences and the site frequency spectrum, as well as common summary statistics of DNA variation. We identify robust genomic signatures of population reconnection after isolation. We utilize our development to infer the recent evolutionary history of human immunodeficiency virus 1 (HIV-1) in Asia and South America, successfully retrieving the successive HIV subtype colonization events in these regions. Our analysis reveals that divergent HIV-1 subtype populations are currently admixing in these regions, suggesting that HIV-1 may be undergoing a process of homogenization, contrary to popular belief.
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Affiliation(s)
- Nicolas Alcala
- Department of Ecology and Evolution, University of Lausanne, Lausanne CH-1015, Switzerland Department of Biology, Stanford University, Stanford, California 94305-5020
| | - Jeffrey D Jensen
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
| | - Amalio Telenti
- Genomic Medicine, The J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, California 92037
| | - Séverine Vuilleumier
- Department of Ecology and Evolution, University of Lausanne, Lausanne CH-1015, Switzerland School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland Institute of Microbiology, University Hospital and University of Lausanne, Lausanne CH-1011, Switzerland
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17
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Seehausen O. Process and pattern in cichlid radiations - inferences for understanding unusually high rates of evolutionary diversification. THE NEW PHYTOLOGIST 2015; 207:304-312. [PMID: 25983053 DOI: 10.1111/nph.13450] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 02/26/2015] [Indexed: 05/15/2023]
Abstract
The cichlid fish radiations in the African Great Lakes differ from all other known cases of rapid speciation in vertebrates by their spectacular trophic diversity and richness of sympatric species, comparable to the most rapid angiosperm radiations. I review factors that may have facilitated these radiations and compare these with insights from recent work on plant radiations. Work to date suggests that it was a coincidence of ecological opportunity, intrinsic ecological versatility and genomic flexibility, rapidly evolving behavioral mate choice and large amounts of standing genetic variation that permitted these spectacular fish radiations. I propose that spatially orthogonal gradients in the fit of phenotypes to the environment facilitate speciation because they allow colonization of alternative fitness peaks during clinal speciation despite local disruptive selection. Such gradients are manifold in lakes because of the interaction of water depth as an omnipresent third spatial dimension with other fitness-relevant variables. I introduce a conceptual model of adaptive radiation that integrates these elements and discuss its applicability to, and predictions for, plant radiations.
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Affiliation(s)
- Ole Seehausen
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- EAWAG Centre for Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland
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18
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Muehlenbein MP, Pacheco MA, Taylor JE, Prall SP, Ambu L, Nathan S, Alsisto S, Ramirez D, Escalante AA. Accelerated diversification of nonhuman primate malarias in Southeast Asia: adaptive radiation or geographic speciation? Mol Biol Evol 2015; 32:422-39. [PMID: 25389206 PMCID: PMC4298170 DOI: 10.1093/molbev/msu310] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Although parasitic organisms are found worldwide, the relative importance of host specificity and geographic isolation for parasite speciation has been explored in only a few systems. Here, we study Plasmodium parasites known to infect Asian nonhuman primates, a monophyletic group that includes the lineage leading to the human parasite Plasmodium vivax and several species used as laboratory models in malaria research. We analyze the available data together with new samples from three sympatric primate species from Borneo: The Bornean orangutan and the long-tailed and the pig-tailed macaques. We find several species of malaria parasites, including three putatively new species in this biodiversity hotspot. Among those newly discovered lineages, we report two sympatric parasites in orangutans. We find no differences in the sets of malaria species infecting each macaque species indicating that these species show no host specificity. Finally, phylogenetic analysis of these data suggests that the malaria parasites infecting Southeast Asian macaques and their relatives are speciating three to four times more rapidly than those with other mammalian hosts such as lemurs and African apes. We estimate that these events took place in approximately a 3-4-Ma period. Based on the genetic and phenotypic diversity of the macaque malarias, we hypothesize that the diversification of this group of parasites has been facilitated by the diversity, geographic distributions, and demographic histories of their primate hosts.
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Affiliation(s)
| | - M Andreína Pacheco
- Center for Evolutionary Medicine and Informatics, The Biodesign Institute, Arizona State University, Tempe
| | - Jesse E Taylor
- Center for Evolutionary Medicine and Informatics, The Biodesign Institute, Arizona State University, Tempe
| | - Sean P Prall
- Department of Anthropology, Indiana University, Bloomington
| | | | | | - Sylvia Alsisto
- Sabah Wildlife Department, Kota Kinabalu, Sabah, Malaysia
| | - Diana Ramirez
- Sabah Wildlife Department, Kota Kinabalu, Sabah, Malaysia
| | - Ananias A Escalante
- Center for Evolutionary Medicine and Informatics, The Biodesign Institute, Arizona State University, Tempe School of Life Sciences, Arizona State University, Tempe
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19
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Alcala N, Vuilleumier S. Turnover and accumulation of genetic diversity across large time-scale cycles of isolation and connection of populations. Proc Biol Sci 2014; 281:20141369. [PMID: 25253456 PMCID: PMC4211446 DOI: 10.1098/rspb.2014.1369] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 08/27/2014] [Indexed: 01/25/2023] Open
Abstract
Major climatic and geological events but also population history (secondary contacts) have generated cycles of population isolation and connection of long and short periods. Recent empirical and theoretical studies suggest that fast evolutionary processes might be triggered by such events, as commonly illustrated in ecology by the adaptive radiation of cichlid fishes (isolation and reconnection of lakes and watersheds) and in epidemiology by the fast adaptation of the influenza virus (isolation and reconnection in hosts). We test whether cyclic population isolation and connection provide the raw material (standing genetic variation) for species evolution and diversification. Our analytical results demonstrate that population isolation and connection can provide, to populations, a high excess of genetic diversity compared with what is expected at equilibrium. This excess is either cyclic (high allele turnover) or cumulates with time depending on the duration of the isolation and the connection periods and the mutation rate. We show that diversification rates of animal clades are associated with specific periods of climatic cycles in the Quaternary. We finally discuss the importance of our results for macroevolutionary patterns and for the inference of population history from genomic data.
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Affiliation(s)
- Nicolas Alcala
- Department of Ecology and Evolution, University of Lausanne, Biophore, 1015 Lausanne, Switzerland
| | - Séverine Vuilleumier
- Department of Ecology and Evolution, University of Lausanne, Biophore, 1015 Lausanne, Switzerland Institute of Microbiology, Lausanne University Hospital and University of Lausanne, CH-1011 Lausanne, Switzerland
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