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Buckley SJ, Brauer CJ, Unmack PJ, Hammer MP, Adams M, Beatty SJ, Morgan DL, Beheregaray LB. Long-term climatic stability drives accumulation and maintenance of divergent freshwater fish lineages in a temperate biodiversity hotspot. Heredity (Edinb) 2024; 133:149-159. [PMID: 38918613 PMCID: PMC11349885 DOI: 10.1038/s41437-024-00700-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 06/17/2024] [Accepted: 06/17/2024] [Indexed: 06/27/2024] Open
Abstract
Anthropogenic climate change is forecast to drive regional climate disruption and instability across the globe. These impacts are likely to be exacerbated within biodiversity hotspots, both due to the greater potential for species loss but also to the possibility that endemic lineages might not have experienced significant climatic variation in the past, limiting their evolutionary potential to respond to rapid climate change. We assessed the role of climatic stability on the accumulation and persistence of lineages in an obligate freshwater fish group endemic to the southwest Western Australia (SWWA) biodiversity hotspot. Using 19,426 genomic (ddRAD-seq) markers and species distribution modelling, we explored the phylogeographic history of western (Nannoperca vittata) and little (Nannoperca pygmaea) pygmy perches, assessing population divergence and phylogenetic relationships, delimiting species and estimating changes in species distributions from the Pliocene to 2100. We identified two deep phylogroups comprising three divergent clusters, which showed no historical connectivity since the Pliocene. We conservatively suggest these represent three isolated species with additional intraspecific structure within one widespread species. All lineages showed long-term patterns of isolation and persistence owing to climatic stability but with significant range contractions likely under future climate change. Our results highlighted the role of climatic stability in allowing the persistence of isolated lineages in the SWWA. This biodiversity hotspot is under compounding threat from ongoing climate change and habitat modification, which may further threaten previously undetected cryptic diversity across the region.
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Affiliation(s)
- Sean James Buckley
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, SA, 5001, Australia
- School of Biological Sciences, University of Western Australia, Perth, WA, 6000, Australia
- Molecular Ecology and Evolution Group, School of Science, Edith Cowan University, Joondalup, WA, 6027, Australia
| | - Chris J Brauer
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, SA, 5001, Australia
| | - Peter J Unmack
- Centre for Applied Water Science, University of Canberra, Canberra, ACT 2601, Australia
- School of Biological Sciences, Monash University, Clayton, VIC, 3800, Australia
| | - Michael P Hammer
- Natural Sciences, Museum and Art Gallery of the Northern Territory, Darwin, NT, 0801, Australia
| | - Mark Adams
- Evolutionary Biology Unit, South Australian Museum, Adelaide, SA, 5000, Australia
- School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5000, Australia
| | - Stephen J Beatty
- Centre for Sustainable Aquatic Ecosystems, Harry Butler Institute, Murdoch University, Murdoch, WA, 6150, Australia
| | - David L Morgan
- Centre for Sustainable Aquatic Ecosystems, Harry Butler Institute, Murdoch University, Murdoch, WA, 6150, Australia
| | - Luciano B Beheregaray
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, SA, 5001, Australia.
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2
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Faurby S, Silvestro D, Werdelin L, Antonelli A. Reliable biogeography requires fossils: insights from a new species-level phylogeny of extinct and living carnivores. Proc Biol Sci 2024; 291:20240473. [PMID: 39106959 DOI: 10.1098/rspb.2024.0473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 05/21/2024] [Indexed: 08/09/2024] Open
Abstract
A central objective of historical biogeography is to understand where clades originated and how they moved across space and over time. However, given the dynamic history of ecosystem changes in response to climate change and geological events, the manifold long-distance dispersals over evolutionary timescales, and regional and global extinctions, it remains uncertain how reliable inferences based solely on extant taxa can be achieved. Using a novel species-level phylogeny of all known extant and extinct species of the mammalian order Carnivora and related extinct groups, we show that far more precise and accurate ancestral areas can be estimated by fully integrating extinct species into the analyses, rather than solely relying on extant species or identifying ancestral areas only based on the geography of the oldest fossils. Through a series of simulations, we further show that this conclusion is robust under realistic scenarios in which the unknown extinct taxa represent a biased subset of all extinct species. Our results highlight the importance of integrating fossil taxa into a phylogenetic framework to further improve our understanding of historical biogeography and reveal the dynamic dispersal and diversification history of carnivores.
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Affiliation(s)
- Søren Faurby
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 40530 Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Box 461, 40530 Gothenburg, Sweden
| | - Daniele Silvestro
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 40530 Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Box 461, 40530 Gothenburg, Sweden
- Department of Biology, University of Fribourg, Fribourg 1700, Switzerland
- Swiss Institute of Bioinformatics, Fribourg 1700, Switzerland
| | - Lars Werdelin
- Department of Palaeobiology, Swedish Museum of Natural History, Box 50007, 10405 Stockholm, Sweden
| | - Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 40530 Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Box 461, 40530 Gothenburg, Sweden
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
- Department of Biology, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
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3
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Ito HC, Sasaki A. The Adaptation Front Equation Explains Innovation-Driven Taxonomic Turnovers and Living Fossilization. Am Nat 2023; 202:E163-E180. [PMID: 38033181 DOI: 10.1086/727046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2023]
Abstract
AbstractEvolutionary taxonomic turnovers are often associated with innovations beneficial in various ecological niches. Such innovations can repeatedly occur in species occupying optimum niches for a focal species group, resulting in their repeated diversifications and species flows from optimum to suboptimum niches, at the expense of less innovated ones. By combining species packing theory and adaptive dynamics theory, we develop an equation that allows analytical prediction for such innovation-driven species flows over a niche space of arbitrary dimension under a unimodal carrying capacity distribution. The developed equation and simulated evolution show that central niches (with the highest carrying capacities) tend to attain the fastest innovation speeds to become biodiversity sources. Species that diverge from the central niches outcompete the indigenous species in peripheral niches. The outcompeted species become extinct or evolve directionally toward far more peripheral niches. Because of this globally acting process over niches, species occupying the most peripheral niches are the least innovated and have deep divergence times from their closest relatives, and thus they correspond to living fossils. The extension of this analysis for multiple geographic regions shows that living fossils are also expected in geographically peripheral regions for the focal species group.
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4
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Velasco JA, Pinto-Ledezma JN. Mapping species diversification metrics in macroecology: Prospects and challenges. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.951271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The intersection of macroecology and macroevolution is one of today’s most active research in biology. In the last decade, we have witnessed a steady increment of macroecological studies that use metrics attempting to capture macroevolutionary processes to explain present-day biodiversity patterns. Evolutionary explanations of current species richness gradients are fundamental for understanding how diversity accumulates in a region. Although multiple hypotheses have been proposed to explain the patterns we observe in nature, it is well-known that the present-day diversity patterns result from speciation, extinction, colonization from nearby areas, or a combination of these macroevolutionary processes. Whether these metrics capture macroevolutionary processes across space is unknown. Some tip-rate metrics calculated directly from a phylogenetic tree (e.g., mean root distance -MRD-; mean diversification rate -mDR-) seem to return very similar geographical patterns regardless of how they are estimated (e.g., using branch lengths explicitly or not). Model-based tip-rate metrics —those estimated using macroevolutionary mixtures, e.g., the BAMM approach— seem to provide better net diversification estimates than only speciation rates. We argue that the lack of appropriate estimates of extinction and dispersal rates in phylogenetic trees may strongly limit our inferences about how species richness gradients have emerged at spatial and temporal scales. Here, we present a literature review about this topic and empirical comparisons between select taxa with several of these metrics. We implemented a simple null model approach to evaluate whether mapping of these metrics deviates from a random sampling process. We show that phylogenetic metrics by themselves are relatively poor at capturing speciation, extinction, and dispersal processes across geographical gradients. Furthermore, we provide evidence of how parametric biogeographic methods can improve our inference of past events and, therefore, our conclusions about the evolutionary processes driving biodiversity patterns. We recommend that further studies include several approaches simultaneously (e.g., spatial diversification modeling, parametric biogeographic methods, simulations) to disentangle the relative role of speciation, extinction, and dispersal in the generation and maintenance of species richness gradients at regional and global scales.
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5
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Jardim de Queiroz L, Doenz CJ, Altermatt F, Alther R, Borko Š, Brodersen J, Gossner MM, Graham C, Matthews B, McFadden IR, Pellissier L, Schmitt T, Selz OM, Villalba S, Rüber L, Zimmermann NE, Seehausen O. Climate, immigration and speciation shape terrestrial and aquatic biodiversity in the European Alps. Proc Biol Sci 2022; 289:20221020. [PMID: 35946161 PMCID: PMC9363983 DOI: 10.1098/rspb.2022.1020] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Quaternary climate fluctuations can affect speciation in regional biodiversity assembly in two non-mutually exclusive ways: a glacial species pump, where isolation in glacial refugia accelerates allopatric speciation, and adaptive radiation in underused adaptive zones during ice-free periods. We detected biogeographic and genetic signatures associated with both mechanisms in the assembly of the biota of the European Alps. Age distributions of endemic and widespread species within aquatic and terrestrial taxa (amphipods, fishes, amphibians, butterflies and flowering plants) revealed that endemic fish evolved only in lakes, are highly sympatric, and mainly of Holocene age, consistent with adaptive radiation. Endemic amphipods are ancient, suggesting preglacial radiation with limited range expansion and local Pleistocene survival, perhaps facilitated by a groundwater-dwelling lifestyle. Terrestrial endemics are mostly of Pleistocene age and are thus more consistent with the glacial species pump. The lack of evidence for Holocene adaptive radiation in the terrestrial biome is consistent with faster recolonization through range expansion of these taxa after glacial retreats. More stable and less seasonal ecological conditions in lakes during the Holocene may also have contributed to Holocene speciation in lakes. The high proportion of young, endemic species makes the Alpine biota vulnerable to climate change, but the mechanisms and consequences of species loss will likely differ between biomes because of their distinct evolutionary histories.
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Affiliation(s)
- Luiz Jardim de Queiroz
- Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum/8600 Dübendorf, Switzerland.,Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Carmela J Doenz
- Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum/8600 Dübendorf, Switzerland.,Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Florian Altermatt
- Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum/8600 Dübendorf, Switzerland.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8006 Zürich, Switzerland
| | - Roman Alther
- Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum/8600 Dübendorf, Switzerland.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8006 Zürich, Switzerland
| | - Špela Borko
- SubBio Lab, Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Jakob Brodersen
- Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum/8600 Dübendorf, Switzerland.,Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Martin M Gossner
- Swiss Federal Institute for Forest, Snow and Landscape Research, 8903 Birmensdorf, Switzerland.,Department of Environmental Systems Science, Swiss Federal Institute of Technology in Zürich, 8092 Zürich, Switzerland
| | - Catherine Graham
- Swiss Federal Institute for Forest, Snow and Landscape Research, 8903 Birmensdorf, Switzerland
| | - Blake Matthews
- Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum/8600 Dübendorf, Switzerland.,Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Ian R McFadden
- Swiss Federal Institute for Forest, Snow and Landscape Research, 8903 Birmensdorf, Switzerland.,Department of Environmental Systems Science, Swiss Federal Institute of Technology in Zürich, 8092 Zürich, Switzerland
| | - Loïc Pellissier
- Swiss Federal Institute for Forest, Snow and Landscape Research, 8903 Birmensdorf, Switzerland.,Department of Environmental Systems Science, Swiss Federal Institute of Technology in Zürich, 8092 Zürich, Switzerland
| | - Thomas Schmitt
- Senckenberg German Entomological Institute, 15374 Müncheberg, Germany.,Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
| | - Oliver M Selz
- Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum/8600 Dübendorf, Switzerland
| | - Soraya Villalba
- Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum/8600 Dübendorf, Switzerland
| | - Lukas Rüber
- Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland.,Naturhistorisches Museum Bern, 3005 Bern, Switzerland
| | - Niklaus E Zimmermann
- Swiss Federal Institute for Forest, Snow and Landscape Research, 8903 Birmensdorf, Switzerland.,Department of Environmental Systems Science, Swiss Federal Institute of Technology in Zürich, 8092 Zürich, Switzerland
| | - Ole Seehausen
- Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum/8600 Dübendorf, Switzerland.,Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
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6
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Goldberg EE, Price T. Effects of plasticity on elevational range size and species richness. Am Nat 2022; 200:316-329. [DOI: 10.1086/720412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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7
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Hauffe T, Pires MM, Quental TB, Wilke T, Silvestro D. A quantitative framework to infer the effect of traits, diversity and environment on dispersal and extinction rates from fossils. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.13845] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Torsten Hauffe
- Department of Biology University of Fribourg and Swiss Institute of Bioinformatics Fribourg Switzerland
| | - Mathias M. Pires
- Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas Campinas Brazil
| | - Tiago B. Quental
- Departamento de Ecologia, Universidade de São Paulo São Paulo Brazil
| | - Thomas Wilke
- Department of Animal Ecology and Systematics, Justus Liebig University Germany
| | - Daniele Silvestro
- Department of Biology University of Fribourg and Swiss Institute of Bioinformatics Fribourg Switzerland
- Department of Biological and Environmental Sciences University of Gothenburg and Gothenburg Global Biodiversity Centre Gothenburg Sweden
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8
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Luza AL, Maestri R, Debastiani VJ, Patterson BD, Hartz SM, Duarte LDS. Is evolution faster at ecotones? A test using rates and tempo of diet transitions in Neotropical Sigmodontinae (Rodentia, Cricetidae). Ecol Evol 2021; 11:18676-18690. [PMID: 35003701 PMCID: PMC8717272 DOI: 10.1002/ece3.8476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 11/27/2021] [Accepted: 12/03/2021] [Indexed: 11/20/2022] Open
Abstract
We evaluated whether evolution is faster at ecotones as niche shifts may be needed to persist under unstable environment. We mapped diet evolution along the evolutionary history of 350 sigmodontine species. Mapping was used in three new tip-based metrics of trait evolution - Transition Rates, Stasis Time, and Last Transition Time - which were spatialized at the assemblage level (aTR, aST, aTL). Assemblages were obtained by superimposing range maps on points located at core and ecotone of the 93 South American ecoregions. Using Linear Mixed Models, we tested whether ecotones have species with more changes from the ancestral diet (higher aTR), have maintained the current diet for a shorter time (lower aST), and have more recent transitions to the current diet (lower aLT) than cores. We found lower aTR, and higher aST and aLT at ecotones than at cores. Although ecotones are more heterogeneous, both environmentally and in relation to selection pressures they exert on organisms, ecotone species change little from the ancestral diet as generalist habits are necessary toward feeding in ephemeral environments. The need to incorporate phylogenetic uncertainty in tip-based metrics was evident from large uncertainty detected. Our study integrates ecology and evolution by analyzing how fast trait evolution is across space.
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Affiliation(s)
- André Luís Luza
- Programa de Pós‐Graduação em EcologiaDepartamento de EcologiaInstituto de BiociênciasUniversidade Federal do Rio Grande do SulBairro AgronomiaRio Grande do SulCEP 91501‐970Brazil
- Departamento de Ecologia e EvoluçãoUniversidade Federal de Santa MariaSanta MariaRio Grande do SulCEP 97105‐900Brazil
| | - Renan Maestri
- Programa de Pós‐Graduação em EcologiaDepartamento de EcologiaInstituto de BiociênciasUniversidade Federal do Rio Grande do SulBairro AgronomiaRio Grande do SulCEP 91501‐970Brazil
- Negaunee Integrative Research CenterField Museum of Natural HistoryChicagoIllinoisUSA
| | - Vanderlei Júlio Debastiani
- Programa de Pós‐Graduação em EcologiaDepartamento de EcologiaInstituto de BiociênciasUniversidade Federal do Rio Grande do SulBairro AgronomiaRio Grande do SulCEP 91501‐970Brazil
| | - Bruce D. Patterson
- Negaunee Integrative Research CenterField Museum of Natural HistoryChicagoIllinoisUSA
| | - Sandra Maria Hartz
- Programa de Pós‐Graduação em EcologiaDepartamento de EcologiaInstituto de BiociênciasUniversidade Federal do Rio Grande do SulBairro AgronomiaRio Grande do SulCEP 91501‐970Brazil
| | - Leandro D. S. Duarte
- Programa de Pós‐Graduação em EcologiaDepartamento de EcologiaInstituto de BiociênciasUniversidade Federal do Rio Grande do SulBairro AgronomiaRio Grande do SulCEP 91501‐970Brazil
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9
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Matos-Maraví P, Wahlberg N, Freitas AVL, Devries P, Antonelli A, Penz CM. Mesoamerica is a cradle and the Atlantic Forest is a museum of Neotropical butterfly diversity: insights from the evolution and biogeography of Brassolini (Lepidoptera: Nymphalidae). Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blab034] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Regional species diversity is explained ultimately by speciation, extinction and dispersal. Here, we estimate dispersal and speciation rates of Neotropical butterflies to propose an explanation for the distribution and diversity of extant species. We focused on the tribe Brassolini (owl butterflies and allies), a Neotropical group that comprises 17 genera and 108 species, most of them endemic to rainforest biomes. We inferred a robust species tree using the multispecies coalescent framework and a dataset including molecular and morphological characters. This formed the basis for three changes in Brassolini classification: (1) Naropina syn. nov. is subsumed within Brassolina; (2) Aponarope syn. nov. is subsumed within Narope; and (3) Selenophanes orgetorix comb. nov. is reassigned from Catoblepia to Selenophanes. By applying biogeographical stochastic mapping, we found contrasting species diversification and dispersal dynamics across rainforest biomes, which might be explained, in part, by the geological and environmental history of each bioregion. Our results revealed a mosaic of biome-specific evolutionary histories within the Neotropics, where butterfly species have diversified rapidly (cradles: Mesoamerica), have accumulated gradually (museums: Atlantic Forest) or have diversified and accumulated alternately (Amazonia). Our study contributes evidence from a major butterfly lineage that the Neotropics are a museum and a cradle of species diversity.
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Affiliation(s)
- Pável Matos-Maraví
- Department of Biological and Environmental Sciences, University of Gothenburg, Carl Skottsbergs gata 22B, 41319 Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Carl Skottsbergs gata 22B, 41319 Gothenburg, Sweden
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 1160/31, 37005 České Budějovice, Czech Republic
| | - Niklas Wahlberg
- Department of Biology, Lund University, Sölvegatan 37, 22362 Lund, Sweden
| | - André V L Freitas
- Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas, Rua Monteiro Lobato 255, CEP 13.083-862 Campinas, São Paulo, Brazil
| | - Phil Devries
- Department of Biological Sciences, University of New Orleans, 2000 Lakeshore Drive, New Orleans, LA 70148, USA
- Courtesy Curators of Lepidoptera, Florida Museum of Natural History, 1659 Museum Road, Gainesville, FL 32611, USA
| | - Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, Carl Skottsbergs gata 22B, 41319 Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Carl Skottsbergs gata 22B, 41319 Gothenburg, Sweden
- Royal Botanical Gardens Kew, Richmond TW9 3AE, UK
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | - Carla M Penz
- Department of Biological Sciences, University of New Orleans, 2000 Lakeshore Drive, New Orleans, LA 70148, USA
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10
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Päckert M, Favre A, Schnitzler J, Martens J, Sun Y, Tietze DT, Hailer F, Michalak I, Strutzenberger P. "Into and Out of" the Qinghai-Tibet Plateau and the Himalayas: Centers of origin and diversification across five clades of Eurasian montane and alpine passerine birds. Ecol Evol 2020; 10:9283-9300. [PMID: 32953061 PMCID: PMC7487248 DOI: 10.1002/ece3.6615] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 06/12/2020] [Accepted: 06/29/2020] [Indexed: 01/06/2023] Open
Abstract
Encompassing some of the major hotspots of biodiversity on Earth, large mountain systems have long held the attention of evolutionary biologists. The region of the Qinghai-Tibet Plateau (QTP) is considered a biogeographic source for multiple colonization events into adjacent areas including the northern Palearctic. The faunal exchange between the QTP and adjacent regions could thus represent a one-way street ("out of" the QTP). However, immigration into the QTP region has so far received only little attention, despite its potential to shape faunal and floral communities of the QTP. In this study, we investigated centers of origin and dispersal routes between the QTP, its forested margins and adjacent regions for five clades of alpine and montane birds of the passerine superfamily Passeroidea. We performed an ancestral area reconstruction using BioGeoBEARS and inferred a time-calibrated backbone phylogeny for 279 taxa of Passeroidea. The oldest endemic species of the QTP was dated to the early Miocene (ca. 20 Ma). Several additional QTP endemics evolved in the mid to late Miocene (12-7 Ma). The inferred centers of origin and diversification for some of our target clades matched the "out of Tibet hypothesis' or the "out of Himalayas hypothesis" for others they matched the "into Tibet hypothesis." Three radiations included multiple independent Pleistocene colonization events to regions as distant as the Western Palearctic and the Nearctic. We conclude that faunal exchange between the QTP and adjacent regions was bidirectional through time, and the QTP region has thus harbored both centers of diversification and centers of immigration.
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Affiliation(s)
- Martin Päckert
- Senckenberg Natural History Collections, Museum of ZoologyDresdenGermany
| | - Adrien Favre
- Entomology IIISenckenberg Research Institute and Natural History Museum FrankfurtFrankfurt am MainGermany
| | - Jan Schnitzler
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
- Department of Molecular Evolution and Plant Systematics & Herbarium (LZ)Institute of BiologyLeipzig UniversityLeipzigGermany
| | - Jochen Martens
- Institute of Organismic and Molecular EvolutionJohannes Gutenberg‐UniversitätMainzGermany
| | - Yue‐Hua Sun
- Key Laboratory of Animal Ecology and ConservationInstitute of ZoologyChinese Academy of SciencesBeijingChina
| | - Dieter Thomas Tietze
- Natural History Museum BaselBaselSwitzerland
- Centrum für NaturkundeUniversität HamburgHamburgGermany
| | - Frank Hailer
- School of BiosciencesCardiff UniversityCardiffUK
- Senckenberg Biodiversity and Climate Research CentreFrankfurt am MainGermany
| | - Ingo Michalak
- Department of Molecular Evolution and Plant Systematics & Herbarium (LZ)Institute of BiologyLeipzig UniversityLeipzigGermany
| | - Patrick Strutzenberger
- Senckenberg Natural History Collections, Museum of ZoologyDresdenGermany
- Department of Botany and Biodiversity ResearchUniversität WienWienAustria
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11
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Landis M, Edwards EJ, Donoghue MJ. Modeling Phylogenetic Biome Shifts on a Planet with a Past. Syst Biol 2020; 70:86-107. [PMID: 32514540 DOI: 10.1093/sysbio/syaa045] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 05/27/2020] [Indexed: 12/30/2022] Open
Abstract
The spatial distribution of biomes has changed considerably over deep time, so the geographical opportunity for an evolutionary lineage to shift into a new biome may depend on how the availability and connectivity of biomes has varied temporally. To better understand how lineages shift between biomes in space and time, we developed a phylogenetic biome shift model in which each lineage shifts between biomes and disperses between regions at rates that depend on the lineage's biome affinity and location relative to the spatial distribution of biomes at any given time. To study the behavior of the biome shift model in an empirical setting, we developed a literature-based representation of paleobiome structure for three mesic forest biomes, six regions, and eight time strata, ranging from the Late Cretaceous (100 Ma) through the present. We then fitted the model to a time-calibrated phylogeny of 119 Viburnum species to compare how the results responded to various realistic or unrealistic assumptions about paleobiome structure. Ancestral biome estimates that account for paleobiome dynamics reconstructed a warm temperate (or tropical) origin of Viburnum, which is consistent with previous fossil-based estimates of ancestral biomes. Imposing unrealistic paleobiome distributions led to ancestral biome estimates that eliminated support for tropical origins, and instead inflated support for cold temperate ancestry throughout the warmer Paleocene and Eocene. The biome shift model we describe is applicable to the study of evolutionary systems beyond Viburnum, and the core mechanisms of our model are extensible to the design of richer phylogenetic models of historical biogeography and/or lineage diversification. We conclude that biome shift models that account for dynamic geographical opportunities are important for inferring ancestral biomes that are compatible with our understanding of Earth history.[Ancestral states; biome shifts; historical biogeography; niche conservatism; phylogenetics].
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Affiliation(s)
- Michael Landis
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, MI 63130, USA.,Department of Ecology & Evolutionary Biology, Yale University, PO Box 208106, New Haven, CT 06520, USA
| | - Erika J Edwards
- Department of Ecology & Evolutionary Biology, Yale University, PO Box 208106, New Haven, CT 06520, USA.,Division of Botany, Yale Peabody Museum of Natural History, P.O. Box 208118, New Haven, CT 06520, USA
| | - Michael J Donoghue
- Department of Ecology & Evolutionary Biology, Yale University, PO Box 208106, New Haven, CT 06520, USA.,Division of Botany, Yale Peabody Museum of Natural History, P.O. Box 208118, New Haven, CT 06520, USA
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12
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Eliason CM, Andersen MJ, Hackett SJ. Using Historical Biogeography Models to Study Color Pattern Evolution. Syst Biol 2019; 68:755-766. [DOI: 10.1093/sysbio/syz012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 02/11/2019] [Accepted: 02/14/2019] [Indexed: 11/14/2022] Open
Abstract
Abstract
Color is among the most striking features of organisms, varying not only in spectral properties like hue and brightness, but also in where and how it is produced on the body. Different combinations of colors on a bird’s body are important in both environmental and social contexts. Previous comparative studies have treated plumage patches individually or derived plumage complexity scores from color measurements across a bird’s body. However, these approaches do not consider the multivariate nature of plumages (allowing for plumage to evolve as a whole) or account for interpatch distances. Here, we leverage a rich toolkit used in historical biogeography to assess color pattern evolution in a cosmopolitan radiation of birds, kingfishers (Aves: Alcedinidae). We demonstrate the utility of this approach and test hypotheses about the tempo and mode of color evolution in kingfishers. Our results highlight the importance of considering interpatch distances in understanding macroevolutionary trends in color diversity and demonstrate how historical biogeography models are a useful way to model plumage color pattern evolution. Furthermore, they show that distinct color mechanisms (pigments or structural colors) spread across the body in different ways and at different rates. Specifically, net rates are higher for structural colors than pigment-based colors. Together, our study suggests a role for both development and selection in driving extraordinary color pattern diversity in kingfishers. We anticipate this approach will be useful for modeling other complex phenotypes besides color, such as parasite evolution across the body.
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Affiliation(s)
- Chad M Eliason
- Integrative Research Center, Field Museum of Natural History, Chicago, IL, USA
| | - Michael J Andersen
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM, USA
| | - Shannon J Hackett
- Integrative Research Center, Field Museum of Natural History, Chicago, IL, USA
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Gomard Y, Cornuault J, Licciardi S, Lagadec E, Belqat B, Dsouli N, Mavingui P, Tortosa P. Evidence of multiple colonizations as a driver of black fly diversification in an oceanic island. PLoS One 2018; 13:e0202015. [PMID: 30096163 PMCID: PMC6086440 DOI: 10.1371/journal.pone.0202015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 07/26/2018] [Indexed: 11/19/2022] Open
Abstract
True oceanic islands typically host reduced species diversity together with high levels of endemism, which make these environmental set-ups ideal for the exploration of species diversification drivers. In the present study, we used black fly species (Diptera: Simuliidae) from Reunion Island as a model to highlight the main drivers of insect species diversification in this young and remote volcanic island located in the Southwestern Indian Ocean. Using local and regional (Comoros and Seychelles archipelagos) samples as well as specimens from continental Africa, we tested the likelihood of two distinct scenarios, i.e. multiple colonizations vs. in-situ diversification. For this, posterior odds were used to test whether species from Reunion did form a monophyletic group and we estimated divergence times between species. Three out of the four previously described Reunion black fly species could be sampled, namely Simulium ruficorne, Simulium borbonense and Simulium triplex. The phylogenies based on nuclear and mitochondrial markers showed that S. ruficorne and S. borbonense are the most closely related species. Interestingly, we report a probable mitochondrial introgression between these two species although they diverged almost six million years ago. Finally, we showed that the three Reunion species did not form a monophyletic group, and, combined with the molecular datation, the results indicated that Reunion black fly diversity resulted from multiple colonization events. Thus, multiple colonizations, rather than in-situ diversification, are likely responsible for an important part of black fly diversity found on this young Darwinian island.
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Affiliation(s)
- Yann Gomard
- Université de La Réunion, UMR PIMIT (Processus Infectieux en Milieu Insulaire Tropical), INSERM 1187, CNRS 9192, IRD 249, Plateforme Technologique CYROI, Sainte-Clotilde, La Réunion, France
- * E-mail:
| | - Josselin Cornuault
- Department of Biodiversity and Conservation, Real Jardín Botánico, RJB-CSIC, Madrid, Spain
| | - Séverine Licciardi
- CIRAD, UMR ASTRE, Sainte-Clotilde, La Réunion, France
- ASTRE, Univ Montpellier, CIRAD, INRA, Montpellier, France
- Groupement d’Intérêt Public Cyclotron Reunion Océan Indien (GIP CYROI), Sainte-Clotilde, La Réunion, France
| | - Erwan Lagadec
- Université de La Réunion, UMR PIMIT (Processus Infectieux en Milieu Insulaire Tropical), INSERM 1187, CNRS 9192, IRD 249, Plateforme Technologique CYROI, Sainte-Clotilde, La Réunion, France
| | - Boutaïna Belqat
- Department of Biology, Faculty of Sciences, University Abdelmalek Essaâdi, Tétouan, Morocco
| | - Najla Dsouli
- Centre de Recherche et de Veille sur les maladies émergentes dans l’Océan Indien (CRVOI), Plateforme Technologique CYROI, Sainte-Clotilde, La Réunion, France
| | - Patrick Mavingui
- Université de La Réunion, UMR PIMIT (Processus Infectieux en Milieu Insulaire Tropical), INSERM 1187, CNRS 9192, IRD 249, Plateforme Technologique CYROI, Sainte-Clotilde, La Réunion, France
- Université de Lyon, Lyon, France; Université Lyon 1, Villeurbanne, France; CNRS, UMR 5557, Ecologie Microbienne, Villeurbanne, France; INRA, UMR1418, Villeurbanne, France
| | - Pablo Tortosa
- Université de La Réunion, UMR PIMIT (Processus Infectieux en Milieu Insulaire Tropical), INSERM 1187, CNRS 9192, IRD 249, Plateforme Technologique CYROI, Sainte-Clotilde, La Réunion, France
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Albert JS, Schoolmaster DR, Tagliacollo V, Duke-Sylvester SM. Barrier Displacement on a Neutral Landscape: Toward a Theory of Continental Biogeography. Syst Biol 2018; 66:167-182. [PMID: 27590192 DOI: 10.1093/sysbio/syw080] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 08/23/2016] [Indexed: 01/07/2023] Open
Abstract
Macroevolutionary theory posits three processes leading to lineage diversification and the formation of regional biotas: dispersal (species geographic range expansion), speciation (species lineage splitting), and extinction (species lineage termination). The Theory of Island Biogeography (TIB) predicts species richness values using just two of these processes; dispersal and extinction. Yet most species on Earth live on continents or continental shelves, and the dynamics of evolutionary diversification at regional and continental scales are qualitatively different from those that govern the formation of species richness on biogeographic islands. Certain geomorphological processes operating perennially on continental platforms displace barriers to gene flow and organismal dispersal, and affect all three terms of macroevolutionary diversification. For example, uplift of a dissected landscape and river capture both merge and separate portions of adjacent areas, allowing dispersal and larger geographic ranges, vicariant speciation and smaller geographic ranges, and extinction when range sizes are subdivided below a minimum persistence threshold. The TIB also does not predict many biogeographic and phylogenetic patterns widely observed in continentally distributed taxa, including: (i) power function-like species-area relationships; (ii) log-normal distribution of species geographic range sizes, in which most species have restricted ranges (are endemic) and few species have broad ranges (are cosmopolitan); (iii) mid-domain effects with more species toward the geographic center, and more early-branching, species-poor clades toward the geographic periphery; (iv) exponential rates of net diversification with log-linear accumulation of lineages through geological time; and (v) power function-like relationships between species-richness and clade diversity, in which most clades are species-poor and few clades are species-rich. Current theory does not provide a robust mechanistic framework to connect these seemingly disparate patterns. Here we present SEAMLESS (Spatially Explicit Area Model of Landscape Evolution by SimulationS) that generates clade diversification by moving geographic barriers on a continuous, neutral landscape. SEAMLESS is a neutral Landscape Evolution Model (LEM) that treats species and barriers as functionally equivalent with respect to model parameters. SEAMLESS differs from other model-based biogeographic methods (e.g., Lagrange, GeoSSE, BayArea, and BioGeoBEARS) by modeling properties of dispersal barriers rather than areas, and by modeling the evolution of species lineages on a continuous landscape, rather than the evolution of geographic ranges along branches of a phylogeny. SEAMLESS shows how dispersal is required to maintain species richness and avoid clade-wide extinction, demonstrates that ancestral range size does not predict species richness, and provides a unified explanation for the suite of commonly observed biogeographic and phylogenetic patterns listed above. SEAMLESS explains how a simple barrier-displacement mechanism affects lineage diversification under neutral conditions, and is advanced here toward the formulation of a general theory of continental biogeography. [Diversification, extinction, geodispersal, macroevolution, river capture, vicariance.].
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Affiliation(s)
- James S Albert
- Department of Biology, University of Louisiana at Lafayette, 104 E. University Circle, Lafayette, LA 70503, USA
| | | | - Victor Tagliacollo
- Universidade Federal do Tocantins Avenida NS 15, 109 Norte Palmas, Tocantins 77001-090, Brazil
| | - Scott M Duke-Sylvester
- Department of Biology, University of Louisiana at Lafayette, 104 E. University Circle, Lafayette, LA 70503, USA
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15
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Huang D, Goldberg EE, Chou LM, Roy K. The origin and evolution of coral species richness in a marine biodiversity hotspot. Evolution 2017; 72:288-302. [PMID: 29178128 DOI: 10.1111/evo.13402] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 10/30/2017] [Accepted: 11/12/2017] [Indexed: 12/25/2022]
Abstract
The Coral Triangle (CT) region of the Indo-Pacific realm harbors an extraordinary number of species, with richness decreasing away from this biodiversity hotspot. Despite multiple competing hypotheses, the dynamics underlying this regional diversity pattern remain poorly understood. Here, we use a time-calibrated evolutionary tree of living reef coral species, their current geographic ranges, and model-based estimates of regional rates of speciation, extinction, and geographic range shifts to show that origination rates within the CT are lower than in surrounding regions, a result inconsistent with the long-standing center of origin hypothesis. Furthermore, endemism of coral species in the CT is low, and the CT endemics are older than relatives found outside this region. Overall, our model results suggest that the high diversity of reef corals in the CT is largely due to range expansions into this region of species that evolved elsewhere. These findings strongly support the notion that geographic range shifts play a critical role in generating species diversity gradients. They also show that preserving the processes that gave rise to the striking diversity of corals in the CT requires protecting not just reefs within the hotspot, but also those in the surrounding areas.
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Affiliation(s)
- Danwei Huang
- Department of Biological Sciences and Tropical Marine Science Institute, National University of Singapore, Singapore 117543, Singapore
| | - Emma E Goldberg
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota 55108
| | - Loke Ming Chou
- Department of Biological Sciences and Tropical Marine Science Institute, National University of Singapore, Singapore 117543, Singapore
| | - Kaustuv Roy
- Section of Ecology, Behavior and Evolution, University of California, San Diego, La Jolla, California 92093
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16
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Cradles and museums of Antarctic teleost biodiversity. Nat Ecol Evol 2017; 1:1379-1384. [DOI: 10.1038/s41559-017-0239-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 06/15/2017] [Indexed: 11/08/2022]
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17
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Poe S, Nieto-montes de oca A, Torres-carvajal O, De Queiroz K, Velasco JA, Truett B, Gray LN, Ryan MJ, Köhler G, Ayala-varela F, Latella I. A Phylogenetic, Biogeographic, and Taxonomic study of all Extant Species of Anolis (Squamata; Iguanidae). Syst Biol 2017; 66:663-697. [DOI: 10.1093/sysbio/syx029] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 01/21/2017] [Indexed: 11/13/2022] Open
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Silvestro D, Zizka A, Bacon CD, Cascales-Miñana B, Salamin N, Antonelli A. Fossil biogeography: a new model to infer dispersal, extinction and sampling from palaeontological data. Philos Trans R Soc Lond B Biol Sci 2016; 371:20150225. [PMID: 26977065 PMCID: PMC4810818 DOI: 10.1098/rstb.2015.0225] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Methods in historical biogeography have revolutionized our ability to infer the evolution of ancestral geographical ranges from phylogenies of extant taxa, the rates of dispersals, and biotic connectivity among areas. However, extant taxa are likely to provide limited and potentially biased information about past biogeographic processes, due to extinction, asymmetrical dispersals and variable connectivity among areas. Fossil data hold considerable information about past distribution of lineages, but suffer from largely incomplete sampling. Here we present a new dispersal–extinction–sampling (DES) model, which estimates biogeographic parameters using fossil occurrences instead of phylogenetic trees. The model estimates dispersal and extinction rates while explicitly accounting for the incompleteness of the fossil record. Rates can vary between areas and through time, thus providing the opportunity to assess complex scenarios of biogeographic evolution. We implement the DES model in a Bayesian framework and demonstrate through simulations that it can accurately infer all the relevant parameters. We demonstrate the use of our model by analysing the Cenozoic fossil record of land plants and inferring dispersal and extinction rates across Eurasia and North America. Our results show that biogeographic range evolution is not a time-homogeneous process, as assumed in most phylogenetic analyses, but varies through time and between areas. In our empirical assessment, this is shown by the striking predominance of plant dispersals from Eurasia into North America during the Eocene climatic cooling, followed by a shift in the opposite direction, and finally, a balance in biotic interchange since the middle Miocene. We conclude by discussing the potential of fossil-based analyses to test biogeographic hypotheses and improve phylogenetic methods in historical biogeography.
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Affiliation(s)
- Daniele Silvestro
- Department of Biological and Environmental Sciences, University of Gothenburg, Carl Skottsbergs gata 22B, Gothenburg 413 19, Sweden Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland
| | - Alexander Zizka
- Department of Biological and Environmental Sciences, University of Gothenburg, Carl Skottsbergs gata 22B, Gothenburg 413 19, Sweden
| | - Christine D Bacon
- Department of Biological and Environmental Sciences, University of Gothenburg, Carl Skottsbergs gata 22B, Gothenburg 413 19, Sweden
| | | | - Nicolas Salamin
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland
| | - Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, Carl Skottsbergs gata 22B, Gothenburg 413 19, Sweden Gothenburg Botanical Garden, Carl Skottsbergs gata 22A, Gothenburg 413 19, Sweden
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19
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Jablonski D, Huang S, Roy K, Valentine JW. Shaping the Latitudinal Diversity Gradient: New Perspectives from a Synthesis of Paleobiology and Biogeography. Am Nat 2016; 189:1-12. [PMID: 28035884 DOI: 10.1086/689739] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
An impediment to understanding the origin and dynamics of the latitudinal diversity gradient (LDG)-the most pervasive large-scale biotic pattern on Earth-has been the tendency to focus narrowly on a single causal factor when a more synthetic, integrative approach is needed. Using marine bivalves as a model system and drawing on other systems where possible, we review paleobiologic and biogeographic support for two supposedly opposing views, that the LDG is shaped primarily by (a) local environmental factors that determine the number of species and higher taxa at a given latitude (in situ hypotheses) or (b) the entry of lineages arising elsewhere into a focal region (spatial dynamics hypotheses). Support for in situ hypotheses includes the fit of present-day diversity trends in many clades to such environmental factors as temperature and the correlation of extinction intensities in Pliocene bivalve faunas with net regional temperature changes. Support for spatial dynamics hypotheses includes the age-frequency distribution of bivalve genera across latitudes, which is consistent with an out-of-the-tropics dynamic, as are the higher species diversities in temperate southeastern Australia and southeastern Japan than in the tropical Caribbean. Thus, both in situ and spatial dynamics processes must shape the bivalve LDG and are likely to operate in other groups as well. The relative strengths of the two processes may differ among groups showing similar LDGs, but dissecting their effects will require improved methods of integrating fossil data with molecular phylogenies. We highlight several potential research directions and argue that many of the most dramatic biotic patterns, past and present, are likely to have been generated by diverse, mutually reinforcing drivers.
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20
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Bromham L. Testing hypotheses in macroevolution. STUDIES IN HISTORY AND PHILOSOPHY OF SCIENCE 2016; 55:47-59. [PMID: 26774069 DOI: 10.1016/j.shpsa.2015.08.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 07/02/2015] [Accepted: 08/17/2015] [Indexed: 06/05/2023]
Abstract
Experimental manipulation of microevolution (changes in frequency of heritable traits in populations) has shed much light on evolutionary processes. But many evolutionary processes occur on scales that are not amenable to experimental manipulation. Indeed, one of the reasons that macroevolution (changes in biodiversity over time, space and lineages) has sometimes been a controversial topic is that processes underlying the generation of biological diversity generally operate at scales that are not open to direct observation or manipulation. Macroevolutionary hypotheses can be tested by using them to generate predictions then asking whether observations from the biological world match those predictions. Each study that identifies significant correlations between evolutionary events, processes or outcomes can generate new predictions that can be further tested with different datasets, allowing a cumulative process that may narrow down on plausible explanations, or lead to rejection of other explanations as inconsistent or unsupported. A similar approach can be taken even for unique events, for example by comparing patterns in different regions, lineages, or time periods. I will illustrate the promise and pitfalls of these approaches using a range of examples, and discuss the problems of inferring causality from significant evolutionary associations.
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Affiliation(s)
- Lindell Bromham
- Centre for Macroevolution and Macroecology, Research School of Biology, Australian National University, Canberra, ACT 0200, Australia.
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21
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Guevara JE, Damasco G, Baraloto C, Fine PVA, Peñuela MC, Castilho C, Vincentini A, Cárdenas D, Wittmann F, Targhetta N, Phillips O, Stropp J, Amaral I, Maas P, Monteagudo A, Jimenez EM, Thomas R, Brienen R, Duque Á, Magnusson W, Ferreira C, Honorio E, Almeida Matos F, Arevalo FR, Engel J, Petronelli P, Vasquez R, Steege H. Low Phylogenetic Beta Diversity and Geographic Neo‐endemism in Amazonian White‐sand Forests. Biotropica 2016. [DOI: 10.1111/btp.12298] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Juan Ernesto Guevara
- Department of Integrative Biology University of California Berkeley CA 94720‐3140 U.S.A
- Museo Ecuatoriano de Ciencias Naturales Quito Ecuador
| | - Gabriel Damasco
- Department of Integrative Biology University of California Berkeley CA 94720‐3140 U.S.A
| | - Christopher Baraloto
- UMR Ecologie des Forêts de Guyane Institut National de la Recherche Agronomique (INRA) Kourou French Guiana
| | - Paul V. A. Fine
- Department of Integrative Biology University of California Berkeley CA 94720‐3140 U.S.A
| | | | - Carolina Castilho
- EMBRAPA Centro de Pesquisa Agroflorestal de Roraima Boa Vista Brazil
| | - Alberto Vincentini
- Instituto Nacional de Pesquisas da Amazônia‐INPA Coordenação de Pesquisas em Ecologia Manaos Brazil
| | - Dairón Cárdenas
- SINCHI Herbario Amazónico Colombiano‐COAH Calle 20 No.5‐44 Bogotá Colombia
| | - Florian Wittmann
- Department of Biochemistry Max Planck Institute for Chemistry Hahn Meitner Weg 1 55128 Mainz Germany
| | - Natalia Targhetta
- Instituto Nacional de Pesquisas da Amazônia‐INPA Coordenação de Pesquisas em Ecologia Manaos Brazil
| | | | - Juliana Stropp
- Institute of Biological and Health Sciences Federal University of Alagoas Maceió AL Brazil
| | - Ieda Amaral
- Instituto Nacional de Pesquisas da Amazônia–INPA Projeto TEAM‐Manaus Manaus Brazil
| | - Paul Maas
- Department of Botany Naturalis Biodiversity Center Leiden The Netherlands
| | - Abel Monteagudo
- Missouri Botanical Garden 4344 Shaw Blvd. St. Louis MO 63110 U.S.A
| | | | - Rachel Thomas
- Iwokrama International Programme for Rainforest Conservation 77 High Street Kingston Georgetown Guiana
| | - Roel Brienen
- School of Geography University of Leeds Leeds U.K
| | - Álvaro Duque
- Departamento de Ciencias Forestales Universidad Nacional de Colombia Medellín Colombia
| | - William Magnusson
- Instituto Nacional de Pesquisas da Amazônia‐INPA Coordenação de Pesquisas em Ecologia Manaos Brazil
| | - Cid Ferreira
- Instituto Nacional de Pesquisas da Amazônia‐INPA Coordenação de Pesquisas em Ecologia Manaos Brazil
| | - Eurídice Honorio
- Instituto de Investigaciones de la Amazonía Peruana Iquitos Peru
| | - Francisca Almeida Matos
- Instituto Nacional de Pesquisas da Amazônia‐INPA Coordenação de Pesquisas em Ecologia Manaos Brazil
| | | | - Julien Engel
- UMR Ecologie des Forêts de Guyane Institut National de la Recherche Agronomique (INRA) Kourou French Guiana
| | - Pascal Petronelli
- UMR Ecologie des Forêts de Guyane Institut National de la Recherche Agronomique (INRA) Kourou French Guiana
| | - Rodolfo Vasquez
- Missouri Botanical Garden 4344 Shaw Blvd. St. Louis MO 63110 U.S.A
| | - Hans Steege
- Naturalis Biodiversity Center Leiden the Netherlands
- Ecology and Biodiversity Group Utrecht University Utrecht The Netherlands
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22
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Bromham L, Hua X, Cardillo M. Detecting Macroevolutionary Self-Destruction from Phylogenies. Syst Biol 2015; 65:109-27. [PMID: 26454872 DOI: 10.1093/sysbio/syv062] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Accepted: 08/18/2015] [Indexed: 12/14/2022] Open
Abstract
Phylogenetic analyses have lent support to the concept of lineage selection: that biological lineages can have heritable traits that influence their capacity to persist and diversify, and thereby affect their representation in biodiversity. While many discussions have focused on "positive" lineage selection, where stably heritable properties of lineages enhance their diversification rate, there are also intriguing examples that seem to represent "negative" lineage selection, where traits reduce the likelihood that a lineage will persist or speciate. In this article, we test whether a particular pattern of negative lineage selection is detectable from the distributions of the trait on a phylogeny. "Self-destructive" traits are those that arise often but then disappear again because they confer either a raised extinction rate or they are prone to a high rate of trait loss. For such a trait, the reconstructed origins will tend to be dispersed across the tips of the phylogeny, rather than defining large clades of related lineages that all share the trait. We examine the utility of four possible measures of "tippiness" as potential indicators of macroevolutionary self-destruction, applying them to phylogenies on which trait evolution has been simulated under different combinations of parameters for speciation, extinction, trait gain, and trait loss. We use an efficient simulation approach that starts with the required number of tips with and without the trait and uses a model to work "backwards" to construct different possible trees that result in that set of tips. We then apply these methods to a number of case studies: salt tolerance in grasses, color polymorphism in birds of prey, and selfing in nightshades. We find that the relative age of species, measured from tip length, can indicate a reduced speciation rate but does not identify traits that increase the extinction rate or the trait loss rate. We show that it is possible to detect cases of macroevolutionary self-destruction by considering the number of tips with the trait that arise from each inferred origin, and the degree to which the trait is scattered across the phylogeny. These metrics, and the methods we present, may be useful for testing macroevolutionary hypotheses from phylogenetic patterns.
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Affiliation(s)
- Lindell Bromham
- Centre for Macroevolution and Macroecology, Division of Ecology, Evolution and Genetics, Research School of Biology, Australian National University, Canberra, ACT 0200, Australia
| | - Xia Hua
- Centre for Macroevolution and Macroecology, Division of Ecology, Evolution and Genetics, Research School of Biology, Australian National University, Canberra, ACT 0200, Australia
| | - Marcel Cardillo
- Centre for Macroevolution and Macroecology, Division of Ecology, Evolution and Genetics, Research School of Biology, Australian National University, Canberra, ACT 0200, Australia
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Islands contribute disproportionately high amounts of evolutionary diversity in passerine birds. Nat Commun 2015; 6:8538. [PMID: 26437360 PMCID: PMC4600755 DOI: 10.1038/ncomms9538] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 09/01/2015] [Indexed: 11/09/2022] Open
Abstract
Island systems generally have fewer species than continental areas due to their small size and geographical isolation. Low island diversity reduces the possibility of exportation of island lineages and island systems are not thought to have a major influence on the build-up of continental diversity. However, the view that islands represent the end of the colonization road has recently been challenged and islands do represent the origin of some specific continental lineages. Here we assess the net contribution of island systems to global diversity patterns of passerine birds, using a complete phylogeny (5,949 species), biogeographical regionalization and null-model comparisons. We show that, in contrast to major continental regions, island regions export relatively more evolutionary lineages than would be expected based on current distributional patterns. This result challenges a central paradigm in island biogeography and changes our perception of the relative importance of islands for the build-up of global diversity.
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Pontarp M, Ripa J, Lundberg P. The Biogeography of Adaptive Radiations and the Geographic Overlap of Sister Species. Am Nat 2015; 186:565-81. [PMID: 26655771 DOI: 10.1086/683260] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The biogeography of speciation and what can be learned about the past mode of speciation from current biogeography of sister species are recurrent problems in evolution. We used a trait- and individual-based, eco-evolutionary model to simulate adaptive radiations and recorded the geographical overlap of species during and after evolutionary branching (speciation). We compared the spatial overlap among sister species in the fully saturated community with the overlap at the speciation event. The mean geographic overlap at speciation varied continuously from complete (sympatry) to none (allopatry), depending on local and regional environmental heterogeneity and the rate of dispersal. The distribution of overlap was, however, in some cases considerably bimodal. This tendency was most expressed at large values of regional heterogeneity, corresponding to sharp environmental contrasts. The mean geographic overlap also varied during the course of a radiation, sometimes with a consistent negative trend over time. The speciations that resulted in currently observable end community sister species were therefore not an unbiased sample of all speciations throughout the radiation. Postspeciation range shifts (causing increased overlap) occurred most frequently when dispersal was high or when local habitat heterogeneity was low. Our results help us understand how the patterns of geographic mode of speciation emerge. We also show the difficulty in inferring the geographical speciation mode from phylogenies and the biogeography of extant species.
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Affiliation(s)
- Mikael Pontarp
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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Crame JA, Beu AG, Ineson JR, Francis JE, Whittle RJ, Bowman VC. The Early Origin of the Antarctic Marine Fauna and Its Evolutionary Implications. PLoS One 2014; 9:e114743. [PMID: 25493546 PMCID: PMC4262473 DOI: 10.1371/journal.pone.0114743] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 11/13/2014] [Indexed: 12/02/2022] Open
Abstract
The extensive Late Cretaceous – Early Paleogene sedimentary succession of Seymour Island, N.E. Antarctic Peninsula offers an unparalleled opportunity to examine the evolutionary origins of a modern polar marine fauna. Some 38 modern Southern Ocean molluscan genera (26 gastropods and 12 bivalves), representing approximately 18% of the total modern benthic molluscan fauna, can now be traced back through at least part of this sequence. As noted elsewhere in the world, the balance of the molluscan fauna changes sharply across the Cretaceous – Paleogene (K/Pg) boundary, with gastropods subsequently becoming more diverse than bivalves. A major reason for this is a significant radiation of the Neogastropoda, which today forms one of the most diverse clades in the sea. Buccinoidea is the dominant neogastropod superfamily in both the Paleocene Sobral Formation (SF) (56% of neogastropod genera) and Early - Middle Eocene La Meseta Formation (LMF) (47%), with the Conoidea (25%) being prominent for the first time in the latter. This radiation of Neogastropoda is linked to a significant pulse of global warming that reached at least 65°S, and terminates abruptly in the upper LMF in an extinction event that most likely heralds the onset of global cooling. It is also possible that the marked Early Paleogene expansion of neogastropods in Antarctica is in part due to a global increase in rates of origination following the K/Pg mass extinction event. The radiation of this and other clades at ∼65°S indicates that Antarctica was not necessarily an evolutionary refugium, or sink, in the Early – Middle Eocene. Evolutionary source – sink dynamics may have been significantly different between the Paleogene greenhouse and Neogene icehouse worlds.
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Affiliation(s)
- J. Alistair Crame
- British Antarctic Survey, Natural Environment Research Council, Cambridge, United Kingdom
- * E-mail:
| | | | - Jon R. Ineson
- Geological Survey of Denmark and Greenland, Copenhagen, Denmark
| | - Jane E. Francis
- British Antarctic Survey, Natural Environment Research Council, Cambridge, United Kingdom
| | - Rowan J. Whittle
- British Antarctic Survey, Natural Environment Research Council, Cambridge, United Kingdom
| | - Vanessa C. Bowman
- British Antarctic Survey, Natural Environment Research Council, Cambridge, United Kingdom
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Relict species: a relict concept? Trends Ecol Evol 2014; 29:655-63. [PMID: 25454211 DOI: 10.1016/j.tree.2014.10.002] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2011] [Revised: 10/01/2014] [Accepted: 10/01/2014] [Indexed: 12/22/2022]
Abstract
Relict species have always beguiled evolutionary biologists and biogeographers, who often view them as fascinating 'living fossils' or remnants of old times. Consequently, they are believed to provide interesting and important information on a vanished past and are used to understand the evolution of clades and biotas. The information that relicts provide can, however, be misleading and overemphasised when it is not remembered that they belong to groups or biotas that are mostly extinct. For example, relict species imply regional extinctions and, for this reason, they cannot simultaneously provide evidence of local biota permanence. Here we consider carefully misconceptions about relict species and highlight more clearly their evolutionary and biogeographical significance.
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Rolland J, Condamine FL, Jiguet F, Morlon H. Faster speciation and reduced extinction in the tropics contribute to the Mammalian latitudinal diversity gradient. PLoS Biol 2014; 12:e1001775. [PMID: 24492316 PMCID: PMC3904837 DOI: 10.1371/journal.pbio.1001775] [Citation(s) in RCA: 170] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Accepted: 12/11/2013] [Indexed: 02/01/2023] Open
Abstract
Jonathan Rolland and colleagues show that the gradient of increased mammalian diversity towards the tropics is driven by both faster speciation and reduced extinction. The increase in species richness from the poles to the tropics, referred to as the latitudinal diversity gradient, is one of the most ubiquitous biodiversity patterns in the natural world. Although understanding how rates of speciation and extinction vary with latitude is central to explaining this pattern, such analyses have been impeded by the difficulty of estimating diversification rates associated with specific geographic locations. Here, we use a powerful phylogenetic approach and a nearly complete phylogeny of mammals to estimate speciation, extinction, and dispersal rates associated with the tropical and temperate biomes. Overall, speciation rates are higher, and extinction rates lower, in the tropics than in temperate regions. The diversity of the eight most species-rich mammalian orders (covering 92% of all mammals) peaks in the tropics, except that of the Lagomorpha (hares, rabbits, and pikas) reaching a maxima in northern-temperate regions. Latitudinal patterns in diversification rates are strikingly consistent with these diversity patterns, with peaks in species richness associated with low extinction rates (Primates and Lagomorpha), high speciation rates (Diprotodontia, Artiodactyla, and Soricomorpha), or both (Chiroptera and Rodentia). Rates of range expansion were typically higher from the tropics to the temperate regions than in the other direction, supporting the “out of the tropics” hypothesis whereby species originate in the tropics and disperse into higher latitudes. Overall, these results suggest that differences in diversification rates have played a major role in shaping the modern latitudinal diversity gradient in mammals, and illustrate the usefulness of recently developed phylogenetic approaches for understanding this famous yet mysterious pattern. Why are there more species in the tropics? This question has fascinated ecologists and evolutionary biologists for decades, generating hundreds of hypotheses, yet basic questions remain: Are rates of speciation higher in the tropics? Are rates of extinction higher in temperate regions? Do the tropics act as a source of diversity for temperate regions? We estimated rates of speciation, extinction, and range expansion associated with mammals living in tropical and temperate regions, using an almost complete mammalian phylogeny. Contrary to what has been suggested before for this class of vertebrates, we found that diversification rates are strikingly consistent with diversity patterns, with latitudinal peaks in species richness being associated with high speciation rates, low extinction rates, or both, depending on the mammalian order (rodents, bats, primates, etc.). We also found evidence for an asymmetry in range expansion, with more expansion “out of” than “into” the tropics. Taken together, these results suggest that tropical regions are not only a reservoir of biodiversity, but also the main place where biodiversity is generated.
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Affiliation(s)
- Jonathan Rolland
- CNRS, UMR 7641 Centre de Mathématiques Appliquées (Ecole Polytechnique), Palaiseau, France
- UMR 7204 MNHN–CNRS–UPMC Centre d'Ecologie et de Sciences de la Conservation, Museum National d'Histoire Naturelle, CP51, Paris, France
- * E-mail: (J.R.); (H.M.)
| | - Fabien L. Condamine
- CNRS, UMR 7641 Centre de Mathématiques Appliquées (Ecole Polytechnique), Palaiseau, France
| | - Frederic Jiguet
- UMR 7204 MNHN–CNRS–UPMC Centre d'Ecologie et de Sciences de la Conservation, Museum National d'Histoire Naturelle, CP51, Paris, France
| | - Hélène Morlon
- CNRS, UMR 7641 Centre de Mathématiques Appliquées (Ecole Polytechnique), Palaiseau, France
- * E-mail: (J.R.); (H.M.)
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Svensson EI, Waller JT. Ecology and Sexual Selection: Evolution of Wing Pigmentation in Calopterygid Damselflies in Relation to Latitude, Sexual Dimorphism, and Speciation. Am Nat 2013; 182:E174-95. [DOI: 10.1086/673206] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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29
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Out of the tropics, but how? Fossils, bridge species, and thermal ranges in the dynamics of the marine latitudinal diversity gradient. Proc Natl Acad Sci U S A 2013; 110:10487-94. [PMID: 23759748 DOI: 10.1073/pnas.1308997110] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Latitudinal diversity gradients are underlain by complex combinations of origination, extinction, and shifts in geographic distribution and therefore are best analyzed by integrating paleontological and neontological data. The fossil record of marine bivalves shows, in three successive late Cenozoic time slices, that most clades (operationally here, genera) tend to originate in the tropics and then expand out of the tropics (OTT) to higher latitudes while retaining their tropical presence. This OTT pattern is robust both to assumptions on the preservation potential of taxa and to taxonomic revisions of extant and fossil species. Range expansion of clades may occur via "bridge species," which violate climate-niche conservatism to bridge the tropical-temperate boundary in most OTT genera. Substantial time lags (∼5 Myr) between the origins of tropical clades and their entry into the temperate zone suggest that OTT events are rare on a per-clade basis. Clades with higher diversification rates within the tropics are the most likely to expand OTT and the most likely to produce multiple bridge species, suggesting that high speciation rates promote the OTT dynamic. Although expansion of thermal tolerances is key to the OTT dynamic, most latitudinally widespread species instead achieve their broad ranges by tracking widespread, spatially-uniform temperatures within the tropics (yielding, via the nonlinear relation between temperature and latitude, a pattern opposite to Rapoport's rule). This decoupling of range size and temperature tolerance may also explain the differing roles of species and clade ranges in buffering species from background and mass extinctions.
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30
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Condamine FL, Rolland J, Morlon H. Macroevolutionary perspectives to environmental change. Ecol Lett 2013; 16 Suppl 1:72-85. [DOI: 10.1111/ele.12062] [Citation(s) in RCA: 183] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Revised: 10/10/2012] [Accepted: 12/04/2012] [Indexed: 11/28/2022]
Affiliation(s)
- Fabien L. Condamine
- CNRS; UMR 7641 Centre de Mathématiques Appliquées (École Polytechnique); Route de Saclay; 91128 Palaiseau; France
| | - Jonathan Rolland
- CNRS; UMR 7641 Centre de Mathématiques Appliquées (École Polytechnique); Route de Saclay; 91128 Palaiseau; France
| | - Hélène Morlon
- CNRS; UMR 7641 Centre de Mathématiques Appliquées (École Polytechnique); Route de Saclay; 91128 Palaiseau; France
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31
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Abstract
The widespread assumption that the origin of polar marine faunas is linked to the onset of major global cooling in the Late Eocene-Early Oligocene is being increasingly challenged. The Antarctic fossil record in particular is suggesting that some modern Southern Ocean taxa may have Early Eocene or even Paleocene origins, i.e. well within the Early Cenozoic greenhouse world. A global analysis of one of the largest marine clades at the present day, the Neogastropoda, indicates that not only is there a decrease in the number of species from the tropics to the poles but also a decrease in the evenness of their distribution. A small number of neogastropod families with predominantly generalist trophic strategies at both poles points to the key role of seasonality in structuring the highest latitude marine assemblages. A distinct latitudinal gradient in seasonality is temperature-invariant and would have operated through periods of global warmth such as the Early Cenozoic. To test this concept a second global analysis was undertaken of earliest Cenozoic (Paleocene) neogastropods and this does indeed show a certain degree of faunal differentiation at both poles. The Buccinidae, s.l. is especially well developed at this time, and this is a major generalist taxon at the present day. There is an element of asymmetry associated with this development of Paleocene polar faunas in that those in the south are more strongly differentiated than their northern counterparts; this can in turn be linked to the already substantial isolation of the southern high latitudes. The key role of seasonality in the formation of polar marine faunas has implications for contemporary ecosystem structure and stability.
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Affiliation(s)
- J Alistair Crame
- British Antarctic Survey, Natural Environment Research Council, Cambridge, United Kingdom.
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32
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Lumbsch T, Kantvilas G, Parnmen S. Molecular data support placement of Cameronia in Ostropomycetidae (Lecanoromycetes, Ascomycota). MycoKeys 2012. [DOI: 10.3897/mycokeys.5.4140] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Carnicer J, Brotons L, Stefanescu C, Peñuelas J. Biogeography of species richness gradients: linking adaptive traits, demography and diversification. Biol Rev Camb Philos Soc 2011; 87:457-79. [PMID: 22129434 DOI: 10.1111/j.1469-185x.2011.00210.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Here we review how adaptive traits contribute to the emergence and maintenance of species richness gradients through their influence on demographic and diversification processes. We start by reviewing how demographic dynamics change along species richness gradients. Empirical studies show that geographical clines in population parameters and measures of demographic variability are frequent along latitudinal and altitudinal gradients. Demographic variability often increases at the extremes of regional species richness gradients and contributes to shape these gradients. Available studies suggest that adaptive traits significantly influence demographic dynamics, and set the limits of species distributions. Traits related to thermal tolerance, resource use, phenology and dispersal seem to play a significant role. For many traits affecting demography and/or diversification processes, complex mechanistic approaches linking genotype, phenotype and fitness are becoming progressively available. In several taxa, species can be distributed along adaptive trait continuums, i.e. a main axis accounting for the bulk of inter-specific variation in some correlated adaptive traits. It is shown that adaptive trait continuums can provide useful mechanistic frameworks to explain demographic dynamics and diversification in species richness gradients. Finally, we review the existence of sequences of adaptive traits in phylogenies, the interactions of adaptive traits and community context, the clinal variation of traits across geographical gradients, and the role of adaptive traits in determining the history of dispersal and diversification of clades. Overall, we show that the study of demographic and evolutionary mechanisms that shape species richness gradients clearly requires the explicit consideration of adaptive traits. To conclude, future research lines and trends in the field are briefly outlined.
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Affiliation(s)
- Jofre Carnicer
- Community and Conservation Ecology Group, Centre for Life Sciences, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.
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35
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Goldberg EE, Lancaster LT, Ree RH. Phylogenetic inference of reciprocal effects between geographic range evolution and diversification. Syst Biol 2011; 60:451-65. [PMID: 21551125 DOI: 10.1093/sysbio/syr046] [Citation(s) in RCA: 240] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Geographic characters--traits describing the spatial distribution of a species-may both affect and be affected by processes associated with lineage birth and death. This is potentially confounding to comparative analyses of species distributions because current models do not allow reciprocal interactions between the evolution of ranges and the growth of phylogenetic trees. Here, we introduce a likelihood-based approach to estimating region-dependent rates of speciation, extinction, and range evolution from a phylogeny, using a new model in which these processes are interdependent. We demonstrate the method with simulation tests that accurately recover parameters relating to the mode of speciation and source-sink dynamics. We then apply it to the evolution of habitat occupancy in Californian plant communities, where we find higher rates of speciation in chaparral than in forests and evidence for expanding habitat tolerances.
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Affiliation(s)
- Emma E Goldberg
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA.
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36
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Heim NA, Peters SE. Regional environmental breadth predicts geographic range and longevity in fossil marine genera. PLoS One 2011; 6:e18946. [PMID: 21573226 PMCID: PMC3087726 DOI: 10.1371/journal.pone.0018946] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2010] [Accepted: 03/25/2011] [Indexed: 11/18/2022] Open
Abstract
Background Geographic range is a good indicator of extinction susceptibility in fossil marine species and higher taxa. The widely-recognized positive correlation between geographic range and taxonomic duration is typically attributed to either accumulating geographic range with age or an extinction buffering effect, whereby cosmopolitan taxa persist longer because they are reintroduced by dispersal from remote source populations after local extinction. The former hypothesis predicts that all taxa within a region should have equal probabilities of extinction regardless of global distributions while the latter predicts that cosmopolitan genera will have greater survivorship within a region than endemics within the same region. Here we test the assumption that all taxa within a region have equal likelihoods of extinction. Methodology/Principal Findings We use North American and European occurrences of marine genera from the Paleobiology Database and the areal extent of marine sedimentary cover in North America to show that endemic and cosmopolitan fossil marine genera have significantly different range-duration relationships and that broad geographic range and longevity are both predicted by regional environmental breadth. Specifically, genera that occur outside of the focal region are significantly longer lived and have larger geographic ranges and environmental breadths within the focal region than do their endemic counterparts, even after controlling for differences in sampling intensity. Analyses of the number of paleoenvironmental zones occupied by endemic and cosmopolitan genera suggest that the number of paleoenvironmental zones occupied is a key factor of geographic range that promotes genus survivorship. Conclusions/Significance Wide environmental tolerances within a single region predict both broad geographic range and increased longevity in marine genera over evolutionary time. This result provides a specific driving mechanism for the spatial and temporal distributions of marine genera at regional and global scales and is consistent with the niche-breadth hypothesis operating on macroevolutionary timescales.
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Affiliation(s)
- Noel A Heim
- Department of Geoscience, University of Wisconsin-Madison, Madison, Wisconsin, United States of America.
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37
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Weir JT, Price TD. Limits to Speciation Inferred from Times to Secondary Sympatry and Ages of Hybridizing Species along a Latitudinal Gradient. Am Nat 2011; 177:462-9. [DOI: 10.1086/658910] [Citation(s) in RCA: 122] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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38
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Anacker BL, Whittall JB, Goldberg EE, Harrison SP. Origins and consequences of serpentine endemism in the California flora. Evolution 2010; 65:365-76. [PMID: 20812977 DOI: 10.1111/j.1558-5646.2010.01114.x] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Habitat specialization plays an important role in the creation and loss of biodiversity over ecological and evolutionary time scales. In California, serpentine soils have a distinctive flora, with 246 serpentine habitat specialists (i.e., endemics). Using molecular phylogenies for 23 genera containing 784 taxa and 51 endemics, we infer few transitions out of the endemic state, which is shown by an analysis of transition rates to simply reflect the low frequency of endemics (i.e., reversal rates were high). The finding of high reversal rates, but a low number of reversals, is consistent with the widely hypothesized trade-off between serpentine tolerance and competitive ability, under which serpentine endemics are physiologically capable of growing in less-stressful habitats but competitors lead to their extirpation. Endemism is also characterized by a decrease in speciation and extinction rates and a decrease in the overall diversification rate. We also find that tolerators (species with nonserpentine and serpentine populations) undergo speciation in serpentine habitats to give rise to new serpentine endemics but are several times more likely to lose serpentine populations to produce serpentine-intolerant taxa. Finally, endemics were younger on average than nonendemics, but this alone does not explain their low diversification.
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Affiliation(s)
- Brian L Anacker
- Department of Environmental Science and Policy, One Shields Avenue, University of California, Davis, California 95616, USA.
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39
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Luna-Vega I, Magallón S. Phylogenetic Composition of Angiosperm Diversity in the Cloud Forests of Mexico. Biotropica 2010. [DOI: 10.1111/j.1744-7429.2009.00606.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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40
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Roy K, Hunt G, Jablonski D, Krug AZ, Valentine JW. A macroevolutionary perspective on species range limits. Proc Biol Sci 2009; 276:1485-93. [PMID: 19324820 DOI: 10.1098/rspb.2008.1232] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Understanding the factors that determine the geographic range limits of species is important for many questions in ecology, evolution and conservation biology. These limits arise from complex interactions among ecology and dispersal ability of species and the physical environment, but many of the underlying traits can be conserved among related species and clades. Thus, the range limits of species are likely to be influenced by their macroevolutionary history. Using palaeontological and biogeographic data for marine bivalves, we find that the range limits of genera are significantly related to their constituent species richness, but the effects of age are weak and inconsistent. In addition, we find a significant phylogenetic signal in the range limits at both genus and family levels, although the strength of this effect shows interoceanic variation. This phylogenetic conservatism of range limits gives rise to an evolutionary pattern where wide-ranging lineages have clusters of species within the biogeographic provinces, with a few extending across major boundaries.
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Affiliation(s)
- Kaustuv Roy
- Section of Ecology, Behavior and Evolution, University of California San Diego, La Jolla, CA 92093-0116, USA.
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41
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Krug AZ, Jablonski D, Valentine JW, Roy K. Generation of Earth's first-order biodiversity pattern. ASTROBIOLOGY 2009; 9:113-124. [PMID: 19215204 DOI: 10.1089/ast.2008.0253] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The first-order biodiversity pattern on Earth today and at least as far back as the Paleozoic is the latitudinal diversity gradient (LDG), a decrease in richness of species and higher taxa from the equator to the poles. LDGs are produced by geographic trends in origination, extinction, and dispersal over evolutionary timescales, so that analyses of static patterns will be insufficient to reveal underlying processes. The fossil record of marine bivalve genera, a model system for the analysis of biodiversity dynamics over large temporal and spatial scales, shows that an origination and range-expansion gradient plays a major role in generating the LDG. Peak origination rates and peak diversities fall within the tropics, with range expansion out of the tropics the predominant spatial dynamic thereafter. The origination-diversity link occurs even in a "contrarian" group whose diversity peaks at midlatitudes, an exception proving the rule that spatial variations in origination are key to latitudinal diversity patterns. Extinction rates are lower in polar latitudes (> or =60 degrees ) than in temperate zones and thus cannot create the observed gradient alone. They may, however, help to explain why origination and immigration are evidently damped in higher latitudes. We suggest that species require more resources in higher latitudes, for the seasonality of primary productivity increases by more than an order of magnitude from equatorial to polar regions. Higher-latitude species are generalists that, unlike potential immigrants, are adapted to garner the large share of resources required for incumbency in those regions. When resources are opened up by extinctions, lineages spread chiefly poleward and chiefly through speciation.
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Affiliation(s)
- Andrew Z Krug
- Department of Geophysical Sciences, University of Chicago, Chicago, Illinois, USA.
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42
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Purvis A. Phylogenetic Approaches to the Study of Extinction. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2008. [DOI: 10.1146/annurev-ecolsys-063008-102010] [Citation(s) in RCA: 127] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Species extinction is both a key process throughout the history of life and a pressing concern in the conservation of present-day biodiversity. These two facets have largely been studied by separate communities using different approaches. This article illustrates with examples some of the ways that considering the evolutionary relationships among species—phylogenies—has helped the study of both past and present species extinction. The focus is on three topics: extinction rates and severities, phylogenetic nonrandomness of extinction, and the testing of hypotheses relating extinction-proneness to attributes of organisms or species. Phylogenetic and taxic approaches to extinction have not fully fused, largely because of the difficulties of relating discrete taxa to the underlying continuity of phylogeny. Phylogeny must be considered in comparative tests of hypotheses about extinction, but care must be taken to avoid overcorrecting for phylogenetic nonindependence among taxa.
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Affiliation(s)
- Andy Purvis
- Division of Biology, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, United Kingdom
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43
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Coates MI, Ruta M, Friedman M. Ever Since Owen: Changing Perspectives on the Early Evolution of Tetrapods. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2008. [DOI: 10.1146/annurev.ecolsys.38.091206.095546] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The traditional notion of a gap between fishes and amphibians has been closed by a wealth of fish-like fossil tetrapods, many discovered since the mid 1980s. This review summarizes these discoveries and explores their significance relative to changing ideas about early tetrapod phylogeny, biogeography, and ecology. Research emphasis can now shift to broader-based questions, including the whole of the early tetrapod radiation, from the divergence from other lobed-finned fishes to the origins of modern amphibians and amniotes. The fish-to-tetrapod morphological transition occurred within the Upper Devonian; the divergence of modern tetrapod groups is an Early Carboniferous event. Modern tetrapods emerged in the aftermath of one of the five major extinction episodes in the fossil record, but the earlier Devonian tetrapod radiation is not well understood. Tetrapod limbs, paired fins, and comparative developmental data are reviewed; again, research emphasis needs to change to explore the origins of tetrapod diversity.
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Affiliation(s)
- Michael I. Coates
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, Illinois 60637
- Committee on Evolutionary Biology, University of Chicago, Chicago, Illinois 60637
| | - Marcello Ruta
- Department of Earth Sciences, University of Bristol, Wills Memorial Building, Queen's Road, Bristol BS8 1RJ, United Kingdom
| | - Matt Friedman
- Committee on Evolutionary Biology, University of Chicago, Chicago, Illinois 60637
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44
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Krug AZ, Jablonski D, Valentine JW. Species-genus ratios reflect a global history of diversification and range expansion in marine bivalves. Proc Biol Sci 2008; 275:1117-23. [PMID: 18270156 DOI: 10.1098/rspb.2007.1729] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The distribution of marine bivalve species among genera and higher taxa takes the form of the classic hollow curve, wherein few lineages are species rich and many are species poor. The distribution of species among genera (S/G ratio) varies with latitude, with temperate S/G's falling within the null expectation, and tropical and polar S/G's exceeding it. Here, we test several hypotheses for this polar overdominance in the species richness of small numbers of genera. We find a significant positive correlation between the latitudinal range of a genus and its species richness, both globally and within regions. Genus age and species richness are also positively related, but this relationship breaks down when the analysis is limited to genera endemic to climate zones or with narrow latitudinal ranges. The data suggest a link between speciation and range-expansion, with genera expanding out of the tropical latitudinal bins tending to speciate more prolifically, both globally and regionally. These genera contain more species within climate zones than taxa endemic to that zone. Range expansion thus appears to be fundamentally coupled with speciation, producing the skewed distribution of species among genera, both globally and regionally, whereas clade longevity is achieved through extinction -- resistance conferred by broad geographical ranges.
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Affiliation(s)
- Andrew Z Krug
- Department of Geophysical Sciences, University of Chicago, Chicago, IL 60637, USA.
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45
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Colloquium paper: extinction and the spatial dynamics of biodiversity. Proc Natl Acad Sci U S A 2008; 105 Suppl 1:11528-35. [PMID: 18695229 DOI: 10.1073/pnas.0801919105] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The fossil record amply shows that the spatial fabric of extinction has profoundly shaped the biosphere; this spatial dimension provides a powerful context for integration of paleontological and neontological approaches. Mass extinctions evidently alter extinction selectivity, with many factors losing effectiveness except for a positive relation between survivorship and geographic range at the clade level (confirmed in reanalyses of end-Cretaceous extinction data). This relation probably also holds during "normal" times, but changes both slope and intercept with increasing extinction. The strong geographical component to clade dynamics can obscure causation in the extinction of a feature or a clade, owing to hitchhiking effects on geographic range, so that multifactorial analyses are needed. Some extinctions are spatially complex, and regional extinctions might either reset a diversity ceiling or create a diversification debt open to further diversification or invasion. Evolutionary recoveries also exhibit spatial dynamics, including regional differences in invasibilty, and expansion of clades from the tropics fuels at least some recoveries, as well as biodiversity dynamics during normal times. Incumbency effects apparently correlate more closely with extinction intensities than with standing diversities, so that regions with higher local and global extinctions are more subject to invasion; the latest Cenozoic temperate zones evidently received more invaders than the tropics or poles, but this dynamic could shift dramatically if tropical diversity is strongly depleted. The fossil record can provide valuable insights, and their application to present-day issues will be enhanced by partitioning past and present-day extinctions by driving mechanism rather than emphasizing intensity.
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Arita HT, Vázquez-Domínguez E. The tropics: cradle, museum or casino? A dynamic null model for latitudinal gradients of species diversity. Ecol Lett 2008; 11:653-63. [PMID: 18445032 DOI: 10.1111/j.1461-0248.2008.01197.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Several ecological and evolutionary hypotheses have been proposed to explain the latitudinal diversity gradient (LDG), but a general model for this conspicuous pattern remains elusive. Mid-domain effect (MDE) models generate gradients of species diversity by randomly placing the geographic ranges of species in one- or two-dimensional spaces, thus excluding both evolutionary processes and the effect of contemporary climate. Traditional MDE models are statistical and static because they determine the size of ranges either randomly or based on empirical frequency distributions. Here we present a simple dynamic null model for the LDG that simulates stochastic processes of range shifts, extinction and speciation. The model predicts higher species diversity and higher extinction and speciation rates in the tropics, and a strong influence of range movements in shaping the LDG. These null expectations should be taken into consideration in studies aimed at understanding the many factors that generate latitudinal diversity gradients.
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Affiliation(s)
- Héctor T Arita
- Instituto de Ecología, Universidad Nacional Autónoma de México, Apartado Postal 70-275, CP 04510, México DF, Mexico.
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Pearman PB, Guisan A, Broennimann O, Randin CF. Niche dynamics in space and time. Trends Ecol Evol 2008; 23:149-58. [PMID: 18289716 DOI: 10.1016/j.tree.2007.11.005] [Citation(s) in RCA: 424] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2007] [Revised: 11/09/2007] [Accepted: 11/09/2007] [Indexed: 10/22/2022]
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Carnicer J, Díaz-Delgado R. Geographic differences between functional groups in patterns of bird species richness in North America. ACTA OECOLOGICA-INTERNATIONAL JOURNAL OF ECOLOGY 2008. [DOI: 10.1016/j.actao.2007.12.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Roy K, Goldberg EE. Origination, Extinction, and Dispersal: Integrative Models for Understanding Present‐Day Diversity Gradients. Am Nat 2007; 170 Suppl 2:S71-85. [PMID: 17874386 DOI: 10.1086/519403] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Species diversity gradients seen today are, to a large degree, a product of history. Spatially nonrandom originations, extinctions, and changes in geographic distributions can create gradients in species and higher-taxon richness, but the relative roles of each of these processes remain poorly documented. Existing explanations of diversity gradients have tended to focus on either macroevolutionary or biogeographic processes; integrative models that include both are largely lacking. We used simple models that incorporate origination and extinction rates along with dispersal of taxa between regions to show that dispersal not only affects regional richness patterns but also has a strong influence on the average age of taxa present in a region. Failure to take into account the effects of dispersal can, in principle, lead to biased estimates of diversification rates and potentially wrong conclusions regarding processes driving latitudinal and other gradients in diversity. Thus, it is critical to include the effects of dispersal when formulating and testing hypotheses about the causes of large-scale gradients in diversity. Finally, the model results, in conjunction with the results of existing empirical studies, suggest that the nature of macroevolutionary and biogeographic processes may differ between terrestrial and marine diversity gradients.
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Affiliation(s)
- Kaustuv Roy
- Section of Ecology, Behavior and Evolution, University of California San Diego, La Jolla, California 92093, USA.
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Affiliation(s)
- John C. Briggs
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR 97333, USA
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