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Wiens JJ. Trait-based species richness: ecology and macroevolution. Biol Rev Camb Philos Soc 2023; 98:1365-1387. [PMID: 37015839 DOI: 10.1111/brv.12957] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 03/21/2023] [Accepted: 03/27/2023] [Indexed: 04/06/2023]
Abstract
Understanding the origins of species richness patterns is a fundamental goal in ecology and evolutionary biology. Much research has focused on explaining two kinds of species richness patterns: (i) spatial species richness patterns (e.g. the latitudinal diversity gradient), and (ii) clade-based species richness patterns (e.g. the predominance of angiosperm species among plants). Here, I highlight a third kind of richness pattern: trait-based species richness (e.g. the number of species with each state of a character, such as diet or body size). Trait-based richness patterns are relevant to many topics in ecology and evolution, from ecosystem function to adaptive radiation to the paradox of sex. Although many studies have described particular trait-based richness patterns, the origins of these patterns remain far less understood, and trait-based richness has not been emphasised as a general category of richness patterns. Here, I describe a conceptual framework for how trait-based richness patterns arise compared to other richness patterns. A systematic review suggests that trait-based richness patterns are most often explained by when each state originates within a group (i.e. older states generally have higher richness), and not by differences in transition rates among states or faster diversification of species with certain states. This latter result contrasts with the widespread emphasis on diversification rates in species-richness research. I show that many recent studies of spatial richness patterns are actually studies of trait-based richness patterns, potentially confounding the causes of these patterns. Finally, I describe a plethora of unanswered questions related to trait-based richness patterns.
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Affiliation(s)
- John J Wiens
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721-0088, USA
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Martín-Hernanz S, Nogales M, Valente L, Fernández-Mazuecos M, Pomeda-Gutiérrez F, Cano E, Marrero P, Olesen JM, Heleno R, Vargas P. Time-calibrated phylogenies reveal mediterranean and pre-mediterranean origin of the thermophilous vegetation of the Canary Islands. ANNALS OF BOTANY 2023; 131:667-684. [PMID: 36594263 PMCID: PMC10147335 DOI: 10.1093/aob/mcac160] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 12/21/2022] [Indexed: 05/20/2023]
Abstract
BACKGROUND AND AIMS The Canary Islands have strong floristic affinities with the Mediterranean Basin. One of the most characteristic and diverse vegetation belts of the archipelago is the thermophilous woodland (between 200 and 900 m.a.s.l.). This thermophilous plant community consists of many non-endemic species shared with the Mediterranean Floristic Region together with Canarian endemic species. Consequently, phytogeographic studies have historically proposed the hypothesis of an origin of the Canarian thermophilous species following the establishment of the summer-dry mediterranean climate in the Mediterranean Basin around 2.8 million years ago. METHODS Time-calibrated phylogenies for 39 plant groups including Canarian thermophilous species were primarily analysed to infer colonization times. In particular, we used 26 previously published phylogenies together with 13 new time-calibrated phylogenies (including newly generated plastid and nuclear DNA sequence data) to assess whether the time interval between stem and crown ages of Canarian thermophilous lineages postdates 2.8 Ma. For lineages postdating this time threshold, we additionally conducted ancestral area reconstructions to infer the potential source area for colonization. KEY RESULTS A total of 43 Canarian thermophilous lineages were identified from 39 plant groups. Both mediterranean (16) and pre-mediterranean (9) plant lineages were found. However, we failed to determine the temporal origin for 18 lineages because a stem-crown time interval overlaps with the 2.8-Ma threshold. The spatial origin of thermophilous lineages was also heterogeneous, including ancestral areas from the Mediterranean Basin (nine) and other regions (six). CONCLUSIONS Our findings reveal an unexpectedly heterogeneous origin of the Canarian thermophilous species in terms of colonization times and mainland source areas. A substantial proportion of the lineages arrived in the Canaries before the summer-dry climate was established in the Mediterranean Basin. The complex temporal and geographic origin of Canarian thermophilous species challenges the view of the Canary Islands (and Madeira) as a subregion within the Mediterranean Floristic Region.
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Affiliation(s)
- Sara Martín-Hernanz
- Department of Biodiversity and Conservation, Real Jardín Botánico de Madrid (RJB-CSIC), 28014 Madrid, Spain
- Departament of Plant Biology and Ecology, Faculty of Pharmacy, Universidad de Sevilla, 41012 Sevilla, Spain
| | - Manuel Nogales
- Island Ecology and Evolution Research Group, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), 38206 San Cristóbal de La Laguna, Tenerife, Canary Islands, Spain
| | - Luis Valente
- Naturalis Biodiversity Center, 2333 Leiden, The Netherlands
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, 9700 AB Groningen, The Netherlands
| | - Mario Fernández-Mazuecos
- Department of Biology (Botany), Faculty of Sciences, Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Fernando Pomeda-Gutiérrez
- Department of Biodiversity and Conservation, Real Jardín Botánico de Madrid (RJB-CSIC), 28014 Madrid, Spain
| | - Emilio Cano
- Department of Biodiversity and Conservation, Real Jardín Botánico de Madrid (RJB-CSIC), 28014 Madrid, Spain
| | - Patricia Marrero
- Department of Biodiversity and Conservation, Real Jardín Botánico de Madrid (RJB-CSIC), 28014 Madrid, Spain
- Island Ecology and Evolution Research Group, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), 38206 San Cristóbal de La Laguna, Tenerife, Canary Islands, Spain
| | - Jens M Olesen
- Department of Biology, Aarhus University, 8000 Aarhus C, Denmark
| | - Ruben Heleno
- Centre for Functional Ecology, TERRA Associate Laboratory, Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal
| | - Pablo Vargas
- Department of Biodiversity and Conservation, Real Jardín Botánico de Madrid (RJB-CSIC), 28014 Madrid, Spain
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Seidl A, Tremetsberger K, Pfanzelt S, Blattner FR, Neuffer B, Friesen N, Hurka H, Shmakov A, Batlai O, Žerdoner Čalasan A, Vesselova PV, Bernhardt KG. The phylogeographic history of Krascheninnikovia reflects the development of dry steppes and semi-deserts in Eurasia. Sci Rep 2021; 11:6645. [PMID: 33758234 PMCID: PMC7988158 DOI: 10.1038/s41598-021-85735-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 03/01/2021] [Indexed: 01/31/2023] Open
Abstract
Constituting one of Earth's major biomes, steppes are characterised by naturally treeless extra-tropical vegetation. The formation of the Eurasian steppe belt, the largest steppe region in the world, began in Central Asia during the Neogene. In the glacial stages of the Pleistocene, steppe displaced forest vegetation, which in turn recolonised the area during the warmer interglacial periods, thus affecting the distribution of plants adapted to these habitats. Krascheninnikovia ceratoides (Chenopodiaceae) is a plant characteristic of dry steppe and semi-desert formations. Earlier studies showed that the ancestor of this autochthonous steppe element originated in Central Asia during the Miocene/Pliocene, i.e., in the same region and at the same time as the first appearance of steppe vegetation. However, as the extant lineages of Krascheninnikovia ceratoides diversified only 2.2 ± 0.9 Mya, it may represent a modern element of current dry steppe and semi-desert formations, rather than a component of the first steppe precursors of the Miocene. As such, it may have capitalised on the climatic conditions of the cold stages of the Quaternary to expand its range and colonise suitable habitats outside of its area of origin. To test this hypothesis, phylogeographic methods were applied to high-resolution genotyping-by-sequencing data. Our results indicate that Krascheninnikovia originated in western Central Asia and the Russian Altai, then spread to Europe in the West, and reached North America in the East. The populations of eastern Central Asia and North America belong to the same clade and are genetically clearly distinct from the Euro-Siberian populations. Among the populations west of the Altai Mountains, the European populations are genetically distinct from all others, which could be the result of the separation of populations east and west of the Urals caused by the Pleistocene transgressions of the Caspian Sea.
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Affiliation(s)
- Anna Seidl
- grid.5173.00000 0001 2298 5320Department of Integrative Biology and Biodiversity Research, Institute of Botany, University of Natural Resources and Life Sciences, Vienna (BOKU), Gregor-Mendel-Straße 33, 1180 Vienna, Austria
| | - Karin Tremetsberger
- grid.5173.00000 0001 2298 5320Department of Integrative Biology and Biodiversity Research, Institute of Botany, University of Natural Resources and Life Sciences, Vienna (BOKU), Gregor-Mendel-Straße 33, 1180 Vienna, Austria
| | - Simon Pfanzelt
- grid.418934.30000 0001 0943 9907Experimental Taxonomy, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466 Gatersleben, Germany
| | - Frank R. Blattner
- grid.418934.30000 0001 0943 9907Experimental Taxonomy, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466 Gatersleben, Germany
| | - Barbara Neuffer
- grid.10854.380000 0001 0672 4366School of Biology/Chemistry, Osnabrück University, Barbarastraße 11, 49076 Osnabrück, Germany
| | - Nikolai Friesen
- grid.10854.380000 0001 0672 4366Botanical Garden of the Osnabrück University, Albrechtstraße 29, 49076 Osnabrück, Germany ,grid.448878.f0000 0001 2288 8774Department of Pharmaceutical and Natural Sciences, I.M. Sechenov First Moscow State Medical University Ministry of Health of the Russian Federation, Izmailovsky Boulevard, 8, Moscow, 105043 Russia
| | - Herbert Hurka
- grid.10854.380000 0001 0672 4366School of Biology/Chemistry, Osnabrück University, Barbarastraße 11, 49076 Osnabrück, Germany
| | - Alexander Shmakov
- grid.77225.350000000112611077South Siberian Botanical Garden, Altai State University, Lenina 61, 656049 Barnaul, Russia
| | - Oyuntsetseg Batlai
- grid.260731.10000 0001 2324 0259Department of Biology, School of Arts and Science, National University of Mongolia, University street 3, 14201 Ulaanbaatar, Mongolia
| | - Anže Žerdoner Čalasan
- grid.10854.380000 0001 0672 4366School of Biology/Chemistry, Osnabrück University, Barbarastraße 11, 49076 Osnabrück, Germany
| | - Polina V. Vesselova
- Institute of Botany and Phytointroduction, Committee of Forestry and Wildlife, Ministry of Ecology, Geology and Natural Resources of the Republic of Kazakhstan, Timiryazeva Street 36D, 050040 Almaty, Kazakhstan
| | - Karl-Georg Bernhardt
- grid.5173.00000 0001 2298 5320Department of Integrative Biology and Biodiversity Research, Institute of Botany, University of Natural Resources and Life Sciences, Vienna (BOKU), Gregor-Mendel-Straße 33, 1180 Vienna, Austria
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Morales-Briones DF, Kadereit G, Tefarikis DT, Moore MJ, Smith SA, Brockington SF, Timoneda A, Yim WC, Cushman JC, Yang Y. Disentangling Sources of Gene Tree Discordance in Phylogenomic Data Sets: Testing Ancient Hybridizations in Amaranthaceae s.l. Syst Biol 2020; 70:219-235. [PMID: 32785686 PMCID: PMC7875436 DOI: 10.1093/sysbio/syaa066] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 03/01/2020] [Accepted: 09/03/2020] [Indexed: 12/26/2022] Open
Abstract
Gene tree discordance in large genomic data sets can be caused by evolutionary processes such as incomplete lineage sorting and hybridization, as well as model violation, and errors in data processing, orthology inference, and gene tree estimation. Species tree methods that identify and accommodate all sources of conflict are not available, but a combination of multiple approaches can help tease apart alternative sources of conflict. Here, using a phylotranscriptomic analysis in combination with reference genomes, we test a hypothesis of ancient hybridization events within the plant family Amaranthaceae s.l. that was previously supported by morphological, ecological, and Sanger-based molecular data. The data set included seven genomes and 88 transcriptomes, 17 generated for this study. We examined gene-tree discordance using coalescent-based species trees and network inference, gene tree discordance analyses, site pattern tests of introgression, topology tests, synteny analyses, and simulations. We found that a combination of processes might have generated the high levels of gene tree discordance in the backbone of Amaranthaceae s.l. Furthermore, we found evidence that three consecutive short internal branches produce anomalous trees contributing to the discordance. Overall, our results suggest that Amaranthaceae s.l. might be a product of an ancient and rapid lineage diversification, and remains, and probably will remain, unresolved. This work highlights the potential problems of identifiability associated with the sources of gene tree discordance including, in particular, phylogenetic network methods. Our results also demonstrate the importance of thoroughly testing for multiple sources of conflict in phylogenomic analyses, especially in the context of ancient, rapid radiations. We provide several recommendations for exploring conflicting signals in such situations. [Amaranthaceae; gene tree discordance; hybridization; incomplete lineage sorting; phylogenomics; species network; species tree; transcriptomics.]
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Affiliation(s)
- Diego F Morales-Briones
- Department of Plant and Microbial Biology, University of Minnesota-Twin Cities, 1445 Gortner Avenue, St. Paul, MN 55108, USA
| | - Gudrun Kadereit
- Institut für Molekulare Physiologie, Johannes Gutenberg-Universität Mainz, D-55099 Mainz, Germany
| | - Delphine T Tefarikis
- Institut für Molekulare Physiologie, Johannes Gutenberg-Universität Mainz, D-55099 Mainz, Germany
| | - Michael J Moore
- Department of Biology, Oberlin College, Science Center K111, 119 Woodland Street, Oberlin, OH 44074-1097, USA
| | - Stephen A Smith
- Department of Ecology & Evolutionary Biology, University of Michigan, 830 North University Avenue, Ann Arbor, MI 48109-1048, USA
| | - Samuel F Brockington
- Department of Plant Sciences, University of Cambridge, Tennis Court Road, Cambridge CB2 3EA, UK
| | - Alfonso Timoneda
- Department of Plant Sciences, University of Cambridge, Tennis Court Road, Cambridge CB2 3EA, UK
| | - Won C Yim
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, 89577, USA
| | - John C Cushman
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, 89577, USA
| | - Ya Yang
- Department of Plant and Microbial Biology, University of Minnesota-Twin Cities, 1445 Gortner Avenue, St. Paul, MN 55108, USA
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