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Luize BG, Palma‐Silva C, Siqueira T, Silva TSF. Tree species occurring in Amazonian wetland forests consistently show broader range sizes and niche breadths than trees in upland forests. Ecol Evol 2024; 14:e11230. [PMID: 38681185 PMCID: PMC11045914 DOI: 10.1002/ece3.11230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 03/11/2024] [Accepted: 03/22/2024] [Indexed: 05/01/2024] Open
Abstract
Generally, species with broad niches also show large range sizes. We investigated the relationship between hydrological niche breadth and geographic range size for Amazonian tree species seeking to understand the role of habitat specialization to Amazonian wetlands and upland forests on the current distribution of tree species. We obtained 571,092 valid occurrence points from GBIF and SpeciesLink to estimate the range size and the niche breadth of 76% of all known Amazonian tree species (5150 tree species). Hydrological niche breadth was measured on different unidimensional axes defined by (1) total annual precipitation; (2) precipitation seasonality; (3) actual evapotranspiration; and (4) water table depth. Geographic range sizes were estimated using alpha-hull adjustments. General linear models were used to relate niche breadth to range size while contrasting tree species occurring and not occurring in wetlands. The hydrological niche breadth of Amazonian tree species varied mostly along the water table depth axis. The average range size for an Amazonian tree species was 751,000 km2 (median of 154,000 km2 and standard deviation of 1,550,000 km2). Niche breadth-range size relationships for Amazonian tree species were positive for all models, and the explanatory power of the models improved when including whether a species occurred in wetlands or in terrestrial uplands. Wetland species had steeper positive slopes for the niche breadth-range size relationship, and consistently larger range sizes for a given niche breadth. Amazonian tree species varied strongly in hydrological niche breadth and range size, but most species had narrow niche breadths and range sizes. Our results suggest that the South American riverscape may have been acting as a corridor for species dispersal in the Neotropical lowlands.
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Affiliation(s)
- Bruno Garcia Luize
- Departamento de Ecologia, Instituto de BiociênciasUniversidade Estadual Paulista (UNESP)Rio ClaroBrazil
- Departamento de Biologia Vegetal, Instituto de BiologiaUniversidade Estadual de Campinas – UNICAMPCampinasBrazil
| | - Clarisse Palma‐Silva
- Departamento de Biologia Vegetal, Instituto de BiologiaUniversidade Estadual de Campinas – UNICAMPCampinasBrazil
| | - Tadeu Siqueira
- Departamento de Ecologia, Instituto de BiociênciasUniversidade Estadual Paulista (UNESP)Rio ClaroBrazil
- School of Biological SciencesUniversity of CanterburyChristchurchNew Zealand
| | - Thiago Sanna Freire Silva
- Departamento de Ecologia, Instituto de BiociênciasUniversidade Estadual Paulista (UNESP)Rio ClaroBrazil
- Biological and Environmental Sciences, Faculty of Natural SciencesUniversity of StirlingStirlingUK
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2
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Berasategui JA, Žerdoner Čalasan A, Zizka A, Kadereit G. Global distribution, climatic preferences and photosynthesis-related traits of C 4 eudicots and how they differ from those of C 4 grasses. Ecol Evol 2023; 13:e10720. [PMID: 37964791 PMCID: PMC10641307 DOI: 10.1002/ece3.10720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 10/25/2023] [Accepted: 10/30/2023] [Indexed: 11/16/2023] Open
Abstract
C₄ is one of three known photosynthetic processes of carbon fixation in flowering plants. It evolved independently more than 61 times in multiple angiosperm lineages and consists of a series of anatomical and biochemical modifications to the ancestral C3 pathway increasing plant productivity under warm and light-rich conditions. The C4 lineages of eudicots belong to seven orders and 15 families, are phylogenetically less constrained than those of monocots and entail an enormous structural and ecological diversity. Eudicot C4 lineages likely evolved the C4 syndrome along different evolutionary paths. Therefore, a better understanding of this diversity is key to understanding the evolution of this complex trait as a whole. By compiling 1207 recognised C4 eudicots species described in the literature and presenting trait data among these species, we identify global centres of species richness and of high phylogenetic diversity. Furthermore, we discuss climatic preferences in the context of plant functional traits. We identify two hotspots of C4 eudicot diversity: arid regions of Mexico/Southern United States and Australia, which show a similarly high number of different C4 eudicot genera but differ in the number of C4 lineages that evolved in situ. Further eudicot C4 hotspots with many different families and genera are in South Africa, West Africa, Patagonia, Central Asia and the Mediterranean. In general, C4 eudicots are diverse in deserts and xeric shrublands, tropical and subtropical grasslands, savannas and shrublands. We found C4 eudicots to occur in areas with less annual precipitation than C4 grasses which can be explained by frequently associated adaptations to drought stress such as among others succulence and salt tolerance. The data indicate that C4 eudicot lineages utilising the NAD-ME decarboxylating enzyme grow in drier areas than those using the NADP-ME decarboxylating enzyme indicating biochemical restrictions of the later system in higher temperatures. We conclude that in most eudicot lineages, C4 evolved in ancestrally already drought-adapted clades and enabled these to further spread in these habitats and colonise even drier areas.
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Affiliation(s)
- Jessica A. Berasategui
- Prinzessin Therese von Bayern Lehrstuhl für Systematik, Biodiversität & Evolution der PflanzenLudwig‐Maximilians Universität MünchenMünchenGermany
- Institute for Molecular PhysiologyJohannes Gutenberg‐University MainzMainzGermany
| | - Anže Žerdoner Čalasan
- Prinzessin Therese von Bayern Lehrstuhl für Systematik, Biodiversität & Evolution der PflanzenLudwig‐Maximilians Universität MünchenMünchenGermany
| | - Alexander Zizka
- Department of BiologyPhilipps‐University MarburgMarburgGermany
| | - Gudrun Kadereit
- Prinzessin Therese von Bayern Lehrstuhl für Systematik, Biodiversität & Evolution der PflanzenLudwig‐Maximilians Universität MünchenMünchenGermany
- Botanischer Garten München‐Nymphenburg und Botanische Staatssammlung MünchenStaatliche Naturwissenschaftliche Sammlungen BayernsMünchenGermany
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Coca-De-La-Iglesia M, Valcárcel V, Medina NG. A Protocol to Retrieve and Curate Spatial and Climatic Data from Online Biodiversity Databases Using R. Bio Protoc 2023; 13:e4847. [PMID: 37900105 PMCID: PMC10603197 DOI: 10.21769/bioprotoc.4847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 08/11/2023] [Accepted: 08/11/2023] [Indexed: 10/31/2023] Open
Abstract
Ecological and evolutionary studies often require high quality biodiversity data. This information is readily available through the many online databases that have compiled biodiversity data from herbaria, museums, and human observations. However, the process of preparing this information for analysis is complex and time consuming. In this study, we have developed a protocol in R language to process spatial data (download, merge, clean, and correct) and extract climatic data, using some genera of the ginseng family (Araliaceae) as an example. The protocol provides an automated way to process spatial and climatic data for numerous taxa independently and from multiple online databases. The script uses GBIF, BIEN, and WorldClim as the online data sources, but can be easily adapted to include other online databases. The script also uses genera as the sampling unit but provides a way to use species as the target. The cleaning process includes a filter to remove occurrences outside the natural range of the taxa, gardens, and other human environments, as well as erroneous locations and a spatial correction for misplaced occurrences (i.e., occurrences within a distance buffer from the coastal boundary). Additionally, each step of the protocol can be run independently. Thus, the protocol can begin with data cleaning, if the database has already been compiled, or with climatic data extraction, if the database has already been parsed. Each line of the R script is commented so that it can also be run by users with little knowledge of R.
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Affiliation(s)
- Marina Coca-De-La-Iglesia
- Departamento de Biología, Universidad Autónoma de Madrid (UAM), Madrid, Spain
- TRAGSATEC, Madrid, Spain
| | - Virginia Valcárcel
- Departamento de Biología, Universidad Autónoma de Madrid (UAM), Madrid, Spain
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Madrid, Spain
| | - Nagore G. Medina
- Departamento de Biología, Universidad Autónoma de Madrid (UAM), Madrid, Spain
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Madrid, Spain
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Colli-Silva M, Richardson JE, Pirani JR. A taxonomic dataset of preserved specimen occurrences of Theobroma and Herrania (Malvaceae, Byttnerioideae) stored in 2020. Biodivers Data J 2023; 11:e99646. [PMID: 38327374 PMCID: PMC10848337 DOI: 10.3897/bdj.11.e99646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 03/22/2023] [Indexed: 02/09/2024] Open
Abstract
Background Species from the "cacao group" are traditionally allocated into two genera, Theobroma and Herrania (Malvaceae, Byttnerioideae), both groups of Neotropical species economically relevant, such as the cacao tree (Theobromacacao), which forms the source of chocolate. This study aimed at compiling and describing a dataset of preserved specimen collections available in the Global Biodiversity Information Facility repository (GBIF) for Tropical Americas. Data were exhaustively revisited and analysed in terms of taxonomic identity, conditions of collection and georeferencing, all of which should enable downstream taxonomic, geographic and evolutionary analyses. New information Our dataset compiles 7975 records of preserved specimen collections found at herbaria. Records are from 18 species of Theobroma and 14 of Herrania, occurring in 60 countries or major territories, with two species endemic to a single country (H.kofanorum from Ecuador and H.laciniifolium from Colombia). Occurrence records are mostly restricted to the Amazon rainforest and species with more occurrence records are cupuí, T.subincanum (1535 records), followed by the cacao tree, T.cacao (1500 records), the latter having cultivated specimens in Africa, Asia and Oceania. In the case of the genus Herrania, H.nitida and H.purpurea are the species with the majority of occurrences (respectively, 431 and 273 records). Most of the botanical samples from these genera are found in American, Brazilian and Colombian collections, with a particular strength for American herbaria. We describe how occurrence records are spread spatially and temporally and highlight key field expeditions responsible for enhancing most of the knowledge of cacao and its wild relatives, especially in countries where they prevail, such as Colombia (with 29 species), Ecuador (23 species), Brazil (18 species) and Peru (15 species). Specifically, expeditions in these countries were led by American and European initiatives in conjunction with local funding in the mid-20th century. We emphasise how initiatives of such kind seems to have weakened in the 21st century and most of the collections of Theobroma and Herrania made afterwards are from various collectors that seek to resample specimens in already explored sites.
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Affiliation(s)
- Matheus Colli-Silva
- Department of Botany, Institute of Biosciences, University of São Paulo, São Paulo, BrazilDepartment of Botany, Institute of Biosciences, University of São PauloSão PauloBrazil
| | - James E. Richardson
- School of Biological, Earth and Environmental Sciences, University College Cork, Cork, IrelandSchool of Biological, Earth and Environmental Sciences, University College CorkCorkIreland
- Tropical Diversity Section, Royal Botanic Garden Edinburgh, Edinburgh, United KingdomTropical Diversity Section, Royal Botanic Garden EdinburghEdinburghUnited Kingdom
- Faculty of Natural Sciences, Rosario University, Bogotá, ColombiaFaculty of Natural Sciences, Rosario UniversityBogotáColombia
| | - José R. Pirani
- Department of Botany, Institute of Biosciences, University of São Paulo, São Paulo, BrazilDepartment of Botany, Institute of Biosciences, University of São PauloSão PauloBrazil
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Galante PJ, Chang Triguero S, Paz A, Aiello‐Lammens M, Gerstner BE, Johnson BA, Kass JM, Merow C, Noguera‐Urbano EA, Pinilla‐Buitrago GE, Blair ME. changeRangeR
: An R package for reproducible biodiversity change metrics from species distribution estimates. CONSERVATION SCIENCE AND PRACTICE 2022. [DOI: 10.1111/csp2.12863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
- Peter J. Galante
- Center for Biodiversity and Conservation American Museum of Natural History New York New York USA
| | - Samuel Chang Triguero
- Department of Environmental Studies and Science Pace University Pleasantville New York USA
| | - Andrea Paz
- Biology Department City College of New York, City University of New York New York New York USA
- Ph.D. Program in Biology, Graduate Center City University of New York New York New York USA
- Department of Environmental Systems Science Institute of Integrative Biology, ETH Zürich Zürich Switzerland
| | - Matthew Aiello‐Lammens
- Department of Environmental Studies and Science Pace University Pleasantville New York USA
| | - Beth E. Gerstner
- Department of Fisheries & Wildlife and Ecology Evolution & Behavior Program, Michigan State University East Lansing Michigan USA
| | - Bethany A. Johnson
- Biology Department City College of New York, City University of New York New York New York USA
| | - Jamie M. Kass
- Biodiversity and Biocomplexity Unit Okinawa Institute of Science and Technology Graduate University Okinawa Japan
| | - Cory Merow
- Eversource Energy Center University of Connecticut Storrs Connecticut USA
| | | | - Gonzalo E. Pinilla‐Buitrago
- Biology Department City College of New York, City University of New York New York New York USA
- Ph.D. Program in Biology, Graduate Center City University of New York New York New York USA
| | - Mary E. Blair
- Center for Biodiversity and Conservation American Museum of Natural History New York New York USA
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6
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Mammalian diversification bursts and biotic turnovers are synchronous with Cenozoic geoclimatic events in Asia. Proc Natl Acad Sci U S A 2022; 119:e2207845119. [PMID: 36442115 PMCID: PMC9894185 DOI: 10.1073/pnas.2207845119] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Asia's rich species diversity has been linked to its Cenozoic geodiversity, including active mountain building and dramatic climatic changes. However, prior studies on the diversification and assembly of Asian faunas have been derived mainly from analyses at taxonomic or geographic scales too limited to offer a comprehensive view of this complex region's biotic evolution. Here, using the class Mammalia, we built historical biogeographic models drawn on phylogenies of 1,543 species occurring across Asia to investigate how and when the mammal diversity in Asian regions and mountain hotspots was assembled. We explore the roles of in situ speciation, colonization, and vicariance and geoclimatic events to explain the buildup of Asia's regional mammal diversity through time. We found that southern Asia has served as the main cradle of Asia's mammal diversity. Present-day species richness in other regions is mainly derived from colonization, but by the Miocene, in situ speciation increased in importance. The high biodiversity present in the mountain hotspots (Himalayas and Hengduan) that flank the Qinghai-Tibetan plateau is a product of high colonization instead of in situ speciation, making them important centers of lineage accumulation. Overall, Neogene was marked by great diversification and migrations across Asia and surrounding continents but Paleogene environments already hosted rich mammal assemblages. Our study revealed that synchronous diversification bursts and biotic turnovers are temporally associated with tectonic events (mountain building, continental collisions) and drastic reorganization of climate (aridification of Asian interior, intensification of Asian monsoons, sea retreat) that took place throughout the Cenozoic in Asia.
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7
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Tack W, Engledow H, Veríssimo Pereira N, Amani C, Bachman SP, Barberá P, Beentje HJ, Bouka GUD, Cheek M, Cosiaux A, Dauby G, De Block P, Ewango CEN, Fischer E, Gereau RE, Hargreaves S, Harvey-Brown Y, Ikabanga DU, Ilunga wa Ilunga E, Kalema J, Kamau P, Lachenaud O, Luke Q, Mwanga Mwanga I, Ndolo Ebika ST, Nkengurutse J, Nsanzurwimo A, Ntore S, Richards SL, Shutsha Ehata R, Simo-Droissart M, Stévart T, Sosef MSM. The ECAT dataset: expert-validated distribution data of endemic and sub-endemic trees of Central Africa (Dem. Rep. Congo, Rwanda, Burundi). PHYTOKEYS 2022; 206:137-151. [PMID: 36761267 PMCID: PMC9849015 DOI: 10.3897/phytokeys.206.77379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 08/15/2022] [Indexed: 06/18/2023]
Abstract
In this data paper, we present a specimen-based occurrence dataset compiled in the framework of the Conservation of Endemic Central African Trees (ECAT) project with the aim of producing global conservation assessments for the IUCN Red List. The project targets all tree species endemic or sub-endemic to the Central African region comprising the Democratic Republic of the Congo (DR Congo), Rwanda, and Burundi. The dataset contains 6361 plant collection records with occurrences of 8910 specimens from 337 taxa belonging to 153 genera in 52 families. Many of these tree taxa have restricted geographic ranges and are only known from a small number of herbarium specimens. As assessments for such taxa can be compromised by inadequate data, we transcribed and geo-referenced specimen label information to obtain a more accurate and complete locality dataset. All specimen data were manually cleaned and verified by botanical experts, resulting in improved data quality and consistency.
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Affiliation(s)
- Wesley Tack
- Meise Botanic Garden, Nieuwelaan 38, 1860 Meise, BelgiumMeise Botanic GardenMeiseBelgium
| | - Henry Engledow
- Meise Botanic Garden, Nieuwelaan 38, 1860 Meise, BelgiumMeise Botanic GardenMeiseBelgium
| | - Nuno Veríssimo Pereira
- Meise Botanic Garden, Nieuwelaan 38, 1860 Meise, BelgiumMeise Botanic GardenMeiseBelgium
| | - Christian Amani
- Université Officielle de Bukavu, Bukavu, Democratic Republic of the CongoIUCN SSC Eastern African Plant Red List Authority (EAPRLA)GlandSwitzerland
- IUCN SSC Eastern African Plant Red List Authority (EAPRLA), Gland, SwitzerlandUniversité Officielle de BukavuBukavuDemocratic Republic of the Congo
| | - Steven P. Bachman
- Royal Botanic Gardens, Kew, Richmond, Surrey, UKRoyal Botanic GardensRichmondUnited Kingdom
| | - Patricia Barberá
- Missouri Botanical Garden, Africa & Madagascar Department, St. Louis, MO 63110, USAMissouri Botanical Garden, Africa & Madagascar DepartmentSt. LouisUnited States of America
| | - Henk J. Beentje
- IUCN SSC Eastern African Plant Red List Authority (EAPRLA), Gland, SwitzerlandUniversité Officielle de BukavuBukavuDemocratic Republic of the Congo
- Royal Botanic Gardens, Kew, Richmond, Surrey, UKRoyal Botanic GardensRichmondUnited Kingdom
| | - Gaël U. D. Bouka
- Laboratoire de Biodiversité, de Gestion des Ecosystèmes et de l’Environnement, Faculté des Sciences et Techniques, Université Marien Ngouabi, BP 69, Brazzaville, Democratic Republic of the CongoUniversité Marien NgouabiBrazzavilleDemocratic Republic of the Congo
| | - Martin Cheek
- IUCN SSC Eastern African Plant Red List Authority (EAPRLA), Gland, SwitzerlandUniversité Officielle de BukavuBukavuDemocratic Republic of the Congo
- Royal Botanic Gardens, Kew, Richmond, Surrey, UKRoyal Botanic GardensRichmondUnited Kingdom
| | - Ariane Cosiaux
- Plant Systematics and Ecology Laboratory, University of Yaoundé I, P.O. Box 047, Yaoundé, CameroonUniversity of Yaoundé IYaoundéCameroon
- Institut de Recherche pour le Développement, Université de Montpellier, Montpellier, FranceUniversité de MontpellierMontpellierFrance
| | - Gilles Dauby
- Institut de Recherche pour le Développement, Université de Montpellier, Montpellier, FranceUniversité de MontpellierMontpellierFrance
| | - Petra De Block
- Meise Botanic Garden, Nieuwelaan 38, 1860 Meise, BelgiumMeise Botanic GardenMeiseBelgium
| | - Corneille E. N. Ewango
- IUCN SSC Eastern African Plant Red List Authority (EAPRLA), Gland, SwitzerlandUniversité Officielle de BukavuBukavuDemocratic Republic of the Congo
- AMAP, Université de Montpellier, CIRAD, CNRS, INRAE, IRD, Montpellier, FranceUniversité de KisanganiKisanganiDemocratic Republic of the Congo
| | - Eberhard Fischer
- Centre de Surveillance de la Biodiversité, Université de Kisangani, Kisangani, Democratic Republic of the CongoUniversity of Koblenz and LandauKoblenzGermany
- University of Koblenz-Landau, Universitätsstraße 1, Koblenz, 56070, GermanyIUCN SSC Central Africa Plant Red List Authority (CARLA)GlandSwitzerland
| | - Roy E. Gereau
- Missouri Botanical Garden, Africa & Madagascar Department, St. Louis, MO 63110, USAMissouri Botanical Garden, Africa & Madagascar DepartmentSt. LouisUnited States of America
- University of Koblenz-Landau, Universitätsstraße 1, Koblenz, 56070, GermanyIUCN SSC Central Africa Plant Red List Authority (CARLA)GlandSwitzerland
| | - Serene Hargreaves
- Royal Botanic Gardens, Kew, Richmond, Surrey, UKRoyal Botanic GardensRichmondUnited Kingdom
| | - Yvette Harvey-Brown
- IUCN SSC Central Africa Plant Red List Authority (CARLA), Gland, SwitzerlandBotanic Gardens Conservation InternationalRichmondUnited Kingdom
| | - Davy U. Ikabanga
- Botanic Gardens Conservation International, Richmond, Surrey, UKUniversity of Sciences and Techniques of MasukuFrancevilleGabon
| | - Edouard Ilunga wa Ilunga
- Department of Biology, Faculty of Sciences, University of Sciences and Techniques of Masuku, BP: 941, Franceville, GabonUniversité de LubumbashiLubumbashiDemocratic Republic of the Congo
| | - James Kalema
- IUCN SSC Eastern African Plant Red List Authority (EAPRLA), Gland, SwitzerlandUniversité Officielle de BukavuBukavuDemocratic Republic of the Congo
- Herbarium de Lubumbashi, Université de Lubumbashi, 1825, Route Kasapa, Lubumbashi, Democratic Republic of the CongoMakerere University Herbarium, Department of Plant Sciences Microbiology and BiotechnologyKampalaUganda
| | - Peris Kamau
- IUCN SSC Eastern African Plant Red List Authority (EAPRLA), Gland, SwitzerlandUniversité Officielle de BukavuBukavuDemocratic Republic of the Congo
- Makerere University Herbarium, Department of Plant Sciences Microbiology and Biotechnology, P.O. Box 7062, Kampala, UgandaEast African Herbarium, National Museums of KenyaNairobiKenya
| | - Olivier Lachenaud
- Meise Botanic Garden, Nieuwelaan 38, 1860 Meise, BelgiumMeise Botanic GardenMeiseBelgium
- East African Herbarium, National Museums of Kenya, P.O. Box 45166-00100, Nairobi, KenyaUniversité Libre de BruxellesBrusselsBelgium
| | - Quentin Luke
- IUCN SSC Eastern African Plant Red List Authority (EAPRLA), Gland, SwitzerlandUniversité Officielle de BukavuBukavuDemocratic Republic of the Congo
- Makerere University Herbarium, Department of Plant Sciences Microbiology and Biotechnology, P.O. Box 7062, Kampala, UgandaEast African Herbarium, National Museums of KenyaNairobiKenya
| | - Ithe Mwanga Mwanga
- Herbarium et Bibliothèque de Botanique africaine, C.P. 265, Université Libre de Bruxelles, Campus de la Plaine, Boulevard du Triomphe 1050, Brussels, BelgiumCentre de Recherche en Sciences Naturelles CRSN/Lwiro, Laboratoire de Systématiquement et Taxonomie végétaleBukavuDemocratic Republic of the Congo
| | - Sydney T. Ndolo Ebika
- Laboratoire de Biodiversité, de Gestion des Ecosystèmes et de l’Environnement, Faculté des Sciences et Techniques, Université Marien Ngouabi, BP 69, Brazzaville, Democratic Republic of the CongoUniversité Marien NgouabiBrazzavilleDemocratic Republic of the Congo
| | - Jacques Nkengurutse
- Centre de Recherche en Sciences Naturelles CRSN/Lwiro, Laboratoire de Systématiquement et Taxonomie végétale, D.S. Bukavu, Democratic Republic of the CongoUniversity of BurundiBujumburaBurundi
| | - Aimable Nsanzurwimo
- Department of Biology, Faculty of Science, University of Burundi, P.O. Box 2700, Bujumbura, BurundiDepartment of Biotechnologies, Faculty of Applied Sciences, INES-RuhengeriRuhengeriRwanda
| | - Salvator Ntore
- Meise Botanic Garden, Nieuwelaan 38, 1860 Meise, BelgiumMeise Botanic GardenMeiseBelgium
- IUCN SSC Eastern African Plant Red List Authority (EAPRLA), Gland, SwitzerlandUniversité Officielle de BukavuBukavuDemocratic Republic of the Congo
- University of Koblenz-Landau, Universitätsstraße 1, Koblenz, 56070, GermanyIUCN SSC Central Africa Plant Red List Authority (CARLA)GlandSwitzerland
| | - Sophie L. Richards
- Royal Botanic Gardens, Kew, Richmond, Surrey, UKRoyal Botanic GardensRichmondUnited Kingdom
| | - Reddy Shutsha Ehata
- AMAP, Université de Montpellier, CIRAD, CNRS, INRAE, IRD, Montpellier, FranceUniversité de KisanganiKisanganiDemocratic Republic of the Congo
| | - Murielle Simo-Droissart
- Plant Systematics and Ecology Laboratory, University of Yaoundé I, P.O. Box 047, Yaoundé, CameroonUniversity of Yaoundé IYaoundéCameroon
- Department of Biotechnologies, Faculty of Applied Sciences, INES-Ruhengeri, B.P.155 Ruhengeri, RwandaUCN SSC Central Africa Plant Red List Authority (CARLA)GlandSwaziland
| | - Tariq Stévart
- Meise Botanic Garden, Nieuwelaan 38, 1860 Meise, BelgiumMeise Botanic GardenMeiseBelgium
- Missouri Botanical Garden, Africa & Madagascar Department, St. Louis, MO 63110, USAMissouri Botanical Garden, Africa & Madagascar DepartmentSt. LouisUnited States of America
- University of Koblenz-Landau, Universitätsstraße 1, Koblenz, 56070, GermanyIUCN SSC Central Africa Plant Red List Authority (CARLA)GlandSwitzerland
- East African Herbarium, National Museums of Kenya, P.O. Box 45166-00100, Nairobi, KenyaUniversité Libre de BruxellesBrusselsBelgium
| | - Marc S. M. Sosef
- Meise Botanic Garden, Nieuwelaan 38, 1860 Meise, BelgiumMeise Botanic GardenMeiseBelgium
- University of Koblenz-Landau, Universitätsstraße 1, Koblenz, 56070, GermanyIUCN SSC Central Africa Plant Red List Authority (CARLA)GlandSwitzerland
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8
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Marcussen T, Ballard HE, Danihelka J, Flores AR, Nicola MV, Watson JM. A Revised Phylogenetic Classification for Viola (Violaceae). PLANTS 2022; 11:plants11172224. [PMID: 36079606 PMCID: PMC9460890 DOI: 10.3390/plants11172224] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 08/15/2022] [Accepted: 08/16/2022] [Indexed: 11/26/2022]
Abstract
The genus Viola (Violaceae) is among the 40–50 largest genera among angiosperms, yet its taxonomy has not been revised for nearly a century. In the most recent revision, by Wilhelm Becker in 1925, the then-known 400 species were distributed among 14 sections and numerous unranked groups. Here, we provide an updated, comprehensive classification of the genus, based on data from phylogeny, morphology, chromosome counts, and ploidy, and based on modern principles of monophyly. The revision is presented as an annotated global checklist of accepted species of Viola, an updated multigene phylogenetic network and an ITS phylogeny with denser taxon sampling, a brief summary of the taxonomic changes from Becker’s classification and their justification, a morphological binary key to the accepted subgenera, sections and subsections, and an account of each infrageneric subdivision with justifications for delimitation and rank including a description, a list of apomorphies, molecular phylogenies where possible or relevant, a distribution map, and a list of included species. We distribute the 664 species accepted by us into 2 subgenera, 31 sections, and 20 subsections. We erect one new subgenus of Viola (subg. Neoandinium, a replacement name for the illegitimate subg. Andinium), six new sections (sect. Abyssinium, sect. Himalayum, sect. Melvio, sect. Nematocaulon, sect. Spathulidium, sect. Xanthidium), and seven new subsections (subsect. Australasiaticae, subsect. Bulbosae, subsect. Clausenianae, subsect. Cleistogamae, subsect. Dispares, subsect. Formosanae, subsect. Pseudorupestres). Evolution within the genus is discussed in light of biogeography, the fossil record, morphology, and particular traits. Viola is among very few temperate and widespread genera that originated in South America. The biggest identified knowledge gaps for Viola concern the South American taxa, for which basic knowledge from phylogeny, chromosome counts, and fossil data is virtually absent. Viola has also never been subject to comprehensive anatomical study. Studies into seed anatomy and morphology are required to understand the fossil record of the genus.
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Affiliation(s)
- Thomas Marcussen
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, P.O. Box 1066 Blindern, NO-0316 Oslo, Norway
- Correspondence:
| | - Harvey E. Ballard
- Department of Environmental and Plant Biology, Ohio University, Athens, OH 45701, USA
| | - Jiří Danihelka
- Department of Botany and Zoology, Masaryk University, Kotlářská 2, CZ-61137 Brno, Czech Republic
- Czech Academy of Sciences, Institute of Botany, Zámek 1, CZ-252 43 Průhonice, Czech Republic
| | - Ana R. Flores
- Independent Researcher, Casilla 161, Los Andes 2100412, Chile
| | - Marcela V. Nicola
- Instituto de Botánica Darwinion (IBODA, CONICET-ANCEFN), Labardén 200, Casilla de Correo 22, San Isidro, Buenos Aires B1642HYD, Argentina
| | - John M. Watson
- Independent Researcher, Casilla 161, Los Andes 2100412, Chile
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9
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Zhang Q, Ye J, Le C, Njenga DM, Rabarijaona NR, Omollo WO, Lu L, Liu B, Chen Z. New insights into the formation of biodiversity hotspots of the Kenyan flora. DIVERS DISTRIB 2022. [DOI: 10.1111/ddi.13624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Qiang Zhang
- State Key Laboratory of Systematic and Evolutionary Botany Institute of Botany, Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
| | - Jian‐Fei Ye
- Beijing Botanical Garden Institute of Botany, Chinese Academy of Sciences Beijing China
| | - Chi‐Toan Le
- Ha Noi Pedagogical University 2 Phuc Yen Vietnam
| | - Dennis Mwithukia Njenga
- State Key Laboratory of Systematic and Evolutionary Botany Institute of Botany, Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
| | - Narindra Romer Rabarijaona
- State Key Laboratory of Systematic and Evolutionary Botany Institute of Botany, Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
| | - Wyckliffe Omondi Omollo
- State Key Laboratory of Systematic and Evolutionary Botany Institute of Botany, Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
| | - Li‐Min Lu
- State Key Laboratory of Systematic and Evolutionary Botany Institute of Botany, Chinese Academy of Sciences Beijing China
| | - Bing Liu
- State Key Laboratory of Systematic and Evolutionary Botany Institute of Botany, Chinese Academy of Sciences Beijing China
- Sino‐Africa Joint Research Center Chinese Academy of Sciences Wuhan China
| | - Zhi‐Duan Chen
- State Key Laboratory of Systematic and Evolutionary Botany Institute of Botany, Chinese Academy of Sciences Beijing China
- Sino‐Africa Joint Research Center Chinese Academy of Sciences Wuhan China
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10
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Kass JM, Guénard B, Dudley KL, Jenkins CN, Azuma F, Fisher BL, Parr CL, Gibb H, Longino JT, Ward PS, Chao A, Lubertazzi D, Weiser M, Jetz W, Guralnick R, Blatrix R, Lauriers JD, Donoso DA, Georgiadis C, Gomez K, Hawkes PG, Johnson RA, Lattke JE, MacGown JA, Mackay W, Robson S, Sanders NJ, Dunn RR, Economo EP. The global distribution of known and undiscovered ant biodiversity. SCIENCE ADVANCES 2022; 8:eabp9908. [PMID: 35921404 PMCID: PMC9348798 DOI: 10.1126/sciadv.abp9908] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 06/21/2022] [Indexed: 05/26/2023]
Abstract
Invertebrates constitute the majority of animal species and are critical for ecosystem functioning and services. Nonetheless, global invertebrate biodiversity patterns and their congruences with vertebrates remain largely unknown. We resolve the first high-resolution (~20-km) global diversity map for a major invertebrate clade, ants, using biodiversity informatics, range modeling, and machine learning to synthesize existing knowledge and predict the distribution of undiscovered diversity. We find that ants and different vertebrate groups have distinct features in their patterns of richness and rarity, underscoring the need to consider a diversity of taxa in conservation. However, despite their phylogenetic and physiological divergence, ant distributions are not highly anomalous relative to variation among vertebrate clades. Furthermore, our models predict that rarity centers largely overlap (78%), suggesting that general forces shape endemism patterns across taxa. This raises confidence that conservation of areas important for small-ranged vertebrates will benefit invertebrates while providing a "treasure map" to guide future discovery.
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Affiliation(s)
- Jamie M. Kass
- Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology, Onna, Okinawa 904-0495, Japan
| | - Benoit Guénard
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Kenneth L. Dudley
- Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology, Onna, Okinawa 904-0495, Japan
| | - Clinton N. Jenkins
- Department of Earth and Environment and Kimberly Green Latin American and Caribbean Center, Florida International University, 11200 SW 8th Street, Miami, FL 33199, USA
| | - Fumika Azuma
- Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology, Onna, Okinawa 904-0495, Japan
| | - Brian L. Fisher
- Entomology, California Academy of Sciences, San Francisco, CA 94118, USA
| | - Catherine L. Parr
- School of Environmental Sciences, University of Liverpool, Liverpool L69 3GP, UK
- Department of Zoology and Entomology, University of Pretoria, Pretoria 0028, South Africa
- School of Animal, Plant, and Environmental Sciences, University of the Witwatersrand, Johannesburg, Wits 2050, South Africa
| | - Heloise Gibb
- Department of Ecology, Environment and Evolution, and Center for Future Landscapes, La Trobe University, Bundoora, Victoria 3086, Australia
| | - John T. Longino
- School of Biology, University of Utah, Salt Lake City, UT 84112, USA
| | - Philip S. Ward
- Department of Entomology and Nematology, University of California, Davis, Davis, CA 95616, USA
| | - Anne Chao
- Institute of Statistics, National Tsing Hua University, Hsin-Chu 30043, Taiwan
| | - David Lubertazzi
- Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Michael Weiser
- Department of Biology and Geographical Ecology Group, University of Oklahoma, Norman, OK 73019, USA
| | - Walter Jetz
- Center for Biodiversity and Global Change and Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA
| | - Robert Guralnick
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Rumsaïs Blatrix
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | | | - David A. Donoso
- Departamento de Biología, Escuela Politécnica Nacional, Quito, Ecuador
| | - Christos Georgiadis
- Section of Zoology–Marine Biology, Department of Biology, National and Kapodistrian University of Athens, Zografou 15772, Greece
| | | | - Peter G. Hawkes
- AfriBugs CC, 341 27th Avenue, Villieria, Pretoria, Gauteng Province 0186, South Africa
- Department of Biological Sciences, University of Venda, Thohoyandou, Limpopo Province, South Africa
| | - Robert A. Johnson
- School of Life Sciences, Arizona State University, Tempe, AZ 852787-4501, USA
| | - John E. Lattke
- Department of Zoology, Universidade Federal do Paraná, Curitiba, CEP 81531-980, PR, Brazil
| | - Joe A. MacGown
- Department of Molecular Biology, Biochemistry, Entomology, and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA
| | - William Mackay
- Biodiversity Collections, Department of Biological Sciences, University of Texas, El Paso, TX, 79968, USA
| | - Simon Robson
- College of Science and Engineering, Central Queensland University, Townsville, QLD 4812, Australia
| | - Nathan J. Sanders
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Robert R. Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, NC 27607, USA
| | - Evan P. Economo
- Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology, Onna, Okinawa 904-0495, Japan
- Radcliffe Institute for Advanced Study, Harvard University, Cambridge, MA 02138, USA
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11
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Führding‐Potschkat P, Kreft H, Ickert‐Bond SM. Influence of different data cleaning solutions of point‐occurrence records on downstream macroecological diversity models. Ecol Evol 2022; 12:e9168. [PMID: 35949539 PMCID: PMC9351331 DOI: 10.1002/ece3.9168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 07/07/2022] [Accepted: 07/12/2022] [Indexed: 11/20/2022] Open
Abstract
Digital point‐occurrence records from the Global Biodiversity Information Facility (GBIF) and other data providers enable a wide range of research in macroecology and biogeography. However, data errors may hamper immediate use. Manual data cleaning is time‐consuming and often unfeasible, given that the databases may contain thousands or millions of records. Automated data cleaning pipelines are therefore of high importance. Taking North American Ephedra as a model, we examined how different data cleaning pipelines (using, e.g., the GBIF web application, and four different R packages) affect downstream species distribution models (SDMs). We also assessed how data differed from expert data. From 13,889 North American Ephedra observations in GBIF, the pipelines removed 31.7% to 62.7% false positives, invalid coordinates, and duplicates, leading to datasets between 9484 (GBIF application) and 5196 records (manual‐guided filtering). The expert data consisted of 704 records, comparable to data from field studies. Although differences in the absolute numbers of records were relatively large, species richness models based on stacked SDMs (S‐SDM) from pipeline and expert data were strongly correlated (mean Pearson's r across the pipelines: .9986, vs. the expert data: .9173). Our results suggest that all R package‐based pipelines reliably identified invalid coordinates. In contrast, the GBIF‐filtered data still contained both spatial and taxonomic errors. Major drawbacks emerge from the fact that no pipeline fully discovered misidentified specimens without the assistance of taxonomic expert knowledge. We conclude that application‐filtered GBIF data will still need additional review to achieve higher spatial data quality. Achieving high‐quality taxonomic data will require extra effort, probably by thoroughly analyzing the data for misidentified taxa, supported by experts.
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Affiliation(s)
- Petra Führding‐Potschkat
- Biodiversity, Macroecology and Conservation Biogeography, Faculty of Forest SciencesUniversity of GöttingenGöttingenGermany
| | - Holger Kreft
- Biodiversity, Macroecology and Conservation Biogeography, Faculty of Forest SciencesUniversity of GöttingenGöttingenGermany
| | - Stefanie M. Ickert‐Bond
- Department of Biology and Wildlife & UA Museum of the NorthUniversity of Alaska FairbanksFairbanksAlaskaUSA
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12
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Abstract
Despite best efforts, the loss of biodiversity has continued at a pace that constitutes a major threat to the efficient functioning of ecosystems. Curbing the loss of biodiversity and assessing its local and global trends requires a vast amount of datasets from a variety of sources. Although the means for generating, aggregating and analyzing big datasets to inform policies are now within the reach of the scientific community, the data-driven nature of a complex multidisciplinary field such as biodiversity science necessitates an overarching framework for engagement. In this review, we propose such a schematic based on the life cycle of data to interrogate the science. The framework considers data generation and collection, storage and curation, access and analysis and, finally, communication as distinct yet interdependent themes for engaging biodiversity science for the purpose of making evidenced-based decisions. We summarize historical developments in each theme, including the challenges and prospects, and offer some recommendations based on best practices.
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13
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Zizka A, Antunes Carvalho F, Calvente A, Rocio Baez-Lizarazo M, Cabral A, Coelho JFR, Colli-Silva M, Fantinati MR, Fernandes MF, Ferreira-Araújo T, Gondim Lambert Moreira F, Santos NMC, Santos TAB, Dos Santos-Costa RC, Serrano FC, Alves da Silva AP, de Souza Soares A, Cavalcante de Souza PG, Calisto Tomaz E, Vale VF, Vieira TL, Antonelli A. No one-size-fits-all solution to clean GBIF. PeerJ 2020; 8:e9916. [PMID: 33062422 PMCID: PMC7528811 DOI: 10.7717/peerj.9916] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 08/20/2020] [Indexed: 12/05/2022] Open
Abstract
Species occurrence records provide the basis for many biodiversity studies. They derive from georeferenced specimens deposited in natural history collections and visual observations, such as those obtained through various mobile applications. Given the rapid increase in availability of such data, the control of quality and accuracy constitutes a particular concern. Automatic filtering is a scalable and reproducible means to identify potentially problematic records and tailor datasets from public databases such as the Global Biodiversity Information Facility (GBIF; http://www.gbif.org), for biodiversity analyses. However, it is unclear how much data may be lost by filtering, whether the same filters should be applied across all taxonomic groups, and what the effect of filtering is on common downstream analyses. Here, we evaluate the effect of 13 recently proposed filters on the inference of species richness patterns and automated conservation assessments for 18 Neotropical taxa, including terrestrial and marine animals, fungi, and plants downloaded from GBIF. We find that a total of 44.3% of the records are potentially problematic, with large variation across taxonomic groups (25–90%). A small fraction of records was identified as erroneous in the strict sense (4.2%), and a much larger proportion as unfit for most downstream analyses (41.7%). Filters of duplicated information, collection year, and basis of record, as well as coordinates in urban areas, or for terrestrial taxa in the sea or marine taxa on land, have the greatest effect. Automated filtering can help in identifying problematic records, but requires customization of which tests and thresholds should be applied to the taxonomic group and geographic area under focus. Our results stress the importance of thorough recording and exploration of the meta-data associated with species records for biodiversity research.
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Affiliation(s)
- Alexander Zizka
- sDiv, German Centre for Integrative Biodiversity Research Halle-Jena-Leipzig (iDiv), Leipzig, Germany.,Naturalis Biodiversity Center, Leiden, The Netherlands
| | - Fernanda Antunes Carvalho
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Alice Calvente
- Departamento de Botânica e Zoologia, Universidade Federal do Rio Grande do Norte, Natal, Brazil
| | | | - Andressa Cabral
- Departamento de Botânica, Universidade de São Paulo, São Paulo, Brazil
| | | | | | - Mariana Ramos Fantinati
- Departamento de Botânica e Zoologia, Universidade Federal do Rio Grande do Norte, Natal, Brazil
| | - Moabe F Fernandes
- Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana, Feira de Santana, Brazil
| | - Thais Ferreira-Araújo
- Departamento de Botânica e Zoologia, Universidade Federal do Rio Grande do Norte, Natal, Brazil
| | | | | | | | | | - Filipe C Serrano
- Departamento de Ecologia, Universidade de São Paulo, São Paulo, Brazil
| | | | - Arthur de Souza Soares
- Departamento de Botânica e Zoologia, Universidade Federal do Rio Grande do Norte, Natal, Brazil
| | | | - Eduardo Calisto Tomaz
- Departamento de Botânica e Zoologia, Universidade Federal do Rio Grande do Norte, Natal, Brazil
| | - Valéria Fonseca Vale
- Departamento de Botânica e Zoologia, Universidade Federal do Rio Grande do Norte, Natal, Brazil
| | - Tiago Luiz Vieira
- Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana, Feira de Santana, Brazil
| | - Alexandre Antonelli
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden.,Department for Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden.,Royal Botanic Gardens Kew, Richmond, United Kingdom
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14
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Pimiento C, Bacon CD, Silvestro D, Hendy A, Jaramillo C, Zizka A, Meyer X, Antonelli A. Selective extinction against redundant species buffers functional diversity. Proc Biol Sci 2020; 287:20201162. [PMID: 32693723 PMCID: PMC7423665 DOI: 10.1098/rspb.2020.1162] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The extinction of species can destabilize ecological processes. A way to assess the ecological consequences of species loss is by examining changes in functional diversity. The preservation of functional diversity depends on the range of ecological roles performed by species, or functional richness, and the number of species per role, or functional redundancy. However, current knowledge is based on short timescales and an understanding of how functional diversity responds to long-term biodiversity dynamics has been limited by the availability of deep-time, trait-based data. Here, we compile an exceptional trait dataset of fossil molluscs from a 23-million-year interval in the Caribbean Sea (34 011 records, 4422 species) and develop a novel Bayesian model of multi-trait-dependent diversification to reconstruct mollusc (i) diversity dynamics, (ii) changes in functional diversity, and (iii) extinction selectivity over the last 23 Myr. Our results identify high diversification between 23–5 Mya, leading to increases in both functional richness and redundancy. Conversely, over the last three million years, a period of high extinction rates resulted in the loss of 49% of species but only 3% of functional richness. Extinction rates were significantly higher in small, functionally redundant species suggesting that competition mediated the response of species to environmental change. Taken together, our results identify long-term diversification and selective extinction against redundant species that allowed functional diversity to grow over time, ultimately buffering the ecological functions of biological communities against extinction.
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Affiliation(s)
- Catalina Pimiento
- Department of Biosciences, Swansea University, Swansea SA2 8PP, UK.,Smithsonian Tropical Research Institute, Box 0843-03092, Balboa, Ancon, Republic of Panama
| | - Christine D Bacon
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, SE-405 30 Gothenburg, Sweden.,Gothenburg Global Biodiversity Centre, Box 461, SE-405 30 Gothenburg, Sweden
| | - Daniele Silvestro
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, SE-405 30 Gothenburg, Sweden.,Gothenburg Global Biodiversity Centre, Box 461, SE-405 30 Gothenburg, Sweden.,Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Austin Hendy
- Natural History Museum of Los Angeles County, Los Angeles, CA 90007, USA
| | - Carlos Jaramillo
- Smithsonian Tropical Research Institute, Box 0843-03092, Balboa, Ancon, Republic of Panama.,Equipe de Paléontologie, Institut des Sciences de l'Évolution de Montpellier, University of Montpellier, Place Eugène Bataillon, 34095 Montpellier Cedex 05, France.,Institut des Sciences de l'Évolution de Montpellier, University of Montpellier, Place Eugène Bataillon, 34095 Montpellier Cedex 05, France
| | - Alexander Zizka
- Gothenburg Global Biodiversity Centre, Box 461, SE-405 30 Gothenburg, Sweden.,German Center for Integrative Biodiversity Research (iDiv) Halle Jena Leipzig, 04103 Leipzig, Germany
| | - Xavier Meyer
- Department of Biology, University of Fribourg, Fribourg, Switzerland.,Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, SE-405 30 Gothenburg, Sweden.,Gothenburg Global Biodiversity Centre, Box 461, SE-405 30 Gothenburg, Sweden.,Royal Botanical Gardens Kew, Richmond TW9 3AE, UK
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15
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Joyce EM, Thiele KR, Slik FJW, Crayn DM. Checklist of the vascular flora of the Sunda-Sahul Convergence Zone. Biodivers Data J 2020; 8:e51094. [PMID: 32508510 PMCID: PMC7248131 DOI: 10.3897/bdj.8.e51094] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 05/05/2020] [Indexed: 11/25/2022] Open
Abstract
Background The Sunda-Sahul Convergence Zone, defined here as the area comprising Australia, New Guinea, and Southeast Asia (Indonesia to Myanmar), straddles the Sunda and Sahul continental shelves and is one of the most biogeographically famous and important regions in the world. Floristically, it is thought to harbour a large amount of the world’s diversity. Despite the importance of the area, a checklist of the flora has never before been published. Here we present the first working checklist of vascular plants for the Sunda-Sahul Convergence Zone. The list was compiled from 24 flora volumes, online databases and unpublished plot data. Taxonomic nomenclature was updated, and each species was coded into nested biogeographic regions. The list includes 60,415 species in 5,135 genera and 363 families of vascular plants. New information This is the first species-level checklist of the region and presents an updated census of the region’s floristic biodiversity. The checklist confirms that species richness of the SSCZ is comparable to that of the Neotropics, and highlights areas in need of further documentation and taxonomic work. This checklist provides a novel dataset for studying floristic ecology and evolution in this biogeographically important region of very high global biodiversity.
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Affiliation(s)
- Elizabeth M Joyce
- Australian Tropical Herbarium, James Cook University, Cairns, 4870, Australia Australian Tropical Herbarium, James Cook University Cairns, 4870 Australia.,College of Science and Engineering, James Cook University, Cairns, 4870, Australia College of Science and Engineering, James Cook University Cairns, 4870 Australia.,Centre for Tropical Environmental Sustainability Science, James Cook University, Cairns, 4870, Australia Centre for Tropical Environmental Sustainability Science, James Cook University Cairns, 4870 Australia
| | - Kevin R Thiele
- School of Biological Sciences, The University of Western Australia, Crawley, 6009, Australia School of Biological Sciences, The University of Western Australia Crawley, 6009 Australia
| | - Ferry J W Slik
- Faculty of Science, Department of Environmental and Life Sciences, Universiti Brunei Darussalam, Gadong BE1410, Brunei Faculty of Science, Department of Environmental and Life Sciences, Universiti Brunei Darussalam Gadong BE1410 Brunei
| | - Darren M Crayn
- Australian Tropical Herbarium, James Cook University, Cairns, 4870, Australia Australian Tropical Herbarium, James Cook University Cairns, 4870 Australia.,College of Science and Engineering, James Cook University, Cairns, 4870, Australia College of Science and Engineering, James Cook University Cairns, 4870 Australia.,Centre for Tropical Environmental Sustainability Science, James Cook University, Cairns, 4870, Australia Centre for Tropical Environmental Sustainability Science, James Cook University Cairns, 4870 Australia
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16
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Batista R, Olsson U, Andermann T, Aleixo A, Ribas CC, Antonelli A. Phylogenomics and biogeography of the world's thrushes (Aves, Turdus): new evidence for a more parsimonious evolutionary history. Proc Biol Sci 2020; 287:20192400. [PMID: 31964299 DOI: 10.1098/rspb.2019.2400] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
To elucidate the relationships and spatial range evolution across the world of the bird genus Turdus (Aves), we produced a large genomic dataset comprising ca 2 million nucleotides for ca 100 samples representing 53 species, including over 2000 loci. We estimated time-calibrated maximum-likelihood and multispecies coalescent phylogenies and carried out biogeographic analyses. Our results indicate that there have been considerably fewer trans-oceanic dispersals within the genus Turdus than previously suggested, such that the Palaearctic clade did not originate in America and the African clade was not involved in the colonization of the Americas. Instead, our findings suggest that dispersal from the Western Palaearctic via the Antilles to the Neotropics might have occurred in a single event, giving rise to the rich Neotropical diversity of Turdus observed today, with no reverse dispersals to the Palaearctic or Africa. Our large multilocus dataset, combined with dense species-level sampling and analysed under probabilistic methods, brings important insights into historical biogeography and systematics, even in a scenario of fast and spatially complex diversification.
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Affiliation(s)
- Romina Batista
- Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva, PPG GCBEv - Instituto Nacional de Pesquisas da Amazônia (INPA) Campus II, Av. André Araújo, 2936, Petrópolis, CEP 69067-375 Manaus, Amazonas, Brazil.,Coordenação de Zoologia, Laboratório de Biologia Molecular, Museu Paraense Emílio Goeldi, CEP 66077-830 Belém, Pará, Brazil.,Gothenburg Global Biodiversity Centre, Box 461, 405 30 Gothenburg, Sweden
| | - Urban Olsson
- Gothenburg Global Biodiversity Centre, Box 461, 405 30 Gothenburg, Sweden.,Department of Biological and Environmental Sciences, University of Gothenburg, SE-413 19 Gothenburg, Sweden
| | - Tobias Andermann
- Gothenburg Global Biodiversity Centre, Box 461, 405 30 Gothenburg, Sweden.,Department of Biological and Environmental Sciences, University of Gothenburg, SE-413 19 Gothenburg, Sweden
| | - Alexandre Aleixo
- Finnish Museum of Natural History, University of Helsinki, P.O. Box 17, 00014 Helsinki, Finland
| | - Camila Cherem Ribas
- Instituto Nacional de Pesquisas da Amazônia, (INPA) Campus II, Av. André Araújo, 2936, CEP 69060-000 Manaus, Amazonas, Brazil
| | - Alexandre Antonelli
- Gothenburg Global Biodiversity Centre, Box 461, 405 30 Gothenburg, Sweden.,Department of Biological and Environmental Sciences, University of Gothenburg, SE-413 19 Gothenburg, Sweden.,Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
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17
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Antonelli A, Ariza M, Albert J, Andermann T, Azevedo J, Bacon C, Faurby S, Guedes T, Hoorn C, Lohmann LG, Matos-Maraví P, Ritter CD, Sanmartín I, Silvestro D, Tejedor M, ter Steege H, Tuomisto H, Werneck FP, Zizka A, Edwards SV. Conceptual and empirical advances in Neotropical biodiversity research. PeerJ 2018; 6:e5644. [PMID: 30310740 PMCID: PMC6174874 DOI: 10.7717/peerj.5644] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 08/27/2018] [Indexed: 01/23/2023] Open
Abstract
The unparalleled biodiversity found in the American tropics (the Neotropics) has attracted the attention of naturalists for centuries. Despite major advances in recent years in our understanding of the origin and diversification of many Neotropical taxa and biotic regions, many questions remain to be answered. Additional biological and geological data are still needed, as well as methodological advances that are capable of bridging these research fields. In this review, aimed primarily at advanced students and early-career scientists, we introduce the concept of "trans-disciplinary biogeography," which refers to the integration of data from multiple areas of research in biology (e.g., community ecology, phylogeography, systematics, historical biogeography) and Earth and the physical sciences (e.g., geology, climatology, palaeontology), as a means to reconstruct the giant puzzle of Neotropical biodiversity and evolution in space and time. We caution against extrapolating results derived from the study of one or a few taxa to convey general scenarios of Neotropical evolution and landscape formation. We urge more coordination and integration of data and ideas among disciplines, transcending their traditional boundaries, as a basis for advancing tomorrow's ground-breaking research. Our review highlights the great opportunities for studying the Neotropical biota to understand the evolution of life.
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Affiliation(s)
- Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Gothenburg Botanical Garden, Gothenburg, Sweden
- Department of Organismic Biology and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - María Ariza
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Laboratory Ecologie et Biologie des Interactions, Team “Ecologie, Evolution, Symbiose”, Université de Poitiers, Poitiers, France
| | - James Albert
- Department of Biology, University of Louisiana at Lafayette, Lafayette, LA, USA
| | - Tobias Andermann
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Josué Azevedo
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Christine Bacon
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Søren Faurby
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Thais Guedes
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Federal University of São Paulo, Diadema, Brazil
- Museum of Zoology, University of São Paulo, São Paulo, Brazil
| | - Carina Hoorn
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
- Universidad Regional Amazonica IKIAM, Napo, Ecuador
| | - Lúcia G. Lohmann
- Instituto de Biociências, Departamento de Botânica, Universidade de São Paulo, São Paulo, Brazil
- Integrative Biology, University of California, Berkeley, CA, USA
| | - Pável Matos-Maraví
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Camila D. Ritter
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | | | - Daniele Silvestro
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Marcelo Tejedor
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Instituto Patagónico de Geología y Paleontología, Puerto Madryn, Guatemala
| | - Hans ter Steege
- Naturalis Biodiversity Center, Leiden, Netherlands
- Systems Ecology, Free University, Amsterdam, Netherlands
| | - Hanna Tuomisto
- Department of Biology, University of Turku, Turku, Finland
| | | | - Alexander Zizka
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Scott V. Edwards
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Department of Organismic Biology and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
- Gothenburg Centre for Advanced Studies in Science and Technology, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden
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18
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Abstract
Amazonia is not only the world’s most diverse rainforest but is also the region in tropical America that has contributed most to its total biodiversity. We show this by estimating and comparing the evolutionary history of a large number of animal and plant species. We find that there has been extensive interchange of evolutionary lineages among different regions and biomes, over the course of tens of millions of years. Amazonia stands out as the primary source of diversity, which can be mainly explained by the total amount of time Amazonian lineages have occupied the region. The exceedingly rich and heterogeneous diversity of the American tropics could only be achieved by high rates of dispersal events across the continent. The American tropics (the Neotropics) are the most species-rich realm on Earth, and for centuries, scientists have attempted to understand the origins and evolution of their biodiversity. It is now clear that different regions and taxonomic groups have responded differently to geological and climatic changes. However, we still lack a basic understanding of how Neotropical biodiversity was assembled over evolutionary timescales. Here we infer the timing and origin of the living biota in all major Neotropical regions by performing a cross-taxonomic biogeographic analysis based on 4,450 species from six major clades across the tree of life (angiosperms, birds, ferns, frogs, mammals, and squamates), and integrate >1.3 million species occurrences with large-scale phylogenies. We report an unprecedented level of biotic interchange among all Neotropical regions, totaling 4,525 dispersal events. About half of these events involved transitions between major environmental types, with a predominant directionality from forested to open biomes. For all taxonomic groups surveyed here, Amazonia is the primary source of Neotropical diversity, providing >2,800 lineages to other regions. Most of these dispersal events were to Mesoamerica (∼1,500 lineages), followed by dispersals into open regions of northern South America and the Cerrado and Chaco biomes. Biotic interchange has taken place for >60 million years and generally increased toward the present. The total amount of time lineages spend in a region appears to be the strongest predictor of migration events. These results demonstrate the complex origin of tropical ecosystems and the key role of biotic interchange for the assembly of regional biotas.
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19
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Antonelli A, Hettling H, Condamine FL, Vos K, Nilsson RH, Sanderson MJ, Sauquet H, Scharn R, Silvestro D, Töpel M, Bacon CD, Oxelman B, Vos RA. Toward a Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa. Syst Biol 2018; 66:152-166. [PMID: 27616324 PMCID: PMC5410925 DOI: 10.1093/sysbio/syw066] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 07/19/2016] [Indexed: 01/06/2023] Open
Abstract
Rapidly growing biological data—including molecular sequences and fossils—hold an unprecedented potential to reveal how evolutionary processes generate and maintain biodiversity. However, researchers often have to develop their own idiosyncratic workflows to integrate and analyze these data for reconstructing time-calibrated phylogenies. In addition, divergence times estimated under different methods and assumptions, and based on data of various quality and reliability, should not be combined without proper correction. Here we introduce a modular framework termed SUPERSMART (Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa), and provide a proof of concept for dealing with the moving targets of evolutionary and biogeographical research. This framework assembles comprehensive data sets of molecular and fossil data for any taxa and infers dated phylogenies using robust species tree methods, also allowing for the inclusion of genomic data produced through next-generation sequencing techniques. We exemplify the application of our method by presenting phylogenetic and dating analyses for the mammal order Primates and for the plant family Arecaceae (palms). We believe that this framework will provide a valuable tool for a wide range of hypothesis-driven research questions in systematics, biogeography, and evolution. SUPERSMART will also accelerate the inference of a “Dated Tree of Life” where all node ages are directly comparable.
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Affiliation(s)
- Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, SE-405 30 Göteborg, Sweden.,Gothenburg Botanical Garden, Carl Skottsbergs Gata 22A, SE-41319 Göteborg, Sweden
| | - Hannes Hettling
- Naturalis Biodiversity Center, Darwinweg 4, 2333 CR Leiden, The Netherlands
| | - Fabien L Condamine
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, SE-405 30 Göteborg, Sweden.,CNRS, UMR 5554 Institut des Sciences de l'Evolution (Université de Montpellier), Place Eugéne Bataillon, 34095 Montpellier, France
| | - Karin Vos
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, SE-405 30 Göteborg, Sweden
| | - R Henrik Nilsson
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, SE-405 30 Göteborg, Sweden
| | - Michael J Sanderson
- Department of Ecology and Evolutionary Biology, University of Arizona, 1041 E. Lowell, Tucson, AZ 85721, USA
| | - Hervé Sauquet
- Université Paris-Sud, Laboratoire Écologie, Systématique, Évolution, CNRS UMR 8079, 91405 Orsay, France
| | - Ruud Scharn
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, SE-405 30 Göteborg, Sweden
| | - Daniele Silvestro
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, SE-405 30 Göteborg, Sweden.,Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
| | - Mats Töpel
- Swedish Bioinformatics Infrastructure for Life Sciences, Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, SE-405 30, Göteborg, Sweden.,Department of Marine Sciences, University of Gothenburg, Box 460, SE-405 30 Göteborg, Sweden
| | - Christine D Bacon
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, SE-405 30 Göteborg, Sweden
| | - Bengt Oxelman
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, SE-405 30 Göteborg, Sweden
| | - Rutger A Vos
- Naturalis Biodiversity Center, Darwinweg 4, 2333 CR Leiden, The Netherlands
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20
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Edler D, Guedes T, Zizka A, Rosvall M, Antonelli A. Infomap Bioregions: Interactive Mapping of Biogeographical Regions from Species Distributions. Syst Biol 2018; 66:197-204. [PMID: 27694311 PMCID: PMC5410963 DOI: 10.1093/sysbio/syw087] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 09/26/2016] [Indexed: 11/24/2022] Open
Abstract
Biogeographical regions (bioregions) reveal how different sets of species are spatially grouped and therefore are important units for conservation, historical biogeography, ecology, and evolution. Several methods have been developed to identify bioregions based on species distribution data rather than expert opinion. One approach successfully applies network theory to simplify and highlight the underlying structure in species distributions. However, this method lacks tools for simple and efficient analysis. Here, we present Infomap Bioregions, an interactive web application that inputs species distribution data and generates bioregion maps. Species distributions may be provided as georeferenced point occurrences or range maps, and can be of local, regional, or global scale. The application uses a novel adaptive resolution method to make best use of often incomplete species distribution data. The results can be downloaded as vector graphics, shapefiles, or in table format. We validate the tool by processing large data sets of publicly available species distribution data of the world’s amphibians using species ranges, and mammals using point occurrences. We then calculate the fit between the inferred bioregions and WWF ecoregions. As examples of applications, researchers can reconstruct ancestral ranges in historical biogeography or identify indicator species for targeted conservation.
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Affiliation(s)
- Daniel Edler
- Integrated Science Lab, Department of Physics, Umeå University, SE-901 87 Umeå, Sweden.,Department of Biological and Environmental Sciences, University of Gothenburg, PO Box 461, SE-405 30 Gothenburg, Sweden
| | - Thaís Guedes
- Department of Biological and Environmental Sciences, University of Gothenburg, PO Box 461, SE-405 30 Gothenburg, Sweden.,Federal University of São Paulo, 09972-270 Diadema, Brazil.,Museum of Zoology of University of São Paulo, 04263-000 São Paulo, Brazil
| | - Alexander Zizka
- Department of Biological and Environmental Sciences, University of Gothenburg, PO Box 461, SE-405 30 Gothenburg, Sweden
| | - Martin Rosvall
- Integrated Science Lab, Department of Physics, Umeå University, SE-901 87 Umeå, Sweden
| | - Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, PO Box 461, SE-405 30 Gothenburg, Sweden.,Gothenburg Botanical Garden, Carl Skottsbergs Gata 22A, 413 19 Gothenburg, Sweden
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21
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Guedes TB, Sawaya RJ, Zizka A, Laffan S, Faurby S, Pyron RA, Bérnils RS, Jansen M, Passos P, Prudente ALC, Cisneros‐Heredia DF, Braz HB, Nogueira CDC, Antonelli A, Meiri S. Patterns, biases and prospects in the distribution and diversity of Neotropical snakes. GLOBAL ECOLOGY AND BIOGEOGRAPHY : A JOURNAL OF MACROECOLOGY 2018; 27:14-21. [PMID: 29398972 PMCID: PMC5765514 DOI: 10.1111/geb.12679] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 09/12/2017] [Accepted: 09/22/2017] [Indexed: 05/19/2023]
Abstract
MOTIVATION We generated a novel database of Neotropical snakes (one of the world's richest herpetofauna) combining the most comprehensive, manually compiled distribution dataset with publicly available data. We assess, for the first time, the diversity patterns for all Neotropical snakes as well as sampling density and sampling biases. MAIN TYPES OF VARIABLES CONTAINED We compiled three databases of species occurrences: a dataset downloaded from the Global Biodiversity Information Facility (GBIF), a verified dataset built through taxonomic work and specialized literature, and a combined dataset comprising a cleaned version of the GBIF dataset merged with the verified dataset. SPATIAL LOCATION AND GRAIN Neotropics, Behrmann projection equivalent to 1° × 1°. TIME PERIOD Specimens housed in museums during the last 150 years. MAJOR TAXA STUDIED Squamata: Serpentes. SOFTWARE FORMAT Geographical information system (GIS). RESULTS The combined dataset provides the most comprehensive distribution database for Neotropical snakes to date. It contains 147,515 records for 886 species across 12 families, representing 74% of all species of snakes, spanning 27 countries in the Americas. Species richness and phylogenetic diversity show overall similar patterns. Amazonia is the least sampled Neotropical region, whereas most well-sampled sites are located near large universities and scientific collections. We provide a list and updated maps of geographical distribution of all snake species surveyed. MAIN CONCLUSIONS The biodiversity metrics of Neotropical snakes reflect patterns previously documented for other vertebrates, suggesting that similar factors may determine the diversity of both ectothermic and endothermic animals. We suggest conservation strategies for high-diversity areas and sampling efforts be directed towards Amazonia and poorly known species.
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Affiliation(s)
- Thaís B. Guedes
- Department of Biological and Environmental SciencesUniversity of GothenburgGöteborgSweden
- Gothenburg Global Biodiversity CenterGöteborgSweden
- Departamento de Ecologia e Biologia EvolutivaUniversidade Federal de São Paulo (UNIFESP)DiademaSão PauloBrazil
- Laboratório de HerpetologiaMuseu de Zoologia da Universidade de São Paulo (MZUSP)São PauloSão PauloBrazil
| | - Ricardo J. Sawaya
- Departamento de Ecologia e Biologia EvolutivaUniversidade Federal de São Paulo (UNIFESP)DiademaSão PauloBrazil
| | - Alexander Zizka
- Department of Biological and Environmental SciencesUniversity of GothenburgGöteborgSweden
- Gothenburg Global Biodiversity CenterGöteborgSweden
| | - Shawn Laffan
- Centre for Ecosystem Science, School of Biological, Earth and Environmental SciencesThe University of New South WalesSydneyNew South WalesAustralia
| | - Søren Faurby
- Department of Biological and Environmental SciencesUniversity of GothenburgGöteborgSweden
- Gothenburg Global Biodiversity CenterGöteborgSweden
| | - R. Alexander Pyron
- Department of Biological SciencesThe George Washington UniversityWashingtonDistrict of Columbia, U.S.A.
| | - Renato S. Bérnils
- Universidade Federal do Espírito Santo (UFES), Campus LitorâneoSão MateusEspírito SantoBrazil
| | - Martin Jansen
- Section of HerpetologySenckenberg Research Institute and Nature MuseumFrankfurt am MainGermany
| | - Paulo Passos
- Departamento de Vertebrados, Museu Nacional (MNRJ)Universidade Federal do Rio de JaneiroRio de JaneiroRio de JaneiroBrazil
| | - Ana L. C. Prudente
- Departamento de ZoologiaLaboratório de Herpetologia, Museu Paraense Emilio Goeldi (MPEG)BelémParáBrazil
| | - Diego F. Cisneros‐Heredia
- Laboratorio de Zoología Terrestre, Colegio de Ciencias Biológicas y Ambientales (COCIBA)Universidad San Francisco de Quito (USFQ)QuitoEcuador
- Department of GeographyKing's College LondonStrandLondonUnited Kingdom
- The Natural History Museum (UK), KensingtonLondonUnited Kingdom
| | - Henrique B. Braz
- School of Life and Environmental Sciences, Faculty of ScienceThe University of SydneySydneyNew South WalesAustralia
| | | | - Alexandre Antonelli
- Department of Biological and Environmental SciencesUniversity of GothenburgGöteborgSweden
- Gothenburg Global Biodiversity CenterGöteborgSweden
- Gothenburg Botanical GardenGöteborgSweden
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22
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Dauby G, Stévart T, Droissart V, Cosiaux A, Deblauwe V, Simo-Droissart M, Sosef MSM, Lowry PP, Schatz GE, Gereau RE, Couvreur TLP. ConR: An R package to assist large-scale multispecies preliminary conservation assessments using distribution data. Ecol Evol 2017; 7:11292-11303. [PMID: 29299301 PMCID: PMC5743656 DOI: 10.1002/ece3.3704] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 09/26/2017] [Accepted: 11/08/2017] [Indexed: 11/10/2022] Open
Abstract
The Red List Categories and the accompanying five criteria developed by the International Union for Conservation of Nature (IUCN) provide an authoritative and comprehensive methodology to assess the conservation status of organisms. Red List criterion B, which principally uses distribution data, is the most widely used to assess conservation status, particularly of plant species. No software package has previously been available to perform large-scale multispecies calculations of the three main criterion B parameters [extent of occurrence (EOO), area of occupancy (AOO) and an estimate of the number of locations] and provide preliminary conservation assessments using an automated batch process. We developed ConR, a dedicated R package, as a rapid and efficient tool to conduct large numbers of preliminary assessments, thereby facilitating complete Red List assessment. ConR (1) calculates key geographic range parameters (AOO and EOO) and estimates the number of locations sensu IUCN needed for an assessment under criterion B; (2) uses this information in a batch process to generate preliminary assessments of multiple species; (3) summarize the parameters and preliminary assessments in a spreadsheet; and (4) provides a visualization of the results by generating maps suitable for the submission of full assessments to the IUCN Red List. ConR can be used for any living organism for which reliable georeferenced distribution data are available. As distributional data for taxa become increasingly available via large open access datasets, ConR provides a novel, timely tool to guide and accelerate the work of the conservation and taxonomic communities by enabling practitioners to conduct preliminary assessments simultaneously for hundreds or even thousands of species in an efficient and time-saving way.
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Affiliation(s)
- Gilles Dauby
- Institut de Recherche pour le Développement (IRD) Université Montpellier, UMR DIADE Montpellier France.,Evolutionary Biology and Ecology Unit Faculté des Sciences Université Libre de Bruxelles Bruxelles Belgium.,French Foundation for Research on Biodiversity (FRB) through its Center for Synthesis and Analysis of Biodiversity data (CESAB) program Domaine du Petit Arbois Aix-en-Provence France
| | - Tariq Stévart
- Africa and Madagascar Department Missouri Botanical Garden St. Louis MO USA.,Botanic Garden Meise Meise Belgium.,Herbarium et Bibliothèque de Botanique Africaine Faculté des Sciences, Université Libre de Bruxelles Bruxelles Belgium
| | - Vincent Droissart
- Herbarium et Bibliothèque de Botanique Africaine Faculté des Sciences, Université Libre de Bruxelles Bruxelles Belgium.,Institut de Recherche pour le Développement (IRD) UMR AMAP Montpellier France
| | - Ariane Cosiaux
- Institut de Recherche pour le Développement (IRD) Université Montpellier, UMR DIADE Montpellier France.,Plant Systematics and Ecology Laboratory Higher Teachers Training College University of Yaoundé I Yaoundé Cameroon
| | - Vincent Deblauwe
- Herbarium et Bibliothèque de Botanique Africaine Faculté des Sciences, Université Libre de Bruxelles Bruxelles Belgium.,Center for Tropical Research Institute of the Environment and Sustainability University of California Los Angeles CA USA.,International Institute of Tropical Agriculture Yaoundé Cameroon
| | - Murielle Simo-Droissart
- Plant Systematics and Ecology Laboratory Higher Teachers Training College University of Yaoundé I Yaoundé Cameroon
| | | | - Porter P Lowry
- Africa and Madagascar Department Missouri Botanical Garden St. Louis MO USA.,Institut de Systématique Évolution et Biodiversité (ISYEB) Unité Mixte de Recherche 7205 (Centre National de la Recherche Scientifique/Muséum National d'Histoire Naturelle/École Pratique des Hautes Études/Université Pierre et Marie Curie) Muséum national d'Histoire naturelle Sorbonne Universités Paris France
| | - George E Schatz
- Africa and Madagascar Department Missouri Botanical Garden St. Louis MO USA
| | - Roy E Gereau
- Africa and Madagascar Department Missouri Botanical Garden St. Louis MO USA
| | - Thomas L P Couvreur
- Institut de Recherche pour le Développement (IRD) Université Montpellier, UMR DIADE Montpellier France.,Plant Systematics and Ecology Laboratory Higher Teachers Training College University of Yaoundé I Yaoundé Cameroon
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23
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Nieto‐Blázquez ME, Antonelli A, Roncal J. Historical Biogeography of endemic seed plant genera in the Caribbean: Did GAARlandia play a role? Ecol Evol 2017; 7:10158-10174. [PMID: 29238545 PMCID: PMC5723623 DOI: 10.1002/ece3.3521] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 09/11/2017] [Accepted: 09/14/2017] [Indexed: 12/16/2022] Open
Abstract
The Caribbean archipelago is a region with an extremely complex geological history and an outstanding plant diversity with high levels of endemism. The aim of this study was to better understand the historical assembly and evolution of endemic seed plant genera in the Caribbean, by first determining divergence times of endemic genera to test whether the hypothesized Greater Antilles and Aves Ridge (GAARlandia) land bridge played a role in the archipelago colonization and second by testing South America as the main colonization source as expected by the position of landmasses and recent evidence of an asymmetrical biotic interchange. We reconstructed a dated molecular phylogenetic tree for 625 seed plants including 32 Caribbean endemic genera using Bayesian inference and ten calibrations. To estimate the geographic range of the ancestors of endemic genera, we performed a model selection between a null and two complex biogeographic models that included timeframes based on geological information, dispersal probabilities, and directionality among regions. Crown ages for endemic genera ranged from Early Eocene (53.1 Ma) to Late Pliocene (3.4 Ma). Confidence intervals for divergence times (crown and/or stem ages) of 22 endemic genera occurred within the GAARlandia time frame. Contrary to expectations, the Antilles appears as the main ancestral area for endemic seed plant genera and only five genera had a South American origin. In contrast to patterns shown for vertebrates and other organisms and based on our sampling, we conclude that GAARlandia did not act as a colonization route for plants between South America and the Antilles. Further studies on Caribbean plant dispersal at the species and population levels will be required to reveal finer-scale biogeographic patterns and mechanisms.
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Affiliation(s)
| | - Alexandre Antonelli
- Department of Biological and Environmental SciencesUniversity of GöteborgGöteborgSweden
- Gothenburg Botanical GardenGöteborgSweden
- Gothenburg Global Biodiversity CentreGöteborgSweden
| | - Julissa Roncal
- Department of BiologyMemorial University of NewfoundlandSt. John'sNLCanada
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24
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Pérez-Escobar OA, Chomicki G, Condamine FL, de Vos JM, Martins AC, Smidt EC, Klitgård B, Gerlach G, Heinrichs J. Multiple Geographical Origins of Environmental Sex Determination enhanced the diversification of Darwin's Favourite Orchids. Sci Rep 2017; 7:12878. [PMID: 29018291 PMCID: PMC5635016 DOI: 10.1038/s41598-017-12300-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 09/06/2017] [Indexed: 11/17/2022] Open
Abstract
Environmental sex determination (ESD) - a change in sexual function during an individual life span driven by environmental cues - is an exceedingly rare sexual system among angiosperms. Because ESD can directly affect reproduction success, it could influence diversification rate as compared with lineages that have alternative reproductive systems. Here we test this hypothesis using a solid phylogenetic framework of Neotropical Catasetinae, the angiosperm lineage richest in taxa with ESD. We assess whether gains of ESD are associated with higher diversification rates compared to lineages with alternative systems while considering additional traits known to positively affect diversification rates in orchids. We found that ESD has evolved asynchronously three times during the last ~5 Myr. Lineages with ESD have consistently higher diversification rates than related lineages with other sexual systems. Habitat fragmentation due to mega-wetlands extinction, and climate instability are suggested as the driving forces for ESD evolution.
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Affiliation(s)
| | - Guillaume Chomicki
- Department of Plant Sciences, University of Oxford, South Park Road, OX1 3RB, Oxford, United Kingdom
| | - Fabien L Condamine
- CNRS, UMR 5554 Institut de Sciences de l'Evolution (Université de Montpellier), Place Eugène Bataillon, 34095, Montpellier, France
| | - Jurriaan M de Vos
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens Kew, Richmond, TW9 3AB, United Kingdom.
- Department of Environmental Sciences - Botany, University of Basel, Totengässlein 3, 4051, Basel, Switzerland.
| | - Aline C Martins
- Department of Botany, Federal University of Paraná, PB 19031, Curitiba, PR, 81531-980, Brazil
| | - Eric C Smidt
- Department of Botany, Federal University of Paraná, PB 19031, Curitiba, PR, 81531-980, Brazil
| | - Bente Klitgård
- Department of Identification and Naming, Royal Botanic Gardens Kew, Richmond, TW9 3AB, UK
| | - Günter Gerlach
- Botanischer Garten München, Menzinger Straße 67, D-80638, München, Germany
| | - Jochen Heinrichs
- Department für Biologie I, Systematische Botanik und Mykologie, Ludwig-Maximilians-Universität, Menzinger Straße 67, D-80638, München, Germany
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25
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Multilocus phylogeny and statistical biogeography clarify the evolutionary history of major lineages of turtles. Mol Phylogenet Evol 2017; 113:59-66. [DOI: 10.1016/j.ympev.2017.05.008] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 04/13/2017] [Accepted: 05/09/2017] [Indexed: 11/19/2022]
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Pérez-Escobar OA, Gottschling M, Chomicki G, Condamine FL, Klitgård BB, Pansarin E, Gerlach G. Andean Mountain Building Did not Preclude Dispersal of Lowland Epiphytic Orchids in the Neotropics. Sci Rep 2017; 7:4919. [PMID: 28687774 PMCID: PMC5501825 DOI: 10.1038/s41598-017-04261-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 05/22/2017] [Indexed: 11/17/2022] Open
Abstract
The Andean uplift is one of the major orographic events in the New World and has impacted considerably the diversification of numerous Neotropical lineages. Despite its importance for biogeography, the specific role of mountain ranges as a dispersal barrier between South and Central American lowland plant lineages is still poorly understood. The swan orchids (Cycnoches) comprise ca 34 epiphytic species distributed in lowland and pre-montane forests of Central and South America. Here, we study the historical biogeography of Cycnoches to better understand the impact of the Andean uplift on the diversification of Neotropical lowland plant lineages. Using novel molecular sequences (five nuclear and plastid regions) and twelve biogeographic models, we infer that the most recent common ancestor of Cycnoches originated in Amazonia ca 5 Mya. The first colonization of Central America occurred from a direct migration event from Amazonia, and multiple bidirectional trans-Andean migrations between Amazonia and Central America took place subsequently. Notably, these rare biological exchanges occurred well after major mountain building periods. The Andes have limited plant migration, yet it has seldom allowed episodic gene exchange of lowland epiphyte lineages such as orchids with great potential for effortless dispersal because of the very light, anemochorous seeds.
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Affiliation(s)
- Oscar Alejandro Pérez-Escobar
- Department Biologie, Systematische Botanik und Mykologie, GeoBio-Center, Ludwig-Maximilians Universität, Menzinger Straße 67, D - 80638, Munich, Germany.
- Identification and Naming department, Royal Botanic Gardens, Kew, TW9 3AB, Surrey, UK.
| | - Marc Gottschling
- Department Biologie, Systematische Botanik und Mykologie, GeoBio-Center, Ludwig-Maximilians Universität, Menzinger Straße 67, D - 80638, Munich, Germany
| | - Guillaume Chomicki
- Department Biologie, Systematische Botanik und Mykologie, GeoBio-Center, Ludwig-Maximilians Universität, Menzinger Straße 67, D - 80638, Munich, Germany
| | - Fabien L Condamine
- CNRS, UMR 5554 Institut de Sciences de l'Evolution (Université de Montpellier), Place Eugène Bataillon, 34095, Montpellier, France
| | - Bente B Klitgård
- Identification and Naming department, Royal Botanic Gardens, Kew, TW9 3AB, Surrey, UK
| | - Emerson Pansarin
- Departamento de Biologia, Facultade de Filosofia, Ciências e Letras, Universidade de Sao Paulo, Ribeirao Preto, SP, 14040-901, Brazil
| | - Günter Gerlach
- Botanischer Garten München, Menzinger Straße 61, D - 80638, Munich, Germany.
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Lehtonen S, Silvestro D, Karger DN, Scotese C, Tuomisto H, Kessler M, Peña C, Wahlberg N, Antonelli A. Environmentally driven extinction and opportunistic origination explain fern diversification patterns. Sci Rep 2017; 7:4831. [PMID: 28684788 PMCID: PMC5500532 DOI: 10.1038/s41598-017-05263-7] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 05/25/2017] [Indexed: 01/16/2023] Open
Abstract
Combining palaeontological and neontological data offers a unique opportunity to investigate the relative roles of biotic and abiotic controls of species diversification, and the importance of origination versus extinction in driving evolutionary dynamics. Ferns comprise a major terrestrial plant radiation with an extensive evolutionary history providing a wealth of modern and fossil data for modelling environmental drivers of diversification. Here we develop a novel Bayesian model to simultaneously estimate correlations between diversification dynamics and multiple environmental trajectories. We estimate the impact of different factors on fern diversification over the past 400 million years by analysing a comprehensive dataset of fossil occurrences and complement these findings by analysing a large molecular phylogeny. We show that origination and extinction rates are governed by fundamentally different processes: originations depend on within-group diversity but are largely unaffected by environmental changes, whereas extinctions are strongly affected by external factors such as climate and geology. Our results indicate that the prime driver of fern diversity dynamics is environmentally driven extinction, with origination being an opportunistic response to diminishing ecospace occupancy.
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Affiliation(s)
- Samuli Lehtonen
- Herbarium, Biodiversity Unit, University of Turku, 20014, Turku, Finland.
- Department of Biology, University of Turku, 20014, Turku, Finland.
| | - Daniele Silvestro
- Department of Biological and Environmental Sciences, University of Gothenburg, Carl Skottsbergs gata 22B, Gothenburg, 413 19, Sweden.
- Gothenburg Global Biodiversity Centre, Box 461, SE-405 30, Gothenburg, Sweden.
- Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, Quartier Sorge, 1015, Lausanne, Switzerland.
| | - Dirk Nikolaus Karger
- Department of Biology, University of Turku, 20014, Turku, Finland
- Department of Systematic and Evolutionary Botany, University of Zurich, 8008, Zurich, Switzerland
| | | | - Hanna Tuomisto
- Department of Biology, University of Turku, 20014, Turku, Finland
| | - Michael Kessler
- Department of Systematic and Evolutionary Botany, University of Zurich, 8008, Zurich, Switzerland
| | - Carlos Peña
- Department of Biology, University of Turku, 20014, Turku, Finland
| | - Niklas Wahlberg
- Department of Biology, University of Turku, 20014, Turku, Finland
- Department of Biology, Lund University, Lund, Sweden
| | - Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, Carl Skottsbergs gata 22B, Gothenburg, 413 19, Sweden
- Gothenburg Global Biodiversity Centre, Box 461, SE-405 30, Gothenburg, Sweden
- Gothenburg Botanical Garden, Carl Skottsbergs gata 22 A, Gothenburg, 413 19, Sweden
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Vanderhoeven S, Adriaens T, Desmet P, Strubbe D, Backeljau T, Barbier Y, Brosens D, Cigar J, Coupremanne M, De Troch R, Eggermont H, Heughebaert A, Hostens K, Huybrechts P, Jacquemart AL, Lens L, Monty A, Paquet JY, Prévot C, Robertson T, Termonia P, Van De Kerchove R, Van Hoey G, Van Schaeybroeck B, Vercayie D, Verleye T, Welby S, Groom Q. Tracking Invasive Alien Species (TrIAS): Building a data-driven framework to inform policy. RESEARCH IDEAS AND OUTCOMES 2017. [DOI: 10.3897/rio.3.e13414] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Imagine a future where dynamically, from year to year, we can track the progression of alien species (AS), identify emerging problem species, assess their current and future risk and timely inform policy in a seamless data-driven workflow. One that is built on open science and open data infrastructures. By using international biodiversity standards and facilities, we would ensure interoperability, repeatability and sustainability. This would make the process adaptable to future requirements in an evolving AS policy landscape both locally and internationally. In recent years, Belgium has developed decision support tools to inform invasive alien species (IAS) policy, including information systems, early warning initiatives and risk assessment protocols. However, the current workflows from biodiversity observations to IAS science and policy are slow, not easily repeatable, and their scope is often taxonomically, spatially and temporally limited. This is mainly caused by the diversity of actors involved and the closed, fragmented nature of the sources of these biodiversity data, which leads to considerable knowledge gaps for IAS research and policy. We will leverage expertise and knowledge from nine former and current BELSPO projects and initiatives: Alien Alert, Invaxen, Diars, INPLANBEL, Alien Impact, Ensis, CORDEX.be, Speedy and the Belgian Biodiversity Platform. The project will be built on two components: 1) The establishment of a data mobilization framework for AS data from diverse data sources and 2) the development of data-driven procedures for risk evaluation based on risk modelling, risk mapping and risk assessment. We will use facilities from the Global Biodiversity Information Facility (GBIF), standards from the Biodiversity Information Standards organization (TDWG) and expertise from Lifewatch to create and facilitate a systematic workflow. Alien species data will be gathered from a large set of regional, national and international initiatives, including citizen science with a wide taxonomic scope from marine, terrestrial and freshwater environments. Observation data will be funnelled in repeatable ways to GBIF. In parallel, a Belgian checklist of AS will be established, benefiting from various taxonomic and project-based checklists foreseen for GBIF publication. The combination of the observation data and the checklist will feed indicators for the identification of emerging species; their level of invasion in Belgium; changes in their invasion status and the identification of areas and species of concern that could be impacted upon by bioinvasions. Data-driven risk evaluation of identified emerging species will be supported by niche and climate modelling and consequent risk mapping using critical climatic variables for the current and projected future climate periods at high resolution. The resulting risk maps will complement risk assessments performed with the recently developed Harmonia+ protocol to assess risks posed by emergent species to biodiversity and human, plant, and animal health. The use of open data will ensure that interested stakeholders in Belgium and abroad can make use of the information we generate. The open science ensures everyone is free to adopt and adapt the workflow for different scenarios and regions. The checklist will be used at national level, but will also serve as the Belgian reference for international databases (IUCN - GRIIS, EASIN) and impact assessments (IPBES, SEBI). The workflow will be showcased through GEO BON, the Invasivesnet network and the COST Actions Alien Challenge and ParrotNet. The observations and outcomes of risk evaluations will be used to provide science-based support for the implementation of IAS policies at the regional, federal and EU levels. The publication of Belgian data and checklists on IAS is particularly timely in light of the currently ongoing EU IAS Regulation and its implementation in Belgium. By proving that automated workflows can provide rapid and repeatable production of information, we will open up this technology for other conservation assessments.
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Sosef MSM, Dauby G, Blach-Overgaard A, van der Burgt X, Catarino L, Damen T, Deblauwe V, Dessein S, Dransfield J, Droissart V, Duarte MC, Engledow H, Fadeur G, Figueira R, Gereau RE, Hardy OJ, Harris DJ, de Heij J, Janssens S, Klomberg Y, Ley AC, Mackinder BA, Meerts P, van de Poel JL, Sonké B, Stévart T, Stoffelen P, Svenning JC, Sepulchre P, Zaiss R, Wieringa JJ, Couvreur TLP. Exploring the floristic diversity of tropical Africa. BMC Biol 2017; 15:15. [PMID: 28264718 PMCID: PMC5339970 DOI: 10.1186/s12915-017-0356-8] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 01/25/2017] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Understanding the patterns of biodiversity distribution and what influences them is a fundamental pre-requisite for effective conservation and sustainable utilisation of biodiversity. Such knowledge is increasingly urgent as biodiversity responds to the ongoing effects of global climate change. Nowhere is this more acute than in species-rich tropical Africa, where so little is known about plant diversity and its distribution. In this paper, we use RAINBIO - one of the largest mega-databases of tropical African vascular plant species distributions ever compiled - to address questions about plant and growth form diversity across tropical Africa. RESULTS The filtered RAINBIO dataset contains 609,776 georeferenced records representing 22,577 species. Growth form data are recorded for 97% of all species. Records are well distributed, but heterogeneous across the continent. Overall, tropical Africa remains poorly sampled. When using sampling units (SU) of 0.5°, just 21 reach appropriate collection density and sampling completeness, and the average number of records per species per SU is only 1.84. Species richness (observed and estimated) and endemism figures per country are provided. Benin, Cameroon, Gabon, Ivory Coast and Liberia appear as the botanically best-explored countries, but none are optimally explored. Forests in the region contain 15,387 vascular plant species, of which 3013 are trees, representing 5-7% of the estimated world's tropical tree flora. The central African forests have the highest endemism rate across Africa, with approximately 30% of species being endemic. CONCLUSIONS The botanical exploration of tropical Africa is far from complete, underlining the need for intensified inventories and digitization. We propose priority target areas for future sampling efforts, mainly focused on Tanzania, Atlantic Central Africa and West Africa. The observed number of tree species for African forests is smaller than those estimated from global tree data, suggesting that a significant number of species are yet to be discovered. Our data provide a solid basis for a more sustainable management and improved conservation of tropical Africa's unique flora, and is important for achieving Objective 1 of the Global Strategy for Plant Conservation 2011-2020. In turn, RAINBIO provides a solid basis for a more sustainable management and improved conservation of tropical Africa's unique flora.
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Affiliation(s)
- Marc S M Sosef
- Botanic Garden Meise, Nieuwelaan 38, BE-1860, Meise, Belgium.
| | - Gilles Dauby
- DIADE, Université Montpellier, IRD, Montpellier, France
- Laboratoire d'Évolution biologique et Écologie, Faculté des Sciences, Université Libre de Bruxelles, Brussels, Belgium
- CESAB/FRB, Domaine du Petit Arbois, Av. Louis Philibert, Aix-en-Provence, 13100, France
| | - Anne Blach-Overgaard
- Section for Ecoinformatics & Biodiversity, Department of Bioscience, Aarhus University, Ny Munkegade 114, DK-8000, Aarhus C, Denmark
| | | | - Luís Catarino
- Centre for Ecology, Evolution and Environmental Changes (CE3C), Faculty of Sciences, University of Lisbon, Campo Grande, 1749-016, Lisbon, Portugal
| | - Theo Damen
- Wageningen University, Biosystematics Group, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Vincent Deblauwe
- DIADE, Université Montpellier, IRD, Montpellier, France
- Herbarium et Bibliothèque de Botanique Africaine, Université Libre de Bruxelles, Boulevard du Triomphe, B-1050, Bruxelles, Belgium
- Laboratoire de Botanique systématique et d'Écologie, Département des Sciences Biologiques, École Normale Supérieure, Université de Yaoundé I, Yaoundé, Cameroon
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, Box 951496, Los Angeles, CA, 90095, USA
- International Institute of Tropical Agriculture, BP 2008 (Messa), Yaounde, Cameroon
| | - Steven Dessein
- Botanic Garden Meise, Nieuwelaan 38, BE-1860, Meise, Belgium
| | | | - Vincent Droissart
- Herbarium et Bibliothèque de Botanique Africaine, Université Libre de Bruxelles, Boulevard du Triomphe, B-1050, Bruxelles, Belgium
- Missouri Botanical Garden, Africa & Madagascar Department, P.O. Box 299, St. Louis, Missouri, 63166-0299, USA
- AMAP, CNRS, INRA, IRD, Université Montpellier, Montpellier, France
| | - Maria Cristina Duarte
- Centre for Ecology, Evolution and Environmental Changes (CE3C), Faculty of Sciences, University of Lisbon, Campo Grande, 1749-016, Lisbon, Portugal
| | - Henry Engledow
- Botanic Garden Meise, Nieuwelaan 38, BE-1860, Meise, Belgium
| | - Geoffrey Fadeur
- Herbarium et Bibliothèque de Botanique Africaine, Université Libre de Bruxelles, Boulevard du Triomphe, B-1050, Bruxelles, Belgium
| | - Rui Figueira
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
- CEABN/InBio, Centro de Ecologia Aplicada "Professor Baeta Neves", Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017, Lisboa, Portugal
| | - Roy E Gereau
- Missouri Botanical Garden, Africa & Madagascar Department, P.O. Box 299, St. Louis, Missouri, 63166-0299, USA
| | - Olivier J Hardy
- Laboratoire d'Évolution biologique et Écologie, Faculté des Sciences, Université Libre de Bruxelles, Brussels, Belgium
| | - David J Harris
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, UK
| | - Janneke de Heij
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR, Leiden, The Netherlands
- Picturae, De Droogmakerij 12, 1851LX, Heiloo, The Netherlands
| | - Steven Janssens
- Botanic Garden Meise, Nieuwelaan 38, BE-1860, Meise, Belgium
| | - Yannick Klomberg
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR, Leiden, The Netherlands
- Department of Ecology, Faculty of Science, Charles University, Vinicna 7, 128 44, Prague 2, Czech Republic
| | - Alexandra C Ley
- Institut für Geobotanik und Botanischer Garten, Im Neuwerk 21, University Halle-Wittenberg, 06108, Halle (Saale), Germany
| | - Barbara A Mackinder
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, UK
| | - Pierre Meerts
- Herbarium et Bibliothèque de Botanique Africaine, Université Libre de Bruxelles, Boulevard du Triomphe, B-1050, Bruxelles, Belgium
- Laboratoire d'Ecologie végétale et Biogéochimie, Université Libre de Bruxelles, Boulevard du Triomphe, B-1050, Bruxelles, Belgium
| | - Jeike L van de Poel
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR, Leiden, The Netherlands
| | - Bonaventure Sonké
- Laboratoire de Botanique systématique et d'Écologie, Département des Sciences Biologiques, École Normale Supérieure, Université de Yaoundé I, Yaoundé, Cameroon
| | - Tariq Stévart
- Botanic Garden Meise, Nieuwelaan 38, BE-1860, Meise, Belgium
- Herbarium et Bibliothèque de Botanique Africaine, Université Libre de Bruxelles, Boulevard du Triomphe, B-1050, Bruxelles, Belgium
- Missouri Botanical Garden, Africa & Madagascar Department, P.O. Box 299, St. Louis, Missouri, 63166-0299, USA
| | - Piet Stoffelen
- Botanic Garden Meise, Nieuwelaan 38, BE-1860, Meise, Belgium
| | - Jens-Christian Svenning
- Section for Ecoinformatics & Biodiversity, Department of Bioscience, Aarhus University, Ny Munkegade 114, DK-8000, Aarhus C, Denmark
| | - Pierre Sepulchre
- Laboratoire des Sciences du Climat et de l'Environnement, LSCE/IPSL, CEA-CNRS-UVSQ, Université Paris-Saclay, F-91191, Gif-sur-Yvette, France
| | - Rainer Zaiss
- AMAP, CNRS, INRA, IRD, Université Montpellier, Montpellier, France
| | - Jan J Wieringa
- Wageningen University, Biosystematics Group, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR, Leiden, The Netherlands
| | - Thomas L P Couvreur
- DIADE, Université Montpellier, IRD, Montpellier, France.
- Laboratoire de Botanique systématique et d'Écologie, Département des Sciences Biologiques, École Normale Supérieure, Université de Yaoundé I, Yaoundé, Cameroon.
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR, Leiden, The Netherlands.
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30
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Maldonado C, Molina CI, Zizka A, Persson C, Taylor CM, Albán J, Chilquillo E, Rønsted N, Antonelli A. Estimating species diversity and distribution in the era of Big Data: to what extent can we trust public databases? GLOBAL ECOLOGY AND BIOGEOGRAPHY : A JOURNAL OF MACROECOLOGY 2015; 24:973-984. [PMID: 27656106 PMCID: PMC5012125 DOI: 10.1111/geb.12326] [Citation(s) in RCA: 138] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
AIM Massive digitalization of natural history collections is now leading to a steep accumulation of publicly available species distribution data. However, taxonomic errors and geographical uncertainty of species occurrence records are now acknowledged by the scientific community - putting into question to what extent such data can be used to unveil correct patterns of biodiversity and distribution. We explore this question through quantitative and qualitative analyses of uncleaned versus manually verified datasets of species distribution records across different spatial scales. LOCATION The American tropics. METHODS As test case we used the plant tribe Cinchoneae (Rubiaceae). We compiled four datasets of species occurrences: one created manually and verified through classical taxonomic work, and the rest derived from GBIF under different cleaning and filling schemes. We used new bioinformatic tools to code species into grids, ecoregions, and biomes following WWF's classification. We analysed species richness and altitudinal ranges of the species. RESULTS Altitudinal ranges for species and genera were correctly inferred even without manual data cleaning and filling. However, erroneous records affected spatial patterns of species richness. They led to an overestimation of species richness in certain areas outside the centres of diversity in the clade. The location of many of these areas comprised the geographical midpoint of countries and political subdivisions, assigned long after the specimens had been collected. MAIN CONCLUSION Open databases and integrative bioinformatic tools allow a rapid approximation of large-scale patterns of biodiversity across space and altitudinal ranges. We found that geographic inaccuracy affects diversity patterns more than taxonomic uncertainties, often leading to false positives, i.e. overestimating species richness in relatively species poor regions. Public databases for species distribution are valuable and should be more explored, but under scrutiny and validation by taxonomic experts. We suggest that database managers implement easy ways of community feedback on data quality.
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Affiliation(s)
- Carla Maldonado
- Natural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
- Herbario Nacional de BoliviaUniversidad Mayor de San AndresLa PazBolivia
| | - Carlos I. Molina
- Natural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
- Instituto de EcologíaUniversidad Mayor de San AndresLa PazBolivia
| | - Alexander Zizka
- Department of Biological and Environmental SciencesUniversity of GothenburgGothenburgSweden
| | - Claes Persson
- Department of Biological and Environmental SciencesUniversity of GothenburgGothenburgSweden
| | | | - Joaquina Albán
- Museo de Historia NaturalUniversidad Nacional Mayor de San MarcosLimaPeru
| | - Eder Chilquillo
- Museo de Historia NaturalUniversidad Nacional Mayor de San MarcosLimaPeru
- Departamento de Biologia VegetalUniversidade Estadual de CampinasSao PauloBrazil
| | - Nina Rønsted
- Natural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
| | - Alexandre Antonelli
- Department of Biological and Environmental SciencesUniversity of GothenburgGothenburgSweden
- Gothenburg Botanical GardenGothenburgSweden
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31
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Antonelli A, Zizka A, Silvestro D, Scharn R, Cascales-Miñana B, Bacon CD. An engine for global plant diversity: highest evolutionary turnover and emigration in the American tropics. Front Genet 2015; 6:130. [PMID: 25904934 PMCID: PMC4389561 DOI: 10.3389/fgene.2015.00130] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 03/18/2015] [Indexed: 11/25/2022] Open
Abstract
Understanding the processes that have generated the latitudinal biodiversity gradient and the continental differences in tropical biodiversity remains a major goal of evolutionary biology. Here we estimate the timing and direction of range shifts of extant flowering plants (angiosperms) between tropical and non-tropical zones, and into and out of the major tropical regions of the world. We then calculate rates of speciation and extinction taking into account incomplete taxonomic sampling. We use a recently published fossil calibrated phylogeny and apply novel bioinformatic tools to code species into user-defined polygons. We reconstruct biogeographic history using stochastic character mapping to compute relative numbers of range shifts in proportion to the number of available lineages through time. Our results, based on the analysis of c. 22,600 species and c. 20 million geo-referenced occurrence records, show no significant differences between the speciation and extinction of tropical and non-tropical angiosperms. This suggests that at least in plants, the latitudinal biodiversity gradient primarily derives from other factors than differential rates of diversification. In contrast, the outstanding species richness found today in the American tropics (the Neotropics), as compared to tropical Africa and tropical Asia, is associated with significantly higher speciation and extinction rates. This suggests an exceedingly rapid evolutionary turnover, i.e., Neotropical species being formed and replaced by one another at unparalleled rates. In addition, tropical America stands out from other continents by having “pumped out” more species than it received through most of the last 66 million years. These results imply that the Neotropics have acted as an engine for global plant diversity.
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Affiliation(s)
- Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg Göteborg, Sweden ; Gothenburg Botanical Garden Göteborg, Sweden
| | - Alexander Zizka
- Department of Biological and Environmental Sciences, University of Gothenburg Göteborg, Sweden
| | - Daniele Silvestro
- Department of Biological and Environmental Sciences, University of Gothenburg Göteborg, Sweden ; Department of Ecology and Evolution, University of Lausanne Lausanne, Switzerland
| | - Ruud Scharn
- Department of Biological and Environmental Sciences, University of Gothenburg Göteborg, Sweden
| | - Borja Cascales-Miñana
- Laboratoire de Paléobiogéologie, Paléobotanique, Paléopalynologie, Département de Géologie, Université de Liège Liège, Belgium
| | - Christine D Bacon
- Department of Biological and Environmental Sciences, University of Gothenburg Göteborg, Sweden ; Laboratório de Biología Molecular (CINBIN), Department of Biology, Universidad Industrial de Santander Bucaramanga, Colombia
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