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Zhigila DA, Elliott TL, Schmiedel U, Muasya AM. Do phylogenetic community metrics reveal the South African quartz fields as terrestrial-habitat islands? ANNALS OF BOTANY 2024; 133:833-850. [PMID: 38401154 PMCID: PMC11082514 DOI: 10.1093/aob/mcae027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 02/23/2024] [Indexed: 02/26/2024]
Abstract
BACKGROUND AND AIMS The quartz fields of the Greater Cape Floristic Region (GCFR) are arid and island-like special habitats, hosting ~142 habitat-specialized plant species, of which 81 % are local endemics, characterized by a rapid turnover of species between and among sites. We use several phylogenetic community metrics: (1) to examine species diversity and phylogenetic structure within and among quartz fields; (2) to investigate whether quartz field specialists are evolutionarily drawn from local species pools, whereas the alternative hypothesis posits that there is no significant evolutionary connection between quartz field specialists and the local species pools; and (3) to determine whether there is an association between certain traits and the presence of species in quartz fields. METHODS We sampled and developed dated phylogenies for six species-rich angiosperm families (Aizoaceae, Asteraceae, Crassulaceae, Cyperaceae, Fabaceae and Santalaceae) represented in the quartz field floras of southern Africa. Specifically, we focused on the flora of three quartz field regions in South Africa (Knersvlakte, Little Karoo and Overberg) and their surrounding species pools to address our research questions by scoring traits associated with harsh environments. KEY RESULTS We found that the Overberg and Little Karoo had the highest level of species overlap for families Aizoaceae and Fabaceae, whereas the Knersvlakte and the Overberg had the highest species overlap for families Asteraceae, Crassulaceae and Santalaceae. Although our phylogenetic community structure and trait analyses showed no clear patterns, relatively low pairwise phylogenetic distances between specialists and their local species pools for Aizoaceae suggest that quartz species could be drawn evolutionarily from their surrounding areas. We also found that families Aizoaceae and Crassulaceae in Knersvlakte and Little Karoo were phylogenetically even. CONCLUSIONS Despite their proximity to one another within the GCFR, the studied areas differ in their species pools and the phylogenetic structure of their specialists. Our work provides further justification for increased conservation focus on these unique habitats under future scenarios of global change.
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Affiliation(s)
- Daniel A Zhigila
- Department of Botany, Gombe State University, PMB 127, Tudun Wada, Gombe, Gombe State, Nigeria
- Bolus Herbarium, Department of Biological Sciences, University of Cape Town, Private Bag X3, Rondebosch, Cape Town 7701, South Africa
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, 22 Divinity Avenue, Cambridge, MA 02138, USA
| | - Tammy L Elliott
- Bolus Herbarium, Department of Biological Sciences, University of Cape Town, Private Bag X3, Rondebosch, Cape Town 7701, South Africa
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlarska 2, 611 37 Brno, Czech Republic
| | - Ute Schmiedel
- Organismic Botany and Mycology, Institute of Plant Science and Microbiology, University of Hamburg, Germany
| | - A Muthama Muasya
- Bolus Herbarium, Department of Biological Sciences, University of Cape Town, Private Bag X3, Rondebosch, Cape Town 7701, South Africa
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2
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Guo WY, Serra-Diaz JM, Eiserhardt WL, Maitner BS, Merow C, Violle C, Pound MJ, Sun M, Slik F, Blach-Overgaard A, Enquist BJ, Svenning JC. Climate change and land use threaten global hotspots of phylogenetic endemism for trees. Nat Commun 2023; 14:6950. [PMID: 37907453 PMCID: PMC10618213 DOI: 10.1038/s41467-023-42671-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 10/18/2023] [Indexed: 11/02/2023] Open
Abstract
Across the globe, tree species are under high anthropogenic pressure. Risks of extinction are notably more severe for species with restricted ranges and distinct evolutionary histories. Here, we use a global dataset covering 41,835 species (65.1% of known tree species) to assess the spatial pattern of tree species' phylogenetic endemism, its macroecological drivers, and how future pressures may affect the conservation status of the identified hotspots. We found that low-to-mid latitudes host most endemism hotspots, with current climate being the strongest driver, and climatic stability across thousands to millions of years back in time as a major co-determinant. These hotspots are mostly located outside of protected areas and face relatively high land-use change and future climate change pressure. Our study highlights the risk from climate change for tree diversity and the necessity to strengthen conservation and restoration actions in global hotspots of phylogenetic endemism for trees to avoid major future losses of tree diversity.
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Affiliation(s)
- Wen-Yong Guo
- Research Center for Global Change and Complex Ecosystems & Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, School of Ecological and Environmental Sciences, East China Normal University, 200241, Shanghai, P. R. China.
- Center for Ecological Dynamics in a Novel Biosphere (ECONOVO) & Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of Biology, Aarhus University, 8000, Aarhus C, Denmark.
- Section for Ecoinformatics & Biodiversity, Department of Biology, Aarhus University, 8000, Aarhus C, Denmark.
| | - Josep M Serra-Diaz
- Eversource Energy Center and Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
- Université de Lorraine, AgroParisTech, INRAE, Silva, Nancy, France
| | - Wolf L Eiserhardt
- Section for Ecoinformatics & Biodiversity, Department of Biology, Aarhus University, 8000, Aarhus C, Denmark
| | - Brian S Maitner
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Cory Merow
- Eversource Energy Center and Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Cyrille Violle
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Matthew J Pound
- Department of Geography and Environmental Sciences, Northumbria University, Newcastle upon Tyne, NE1 8ST, United Kingdom
| | - Miao Sun
- Section for Ecoinformatics & Biodiversity, Department of Biology, Aarhus University, 8000, Aarhus C, Denmark
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, 430070, P. R. China
| | - Ferry Slik
- Environmental and Life Sciences, Faculty of Science, Universiti Brunei Darussalam, Jalan Tungku Link, BE1410, Gadong, Brunei Darussalam
| | - Anne Blach-Overgaard
- Center for Ecological Dynamics in a Novel Biosphere (ECONOVO) & Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of Biology, Aarhus University, 8000, Aarhus C, Denmark
- Section for Ecoinformatics & Biodiversity, Department of Biology, Aarhus University, 8000, Aarhus C, Denmark
| | - Brian J Enquist
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
- The Santa Fe Institute, 1399 Hyde Park Rd, Santa Fe, NM, 87501, USA
| | - Jens-Christian Svenning
- Center for Ecological Dynamics in a Novel Biosphere (ECONOVO) & Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of Biology, Aarhus University, 8000, Aarhus C, Denmark
- Section for Ecoinformatics & Biodiversity, Department of Biology, Aarhus University, 8000, Aarhus C, Denmark
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3
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Ramírez-Verdugo P, Tapia A, Forest F, Scherson RA. Evolutionary diversity of the endemic genera of the vascular flora of Chile and its implications for conservation. PLoS One 2023; 18:e0287957. [PMID: 37406022 DOI: 10.1371/journal.pone.0287957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 06/19/2023] [Indexed: 07/07/2023] Open
Abstract
As a direct consequence of global change, both natural and human-induced, a high percentage of biodiversity is now under threat worldwide. This has urged conservation planners to formulate and/or improve existing strategies to preserve species and their ecosystems. In this context, the present study focuses on two strategies using phylogeny-based measures of biodiversity to account for the processes that led to the biodiversity patterns observed today. It will contribute additional information that can aid decision-making regarding the assignment of threat status for some species, thus strengthening measures currently in use and facilitate the allocation of often scarce conservation resources. The Evolutionarily Distinct (ED) index prioritises species that are on long branches of the tree of life with few descendants, and the Evolutionarily Distinct and Globally Endangered (EDGE) index integrates evolutionary history with IUCN Red List threat status of species. It has been used mostly in animal groups, but since the threats faced by many plants have not been evaluated, it has been more difficult to compile for plants worldwide. Here, we apply the EDGE metric to species of the endemic genera of Chile. However, more than 50% of the endemic flora of the country are still lacking official threat status. We thus used an alternative measure (Relative Evolutionary Distinctness-RED), based on a range-weighted phylogenetic tree, which uses geographic ranges to adjust branch lengths, and calculate ED. The RED index was shown to be a suitable measure, yielding similar results compared to EDGE, at least for this group of species. Given the urgency to halt biodiversity loss and the time it would take to evaluate all species, we propose that this index is used to set conservation priorities until we can calculate EDGE for these unique endemic species. This would allow guiding decision-making until we can gather more data to assess and assign conservation status to new species.
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Affiliation(s)
- Pamela Ramírez-Verdugo
- Herbario VALPL y Laboratorio de Botánica, Departamento de Ciencias y Geografía, Universidad de Playa Ancha, Valparaíso, Chile
- Jardín Botánico Nacional, Viña del Mar, Chile
- Laboratorio de Evolución y Sistemática, Departamento de Silvicultura y Conservación de la Naturaleza, Universidad de Chile, Santiago, Chile
| | - Alexis Tapia
- Departamento de Matemática, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - Félix Forest
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, United Kingdom
| | - Rosa A Scherson
- Laboratorio de Evolución y Sistemática, Departamento de Silvicultura y Conservación de la Naturaleza, Universidad de Chile, Santiago, Chile
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4
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Ceron K, Sales LP, Santana DJ, Pires MM. Decoupled responses of biodiversity facets driven from anuran vulnerability to climate and land‐use changes. Ecol Lett 2023; 26:869-882. [DOI: 10.1111/ele.14207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 03/03/2023] [Accepted: 03/06/2023] [Indexed: 03/29/2023]
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5
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Jambura PL, Villalobos-Segura E, Türtscher J, Begat A, Staggl MA, Stumpf S, Kindlimann R, Klug S, Lacombat F, Pohl B, Maisey JG, Naylor GJP, Kriwet J. Systematics and Phylogenetic Interrelationships of the Enigmatic Late Jurassic Shark Protospinax annectans Woodward, 1918 with Comments on the Shark-Ray Sister Group Relationship. DIVERSITY 2023; 15:311. [PMID: 36950326 PMCID: PMC7614347 DOI: 10.3390/d15030311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
The Late Jurassic elasmobranch Protospinax annectans is often regarded as a key species to our understanding of crown group elasmobranch interrelationships and the evolutionary history of this group. However, since its first description more than 100 years ago, its phylogenetic position within the Elasmobranchii (sharks and rays) has proven controversial, and a closer relationship between Protospinax and each of the posited superorders (Batomorphii, Squalomorphii, and Galeomorphii) has been proposed over the time. Here we revise this controversial taxon based on new holomorphic specimens from the Late Jurassic Konservat-Lagerstätte of the Solnhofen Archipelago in Bavaria (Germany) and review its skeletal morphology, systematics, and phylogenetic interrelationships. A data matrix with 224 morphological characters was compiled and analyzed under a molecular backbone constraint. Our results indicate a close relationship between Protospinax, angel sharks (Squatiniformes), and saw sharks (Pristiophoriformes). However, the revision of our morphological data matrix within a molecular framework highlights the lack of morphological characters defining certain groups, especially sharks of the order Squaliformes, hampering the phylogenetic resolution of Protospinax annectans with certainty. Furthermore, the monophyly of modern sharks retrieved by molecular studies is only weakly supported by morphological data, stressing the need for more characters to align morphological and molecular studies in the future.
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Affiliation(s)
- Patrick L. Jambura
- Department of Palaeontology, University of Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria
- Vienna Doctoral School of Ecology and Evolution (VDSEE), University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
- Correspondence:
| | | | - Julia Türtscher
- Department of Palaeontology, University of Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria
- Vienna Doctoral School of Ecology and Evolution (VDSEE), University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Arnaud Begat
- Department of Palaeontology, University of Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria
- Vienna Doctoral School of Ecology and Evolution (VDSEE), University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Manuel Andreas Staggl
- Department of Palaeontology, University of Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria
- Vienna Doctoral School of Ecology and Evolution (VDSEE), University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Sebastian Stumpf
- Department of Palaeontology, University of Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria
| | - René Kindlimann
- Haimuseum und Sammlung R. Kindlimann, 8607 Aathal-Seegräben, Switzerland
| | - Stefanie Klug
- School of Science (GAUSS), Georg–August Universität Göttingen, 37077 Göttingen, Germany
| | | | - Burkhard Pohl
- Interprospekt Group, 1724 Ferpicloz, Switzerland
- Wyoming Dinosaur Center, Thermopolis, WY 82443, USA
| | - John G. Maisey
- Department of Vertebrate Paleontology, American Natural History Museum, New York, NY 10024, USA
| | - Gavin J. P. Naylor
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Jürgen Kriwet
- Department of Palaeontology, University of Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria
- Vienna Doctoral School of Ecology and Evolution (VDSEE), University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
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Griffith P, Lang JW, Turvey ST, Gumbs R. Using functional traits to identify conservation priorities for the world's crocodylians. Funct Ecol 2022. [DOI: 10.1111/1365-2435.14140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Phoebe Griffith
- Institute of Zoology Zoological Society of London London UK
- Wildlife Conservation Research Unit The Recanati‐Kaplan Centre, Department of Zoology, University of Oxford Oxford UK
| | - Jeffrey W. Lang
- Gharial Ecology Project Madras Crocodile Bank Trust Mamallapuram Tamil Nadu India
| | | | - Rikki Gumbs
- EDGE of Existence Programme Conservation and Policy, Zoological Society of London London UK
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7
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Cavender-Bares J, Schneider FD, Santos MJ, Armstrong A, Carnaval A, Dahlin KM, Fatoyinbo L, Hurtt GC, Schimel D, Townsend PA, Ustin SL, Wang Z, Wilson AM. Integrating remote sensing with ecology and evolution to advance biodiversity conservation. Nat Ecol Evol 2022; 6:506-519. [PMID: 35332280 DOI: 10.1038/s41559-022-01702-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 02/10/2022] [Indexed: 12/31/2022]
Abstract
Remote sensing has transformed the monitoring of life on Earth by revealing spatial and temporal dimensions of biological diversity through structural, compositional and functional measurements of ecosystems. Yet, many aspects of Earth's biodiversity are not directly quantified by reflected or emitted photons. Inclusive integration of remote sensing with field-based ecology and evolution is needed to fully understand and preserve Earth's biodiversity. In this Perspective, we argue that multiple data types are necessary for almost all draft targets set by the Convention on Biological Diversity. We examine five key topics in biodiversity science that can be advanced by integrating remote sensing with in situ data collection from field sampling, experiments and laboratory studies to benefit conservation. Lowering the barriers for bringing these approaches together will require global-scale collaboration.
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Affiliation(s)
| | - Fabian D Schneider
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
| | | | - Amanda Armstrong
- Biospheric Sciences Laboratory, NASA Goddard Space Flight Center, Greenbelt, MD, USA
| | - Ana Carnaval
- Department of Biology, Ph.D. Program in Biology, City University of New York and The Graduate Center of CUNY, New York City, NY, USA
| | - Kyla M Dahlin
- Department of Geography, Environment, and Spatial Sciences, Michigan State University, East Lansing, MI, USA
| | - Lola Fatoyinbo
- Biospheric Sciences Laboratory, NASA Goddard Space Flight Center, Greenbelt, MD, USA
| | - George C Hurtt
- Department of Geographical Sciences, University of Maryland, College Park, MD, USA
| | - David Schimel
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
| | - Philip A Townsend
- Department of Forest and Wildlife Ecology, Univ. of Wisconsin-Madison, Madison, WI, USA
| | - Susan L Ustin
- Department of Land, Air and Water Resources and the John Muir Institute of the Environment, University of California, Davis, CA, USA
| | - Zhihui Wang
- Key Lab of Guangdong for Utilization of Remote Sensing and Geographical Information System, Guangdong Open Laboratory of Geospatial Information Technology and Application, Guangzhou Institute of Geography, Guangdong Academy of Sciences, Guangzhou, China
| | - Adam M Wilson
- Department of Geography, University at Buffalo, Buffalo, NY, USA
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8
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Bundalovic-Torma C, Desveaux D, Guttman DS. RecPD: A Recombination-aware measure of phylogenetic diversity. PLoS Comput Biol 2022; 18:e1009899. [PMID: 35192600 PMCID: PMC8896707 DOI: 10.1371/journal.pcbi.1009899] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 03/04/2022] [Accepted: 02/07/2022] [Indexed: 12/22/2022] Open
Abstract
A critical step in studying biological features (e.g., genetic variants, gene families, metabolic capabilities, or taxa) is assessing their diversity and distribution among a sample of individuals. Accurate assessments of these patterns are essential for linking features to traits or outcomes of interest and understanding their functional impact. Consequently, it is of crucial importance that the measures employed for quantifying feature diversity can perform robustly under any evolutionary scenario. However, the standard measures used for quantifying and comparing the distribution of features, such as prevalence, phylogenetic diversity, and related approaches, either do not take into consideration evolutionary history, or assume strictly vertical patterns of inheritance. Consequently, these approaches cannot accurately assess diversity for features that have undergone recombination or horizontal transfer. To address this issue, we have devised RecPD, a novel recombination-aware phylogenetic-diversity statistic for measuring the distribution and diversity of features under all evolutionary scenarios. RecPD utilizes ancestral-state reconstruction to map the presence / absence of features onto ancestral nodes in a species tree, and then identifies potential recombination events in the evolutionary history of the feature. We also derive several related measures from RecPD that can be used to assess and quantify evolutionary dynamics and correlation of feature evolutionary histories. We used simulation studies to show that RecPD reliably reconstructs feature evolutionary histories under diverse recombination and loss scenarios. We then applied RecPD in two diverse real-world scenarios including a preliminary study type III effector protein families secreted by the plant pathogenic bacterium Pseudomonas syringae and growth phenotypes of the Pseudomonas genus and demonstrate that prevalence is an inadequate measure that obscures the potential impact of recombination. We believe RecPD will have broad utility for revealing and quantifying complex evolutionary processes for features at any biological level. Phylogenetic diversity is an important concept utilized in evolutionary ecology which has extensive applications in population genetics to help us understand how evolutionary processes have distributed genetic variation among individuals of a species, and how this impacts phenotypic diversification over time. However, existing approaches for studying phylogenetic diversity largely assume that the genetic features follow vertical inheritance, which is frequently violated in the case of microbial genomes due to horizontal transfer. To address this shortcoming, we present RecPD, a recombination-aware phylogenetic diversity measure, which incorporates ancestral state reconstruction to quantify the phylogenetic diversity of genetic features mapped onto a species phylogeny. Through simulation experiments we show that RecPD robustly reconstructs the evolutionary histories of features evolving under various scenarios of recombination and loss. When applied to a real-world example of type III secreted effector protein families from the plant pathogenic bacterium Pseudomonas syringae, RecPD reveals that horizontal transfer has played an important role in shaping the phylogenetic distributions of a substantial proportion of families across the P. syringae species complex. Furthermore, we demonstrate that the traditional measures of feature prevalence are unsuitable as a measure for comparing feature diversity. We also provide a R package implementation of RecPD for public use: https://github.com/cedatorma/recpd.
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Affiliation(s)
| | - Darrell Desveaux
- Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario, Canada
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, Ontario, Canada
| | - David S. Guttman
- Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario, Canada
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, Ontario, Canada
- * E-mail:
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9
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Wu ETY, Liu Y, Jennings L, Dong S, Davies TJ. Detecting the phylogenetic signal of glacial refugia in a bryodiversity hotspot outside the tropics. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13449] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Ernest T. Y. Wu
- Department of Forest and Conservation Sciences Faculty of Forestry University of British Columbia Vancouver British Columbia Canada
- Department of Plant Sciences University of Oxford Oxford UK
| | - Yang Liu
- Fairy Lake Botanical Garden Chinese Academy of Sciences Shenzhen Guangdong China
| | - Linda Jennings
- Department of Botany Faculty of Sciences University of British Columbia Vancouver British Columbia Canada
- Herbarium, Beaty Biodiversity Museum University of British Columbia Vancouver British Columbia Canada
| | - Shanshan Dong
- Fairy Lake Botanical Garden Chinese Academy of Sciences Shenzhen Guangdong China
| | - T. Jonathan Davies
- Department of Forest and Conservation Sciences Faculty of Forestry University of British Columbia Vancouver British Columbia Canada
- Department of Botany Faculty of Sciences University of British Columbia Vancouver British Columbia Canada
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10
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Ellis RJ, Iudicello JE, Heaton RK, Isnard S, Lin J, Routy JP, Gianella S, Hoenigl M, Knight R. Markers of Gut Barrier Function and Microbial Translocation Associate with Lower Gut Microbial Diversity in People with HIV. Viruses 2021; 13:1891. [PMID: 34696320 PMCID: PMC8537977 DOI: 10.3390/v13101891] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/14/2021] [Accepted: 09/18/2021] [Indexed: 12/14/2022] Open
Abstract
People with human immunodeficiency virus (HIV) (PWH) have reduced gut barrier integrity ("leaky gut") that permits diffusion of microbial antigens (microbial translocation) such as lipopolysaccharide (LPS) into the circulation, stimulating inflammation. A potential source of this disturbance, in addition to gut lymphoid tissue CD4+ T-cell depletion, is the interaction between the gut barrier and gut microbes themselves. We evaluated the relationship of gut barrier integrity, as indexed by plasma occludin levels (higher levels corresponding to greater loss of occludin from the gut barrier), to gut microbial diversity. PWH and people without HIV (PWoH) participants were recruited from community sources and provided stool, and 16S rRNA amplicon sequencing was used to characterize the gut microbiome. Microbial diversity was indexed by Faith's phylogenetic diversity (PD). Participants were 50 PWH and 52 PWoH individuals, mean ± SD age 45.6 ± 14.5 years, 28 (27.5%) women, 50 (49.0%) non-white race/ethnicity. PWH had higher gut microbial diversity (Faith's PD 14.2 ± 4.06 versus 11.7 ± 3.27; p = 0.0007), but occludin levels were not different (1.84 ± 0.311 versus 1.85 ± 0.274; p = 0.843). Lower gut microbial diversity was associated with higher plasma occludin levels in PWH (r = -0.251; p = 0.0111), but not in PWoH. A multivariable model demonstrated an interaction (p = 0.0459) such that the correlation between Faith's PD and plasma occludin held only for PWH (r = -0.434; p = 0.0017), but not for PWoH individuals (r = -0.0227; p = 0.873). The pattern was similar for Shannon alpha diversity. Antiretroviral treatment and viral suppression status were not associated with gut microbial diversity (ps > 0.10). Plasma occludin levels were not significantly related to age, sex or ethnicity, nor to current or nadir CD4 or plasma viral load. Higher occludin levels were associated with higher plasma sCD14 and LPS, both markers of microbial translocation. Together, the findings suggest that damage to the gut epithelial barrier is an important mediator of microbial translocation and inflammation in PWH, and that reduced gut microbiome diversity may have an important role.
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Affiliation(s)
- Ronald J. Ellis
- Departments of Neurosciences and Psychiatry, University of California, San Diego, CA 92093, USA
| | - Jennifer E. Iudicello
- Department of Psychiatry, University of California, San Diego, CA 92093, USA; (J.E.I.); (R.K.H.)
| | - Robert K. Heaton
- Department of Psychiatry, University of California, San Diego, CA 92093, USA; (J.E.I.); (R.K.H.)
| | - Stéphane Isnard
- Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada; (S.I.); (J.L.); (J.-P.R.)
| | - John Lin
- Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada; (S.I.); (J.L.); (J.-P.R.)
| | - Jean-Pierre Routy
- Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada; (S.I.); (J.L.); (J.-P.R.)
| | - Sara Gianella
- Department of Medicine, University of California, San Diego, CA 92093, USA; (S.G.); (M.H.)
| | - Martin Hoenigl
- Department of Medicine, University of California, San Diego, CA 92093, USA; (S.G.); (M.H.)
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, CA 92093, USA;
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11
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Robuchon M, Pavoine S, Véron S, Delli G, Faith DP, Mandrici A, Pellens R, Dubois G, Leroy B. Revisiting species and areas of interest for conserving global mammalian phylogenetic diversity. Nat Commun 2021; 12:3694. [PMID: 34140481 PMCID: PMC8211746 DOI: 10.1038/s41467-021-23861-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 05/11/2021] [Indexed: 02/05/2023] Open
Abstract
Various prioritisation strategies have been developed to cope with accelerating biodiversity loss and limited conservation resources. These strategies could become more engaging for decision-makers if they reflected the positive effects conservation can have on future projected biodiversity, by targeting net positive outcomes in future projected biodiversity, rather than reflecting the negative consequences of further biodiversity losses only. Hoping to inform the post-2020 biodiversity framework, we here apply this approach of targeting net positive outcomes in future projected biodiversity to phylogenetic diversity (PD) to re-identify species and areas of interest for conserving global mammalian PD. We identify priority species/areas as those whose protection would maximise gains in future projected PD. We also identify loss-significant species/areas as those whose/where extinction(s) would maximise losses in future projected PD. We show that our priority species/areas differ from loss-significant species/areas. While our priority species are mostly similar to those identified by the EDGE of Existence Programme, our priority areas generally differ from previously-identified ones for global mammal conservation. We further highlight that these newly-identified species/areas of interest currently lack protection and offer some guidance for their future management.
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Affiliation(s)
- Marine Robuchon
- Centre d'Ecologie et des Sciences de la Conservation (CESCO), Muséumnational d'Histoire naturelle, Centre National de la Recherche Scientifique, Sorbonne Université, Paris, France.
- Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Muséum national d'Histoire naturelle, Centre National de la Recherche Scientifique, Institut de Recherche pour le Développement, Sorbonne Université, Université Caen-Normandie, Université des Antilles, Paris, France.
- Joint Research Centre (JRC) of the European Commission, Directorate for Sustainable Resources, Ispra (VA), Italy.
| | - Sandrine Pavoine
- Centre d'Ecologie et des Sciences de la Conservation (CESCO), Muséumnational d'Histoire naturelle, Centre National de la Recherche Scientifique, Sorbonne Université, Paris, France
| | - Simon Véron
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, Centre National de la Recherche Scientifique, Sorbonne Université, Ecole Pratique des Hautes Etudes, Université des Antilles, Paris, France
| | - Giacomo Delli
- Joint Research Centre (JRC) of the European Commission, Directorate for Sustainable Resources, Ispra (VA), Italy
| | | | - Andrea Mandrici
- Joint Research Centre (JRC) of the European Commission, Directorate for Sustainable Resources, Ispra (VA), Italy
| | - Roseli Pellens
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, Centre National de la Recherche Scientifique, Sorbonne Université, Ecole Pratique des Hautes Etudes, Université des Antilles, Paris, France
| | - Grégoire Dubois
- Joint Research Centre (JRC) of the European Commission, Directorate for Sustainable Resources, Ispra (VA), Italy
| | - Boris Leroy
- Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Muséum national d'Histoire naturelle, Centre National de la Recherche Scientifique, Institut de Recherche pour le Développement, Sorbonne Université, Université Caen-Normandie, Université des Antilles, Paris, France
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12
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Obregón Alvarez D, Mendes KF, Tosi M, Fonseca de Souza L, Campos Cedano JC, de Souza Falcão NP, Dunfield K, Tsai SM, Tornisielo VL. Sorption-desorption and biodegradation of sulfometuron-methyl and its effects on the bacterial communities in Amazonian soils amended with aged biochar. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 207:111222. [PMID: 32890950 DOI: 10.1016/j.ecoenv.2020.111222] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 08/11/2020] [Accepted: 08/23/2020] [Indexed: 06/11/2023]
Abstract
Sulfometuron-methyl is a broad-spectrum herbicide, used throughout Brazil; however, its environmental impacts in biochar (BC) amended soils is not fully understood. Biochar is known to enhance soil quality but can also have undesired effects such as altering the bioavailability and behavior of herbicides. Microbial communities can degrade herbicides such as sulfometuron-methyl in soils; however, they are known to be affected by BC. Therefore, it is important to understand the tripartite interaction between these factors. This research aimed to evaluate the sorption-desorption and biodegradation of sulfometuron-methyl in Amazonian soils amended with BC, and to assess the effects of the interactions between BC and sulfometuron-methyl on soil bacterial communities. Soil samples were collected from field plots amended with BC at three doses (0, 40 and 80 t ha-1) applied ten years ago. The herbicide sorption and desorption were evaluated using a batch equilibrium method. Mineralization and biodegradation studies were conducted in microcosms incubated with 14C-sulfometuron-methyl for 80 days. Systematic soil sampling, followed by DNA extraction, quantification (qPCR) and 16S rRNA amplicon sequencing were performed. The presence of BC increased the sorption of the herbicide to the soil by 11% (BC40) and 16% (BC80) compared to unamended soil. The presence of BC also affected the degradation of 14C-sulfometuron-methyl, reducing the mineralization rate and increasing the degradation half-life times (DT50) from 36.67 days in unamended soil to 52.11 and 55.45 days in BC40 and BC80 soils, respectively. The herbicide application altered the bacterial communities, affecting abundance and richness, and changing the taxonomic diversity (i.e., some taxa were promoted and other inhibited). A tripartite interaction was found between BC, the herbicide and soil bacterial communities, suggesting that it is important to consider the environmental impact of soil applied herbicides in biochar amended soils.
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Affiliation(s)
- Dasiel Obregón Alvarez
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture (CENA), University of São Paulo (USP), Av. Centenário, N° 303, Piracicaba, São Paulo, 13400-970, Brazil; School of Environmental Sciences, University of Guelph, Guelph, ON, N1G 2W1, Canada.
| | - Kassio Ferreira Mendes
- Department of Agronomy, Federal University of Viçosa, Avenida Peter Henry Rolfs, S/n, Viçosa, Minas Gerais, 36570-000, Brazil.
| | - Micaela Tosi
- School of Environmental Sciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Leandro Fonseca de Souza
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture (CENA), University of São Paulo (USP), Av. Centenário, N° 303, Piracicaba, São Paulo, 13400-970, Brazil
| | - Johnny Carlos Campos Cedano
- Department of Agricultural Sciences, National Institute of Amazonian Research (INPA), Av. André Araújo, 2936, Aleixo, Manaus, Amazonas, 69060-001, Brazil
| | - Newton Paulo de Souza Falcão
- Department of Agricultural Sciences, National Institute of Amazonian Research (INPA), Av. André Araújo, 2936, Aleixo, Manaus, Amazonas, 69060-001, Brazil
| | - Kari Dunfield
- School of Environmental Sciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Siu Mui Tsai
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture (CENA), University of São Paulo (USP), Av. Centenário, N° 303, Piracicaba, São Paulo, 13400-970, Brazil
| | - Valdemar Luiz Tornisielo
- Ecotoxicology Laboratory, Center for Nuclear Energy in Agriculture (CENA), University of São Paulo (USP), Av. Centenário, N° 303, Piracicaba, São Paulo, 13400-970 Brazil
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13
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Bartish IV, Ozinga WA, Bartish MI, Wamelink GW, Hennekens SM, Yguel B, Prinzing A. Anthropogenic threats to evolutionary heritage of angiosperms in the Netherlands through an increase in high-competition environments. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2020; 34:1536-1548. [PMID: 32463531 PMCID: PMC7754312 DOI: 10.1111/cobi.13556] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 02/26/2020] [Accepted: 03/02/2020] [Indexed: 06/01/2023]
Abstract
Present biodiversity comprises the evolutionary heritage of Earth's epochs. Lineages from particular epochs are often found in particular habitats, but whether current habitat decline threatens the heritage from particular epochs is unknown. We hypothesized that within a given region, humans threaten specifically habitats that harbor lineages from a particular geological epoch. We expect so because humans threaten environments that dominated and lineages that diversified during these epochs. We devised a new approach to quantify, per habitat type, diversification of lineages from different epochs. For Netherlands, one of the floristically and ecologically best-studied regions, we quantified the decline of habitat types and species in the past century. We defined habitat types based on vegetation classification and used existing ranking of decline of vegetation classes and species. Currently, most declining habitat types and the group of red-listed species are characterized by increased diversification of lineages dating back to Paleogene, specifically to Paleocene-Eocene and Oligocene. Among vulnerable habitat types with large representation of lineages from these epochs were sublittoral and eulittoral zones of temperate seas and 2 types of nutrient-poor, open habitats. These losses of evolutionary heritage would go unnoticed with classical measures of evolutionary diversity. Loss of heritage from Paleocene-Eocene became unrelated to decline once low competition, shade tolerance, and low proportion of non-Apiaceae were accounted for, suggesting that these variables explain the loss of heritage from Paleocene-Eocene. Losses of heritage from Oligocene were partly explained by decline of habitat types occupied by weak competitors and shade-tolerant species. Our results suggest a so-far unappreciated human threat to evolutionary heritage: habitat decline threatens descendants from particular epochs. If the trends persist into the future uncontrolled, there may be no habitats within the region for many descendants of evolutionary ancient epochs, such as Paleogene.
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Affiliation(s)
- Igor V. Bartish
- Department of Genetic Ecology, Institute of BotanyAcademy of Sciences of Czech RepublicZamek 1Průhonice25243Czech Republic
| | - Wim A. Ozinga
- Wageningen Environmental Research (Alterra)P.O. Box 47WageningenNL‐6700 AAThe Netherlands
- Experimental Plant EcologyRadboud University NijmegenP.O. Box 9010Nijmegen6500 GLThe Netherlands
| | | | - G.W. Wieger Wamelink
- Wageningen Environmental Research (Alterra)P.O. Box 47WageningenNL‐6700 AAThe Netherlands
| | - Stephan M. Hennekens
- Wageningen Environmental Research (Alterra)P.O. Box 47WageningenNL‐6700 AAThe Netherlands
| | - Benjamin Yguel
- Centre d'Ecologie et des Sciences de la Conservation (CESCO‐UMR 7204)Sorbonne Universités‐MNHN‐CNRS‐UPMCCP51, 55‐61 rue BuffonParis75005France
| | - Andreas Prinzing
- University Rennes 1Centre National de la Recherche Scientifique, Research Unit "Ecosystèmes, Biodiversité, Evolution"Evolution (UMR 6553), Campus Beaulieu, Bâtiment 14 ARennes35042France
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14
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Mendez R, Kesh K, Arora N, Di Martino L, McAllister F, Merchant N, Banerjee S, Banerjee S. Microbial dysbiosis and polyamine metabolism as predictive markers for early detection of pancreatic cancer. Carcinogenesis 2020; 41:561-570. [PMID: 31369062 DOI: 10.1093/carcin/bgz116] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 05/29/2019] [Accepted: 06/17/2019] [Indexed: 12/15/2022] Open
Abstract
The lack of tools for early detection of pancreatic ductal adenocarcinoma (PDAC) is directly correlated with the abysmal survival rates in patients. In addition to several potential detection tools under active investigation, we tested the gut microbiome and its metabolic complement as one of the earliest detection tools that could be useful in patients at high risk for PDAC. We used a combination of 16s rRNA pyrosequencing and whole-genome sequencing of gut fecal microbiota in a genetically engineered PDAC murine model (KRASG12DTP53R172HPdxCre or KPC). Metabolic reconstruction of microbiome was done using the HUMAnN2 pipeline. Serum polyamine levels were measured from murine and patient samples using chromogenic assay. Our results showed a Proteobacterial and Firmicutes dominance in gut microbiota in early stages of PDAC development. Upon in silico reconstruction of active metabolic pathways within the altered microbial flora, polyamine and nucleotide biosynthetic pathways were significantly elevated. These metabolic products are known to be actively assimilated by the host and eventually utilized by rapidly dividing cells for proliferation validating their importance in the context of tumorigenesis. In KPC mice, as well as PDAC patients, we show significantly elevated serum polyamine concentrations. Therefore, at the early stages of tumorigenesis, there is a strong correlation between microbial changes and release of metabolites that foster host tumorigenesis, thereby fulfilling the 'vicious cycle hypothesis' of the role of microbiome in health and disease states. Our results provide a potential, precise, noninvasive tool for early detection of PDAC, which may result in improved outcomes.
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Affiliation(s)
- Roberto Mendez
- Department of Surgery, University of Miami, Miami, FL, USA
| | - Kousik Kesh
- Department of Surgery, University of Miami, Miami, FL, USA
| | - Nivedita Arora
- Department of Surgery, University of Minnesota, Minneapolis, MN, USA
| | - Leá Di Martino
- Department of Surgery, University of Miami, Miami, FL, USA.,Université Grenoble Alpes, Isère, France
| | - Florencia McAllister
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Miami, FL, USA
| | - Nipun Merchant
- Department of Surgery, University of Miami, Miami, FL, USA.,Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - Sulagna Banerjee
- Department of Surgery, University of Miami, Miami, FL, USA.,Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - Santanu Banerjee
- Department of Surgery, University of Miami, Miami, FL, USA.,Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
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15
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Ritchie AM, Hua X, Cardillo M, Yaxley KJ, Dinnage R, Bromham L. Phylogenetic diversity metrics from molecular phylogenies: modelling expected degree of error under realistic rate variation. DIVERS DISTRIB 2020. [DOI: 10.1111/ddi.13179] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Andrew M. Ritchie
- Research School of Biological Sciences Australian National University Canberra ACT Australia
| | - Xia Hua
- Research School of Biological Sciences Australian National University Canberra ACT Australia
- Mathematical Sciences Institute Australian National University Canberra ACT Australia
| | - Marcel Cardillo
- Research School of Biological Sciences Australian National University Canberra ACT Australia
| | - Keaghan J. Yaxley
- Research School of Biological Sciences Australian National University Canberra ACT Australia
| | - Russell Dinnage
- Research School of Biological Sciences Australian National University Canberra ACT Australia
| | - Lindell Bromham
- Research School of Biological Sciences Australian National University Canberra ACT Australia
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16
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Mammeri M, Obregón DA, Chevillot A, Polack B, Julien C, Pollet T, Cabezas-Cruz A, Adjou KT. Cryptosporidium parvum Infection Depletes Butyrate Producer Bacteria in Goat Kid Microbiome. Front Microbiol 2020; 11:548737. [PMID: 33178145 PMCID: PMC7596689 DOI: 10.3389/fmicb.2020.548737] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 09/11/2020] [Indexed: 01/09/2023] Open
Abstract
Cryptosporidium parvum is an important apicomplexan parasite infecting ruminants and humans. We characterized the impact of C. parvum infection on the goat kid microbiome. C. parvum was orally administered to parasite-naïve goats, and infection was monitored for 26 days in fecal samples using immunofluorescence assay and qPCR tests. Age-matched goats served as uninfected controls. A reduction in body weight gain, diarrhea, and dehydration were observed in infected goats compared to the uninfected controls. Infection decreased the bacterial diversity 5 days post-infection (dpi), but this parameter recovered at 15 dpi. The infection altered the relative abundance of several taxa. A total of 38 taxa displayed significant differences in abundance between control and infected goats at both 5 and 15 dpi. Co-occurrence network analysis revealed that the infection resulted in a differential pattern of taxa interactions and that C. parvum infection increased the relative abundance of specific taxa. The 16S data set was used for metagenome predictions using the software package PICRUSt2. As many as 34 and 40 MetaCyc pathways (from 387 total) were significantly affected by the infection at 5 and 15 dpi, respectively. Notably, C. parvum decreased the abundance of butyrate-producing pathways in bacteria. Low levels of butyrate may increase mucosal inflammation and tissue repair. Our results suggest that the gut inflammation induced by C. parvum infection is associated with the reduction of butyrate-producing bacteria. This insight could be the basis for the development of novel control strategies to improve animal health.
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Affiliation(s)
- Mohamed Mammeri
- UMR BIPAR, Ecole Nationale Vétérinaire d’Alfort, ANSES, INRAE, Université Paris-Est, Maisons-Alfort, France
- Phileo by Lesaffre, Marcq-en-Barœul, France
| | - Dasiel Alvarez Obregón
- Centre for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, Brazil
- School of Environmental Sciences, University of Guelph, Guelph, ON, Canada
| | - Aurélie Chevillot
- UMR BIPAR, Ecole Nationale Vétérinaire d’Alfort, ANSES, INRAE, Université Paris-Est, Maisons-Alfort, France
| | - Bruno Polack
- UMR BIPAR, Ecole Nationale Vétérinaire d’Alfort, ANSES, INRAE, Université Paris-Est, Maisons-Alfort, France
| | | | - Thomas Pollet
- UMR BIPAR, Ecole Nationale Vétérinaire d’Alfort, ANSES, INRAE, Université Paris-Est, Maisons-Alfort, France
- UMR ASTRE, INRAE, CIRAD, Université Montpellier, Montpellier, France
| | - Alejandro Cabezas-Cruz
- UMR BIPAR, Ecole Nationale Vétérinaire d’Alfort, ANSES, INRAE, Université Paris-Est, Maisons-Alfort, France
| | - Karim Tarik Adjou
- UMR BIPAR, Ecole Nationale Vétérinaire d’Alfort, ANSES, INRAE, Université Paris-Est, Maisons-Alfort, France
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17
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DNA barcoding for identification of fish species from freshwater in Enugu and Anambra States of Nigeria. CONSERV GENET RESOUR 2020. [DOI: 10.1007/s12686-020-01155-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
AbstractWithin Enugu and Anambra States, Nigeria, identification of fishes has been based on morphological traits and do not account for existing biodiversity. For DNA barcoding, assessment of biodiversity, conservation and fishery management, 44 fish sampled from Enugu and Anambra States were isolated, amplified and sequenced with mitochondrial cytochrome oxidase subunit I (COI). Twenty groups clustering at 100% bootstrap value including monophyletic ones were identified. The phylogenetic diversity (PD) ranged from 0.0397 (Synodontis obesus) to 0.2147 (Parachanna obscura). The highest percentage of genetic distance based on Kimura 2-parameter was 37.00 ± 0.0400. Intergeneric distances ranged from 15.8000 to 37.0000%. Congeneric distances were 6.9000 ± 0.0140–28.1000 ± 0.0380, with Synodontis as the existing synonymous genus. Confamilial distances in percentage were 16.0000 ± 0.0140 and 25.7000 ± 0.0300. Forty-two haplotypes and haplotype diversity of 0.9990 ± 0.0003 were detected. Nucleotide diversity was 0.7372, while Fu and Li’s D* test statistic was 2.1743 (P < 0.02). Tajima’s D was 0.2424 (P > 0.10) and nucleotide frequencies were C (17.70%), T (29.40%), A (24.82%), G (18.04%) and A + T (54.22%). Transitional mutations were more than transversions. Twenty species (99–100%) were identified with the e-value, maximum coverage and bit-score of 1e−43, 99–100 and 185–1194, respectively. Seventeen genera and 12 families were found and Clariidae (n = 14) was the most dominant among other families. The fish species resolution, diversity assessment and phylogenetic relationships were successfully obtained with the COI marker. Clariidae had the highest number of genera and families. Phylogenetic diversity analysis identified Parachanna obscura as the most evolutionarily divergent one. This study will contribute to fishery management, and conservation of freshwater fishes in Enugu and Anambra States, Nigeria.
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18
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Gumbs R, Gray CL, Böhm M, Hoffmann M, Grenyer R, Jetz W, Meiri S, Roll U, Owen NR, Rosindell J. Global priorities for conservation of reptilian phylogenetic diversity in the face of human impacts. Nat Commun 2020; 11:2616. [PMID: 32457412 PMCID: PMC7250838 DOI: 10.1038/s41467-020-16410-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 04/24/2020] [Indexed: 11/09/2022] Open
Abstract
Phylogenetic diversity measures are increasingly used in conservation planning to represent aspects of biodiversity beyond that captured by species richness. Here we develop two new metrics that combine phylogenetic diversity and the extent of human pressure across the spatial distribution of species - one metric valuing regions and another prioritising species. We evaluate these metrics for reptiles, which have been largely neglected in previous studies, and contrast these results with equivalent calculations for all terrestrial vertebrate groups. We find that regions under high human pressure coincide with the most irreplaceable areas of reptilian diversity, and more than expected by chance. The highest priority reptile species score far above the top mammal and bird species, and reptiles include a disproportionate number of species with insufficient extinction risk data. Data Deficient species are, in terms of our species-level metric, comparable to Critically Endangered species and therefore may require urgent conservation attention.
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Affiliation(s)
- Rikki Gumbs
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire, SL5 7PY, UK.
- Science and Solutions for a Changing Planet DTP, Grantham Institute, Imperial College London, Exhibition Road, South Kensington, London, SW7 2AZ, UK.
- EDGE of Existence Programme, Zoological Society of London, Regent's Park, London, NW1 4RY, UK.
| | - Claudia L Gray
- EDGE of Existence Programme, Zoological Society of London, Regent's Park, London, NW1 4RY, UK
| | - Monika Böhm
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK
| | - Michael Hoffmann
- Conservation and Policy, Zoological Society of London, Regent's Park, London, NW1 4RY, UK
| | - Richard Grenyer
- School of Geography and the Environment, University of Oxford, Oxford, OX1 3QY, UK
| | - Walter Jetz
- Ecology and Evolutionary Biology Department, Yale University, 165 Prospect Street, New Haven, CT, 06511, USA
- Center for Biodiversity and Global Change, Yale University, 165 Prospect Street, New Haven, CT, 06511, USA
| | - Shai Meiri
- School of Zoology, Tel Aviv University, 6997801, Tel Aviv, Israel
- Steinhardt Museum of Natural History, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Uri Roll
- Mitrani Department of Desert Ecology, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, 8499000, Israel
| | - Nisha R Owen
- On The EDGE Conservation, 152a Walton St, Chelsea, London, SW3 2JJ, UK
| | - James Rosindell
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire, SL5 7PY, UK
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Dopheide A, Makiola A, Orwin KH, Holdaway RJ, Wood JR, Dickie IA. Rarity is a more reliable indicator of land-use impacts on soil invertebrate communities than other diversity metrics. eLife 2020; 9:e52787. [PMID: 32423527 PMCID: PMC7237214 DOI: 10.7554/elife.52787] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 04/15/2020] [Indexed: 02/04/2023] Open
Abstract
The effects of land use on soil invertebrates - an important ecosystem component - are poorly understood. We investigated land-use impacts on a comprehensive range of soil invertebrates across New Zealand, measured using DNA metabarcoding and six biodiversity metrics. Rarity and phylogenetic rarity - direct measures of the number of species or the portion of a phylogeny unique to a site - showed stronger, more consistent responses across taxa to land use than widely used metrics of species richness, effective species numbers, and phylogenetic diversity. Overall, phylogenetic rarity explained the highest proportion of land use-related variance. Rarity declined from natural forest to planted forest, grassland, and perennial cropland for most soil invertebrate taxa, demonstrating pervasive impacts of agricultural land use on soil invertebrate communities. Commonly used diversity metrics may underestimate the impacts of land use on soil invertebrates, whereas rarity provides clearer and more consistent evidence of these impacts.
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Affiliation(s)
| | - Andreas Makiola
- Bio-Protection Research Centre, Lincoln UniversityLincolnNew Zealand
| | - Kate H Orwin
- Manaaki Whenua – Landcare ResearchLincolnNew Zealand
| | | | - Jamie R Wood
- Manaaki Whenua – Landcare ResearchLincolnNew Zealand
| | - Ian A Dickie
- Bio-Protection Research Centre, School of Biological Sciences, University of CanterburyChristchurchNew Zealand
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20
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Georgiev KB, Chao A, Castro J, Chen Y, Choi C, Fontaine JB, Hutto RL, Lee E, Müller J, Rost J, Żmihorski M, Thorn S. Salvage logging changes the taxonomic, phylogenetic and functional successional trajectories of forest bird communities. J Appl Ecol 2020. [DOI: 10.1111/1365-2664.13599] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kostadin B. Georgiev
- Field Station Fabrikschleichach Biocenter University of Würzburg Rauhenebrach Germany
- Bavarian Forest National Park Grafenau Germany
| | - Anne Chao
- Institute of Statistics National Tsing Hua University Hsin‐Chu Taiwan
| | - Jorge Castro
- Department of Ecology University of Granada Granada Spain
| | - Yan‐Han Chen
- Institute of Statistics National Tsing Hua University Hsin‐Chu Taiwan
| | - Chang‐Yong Choi
- Research Institute of Agriculture and Life Sciences Seoul National University Seoul Korea
| | - Joseph B. Fontaine
- Environmental and Conservation Sciences Murdoch University Murdoch WA Australia
| | - Richard L. Hutto
- Division of Biological Sciences University of Montana Missoula MT USA
| | - Eun‐Jae Lee
- Urban Planning Research Group Daejeon Sejong Research Institute Daejeon Korea
| | - Jörg Müller
- Field Station Fabrikschleichach Biocenter University of Würzburg Rauhenebrach Germany
- Bavarian Forest National Park Grafenau Germany
| | - Josep Rost
- Department of Environmental Sciences and Food Industries University of Vic‐Central University of Catalonia Catalonia Spain
| | - Michal Żmihorski
- Mammal Research Institute Polish Academy of Sciences Białowieża Poland
| | - Simon Thorn
- Field Station Fabrikschleichach Biocenter University of Würzburg Rauhenebrach Germany
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21
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Gobbi A, Kyrkou I, Filippi E, Ellegaard-Jensen L, Hansen LH. Seasonal epiphytic microbial dynamics on grapevine leaves under biocontrol and copper fungicide treatments. Sci Rep 2020; 10:681. [PMID: 31959791 PMCID: PMC6971271 DOI: 10.1038/s41598-019-56741-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 12/10/2019] [Indexed: 02/01/2023] Open
Abstract
Winemakers have long used copper as a conventional fungicide treatment on grapevine and only recently, the use of biocontrol agents depicted a promising alternative. Most of the studies that investigate the impact of fungicide treatments, focus on specific pathogenic microbes. In the present work instead, a field experiment conducted in South Africa shows the seasonal microbial change occurring on grapevine leaves, periodically treated with two different fungicide treatments: copper sulphate and Lactobacillus plantarum MW-1. In this work, NGS data were combined with strain-specific and community qPCRs to reveal the shift of the microbial communities throughout the growing season and highlight the impact of fungicides on the microbiota. Only the family of Lactobacillaceae systematically changed between treatments, while the bacterial community remained relatively stable over time. MW-1 was exclusively detected on biocontrol-sprayed leaves. Conversely, the fungal community was largely shaped by sampling time, underlining the succession of different dominant taxa over the months. Between treatments, only a few fungal taxa appeared to change significantly and the fungal load was also comparable. Monitoring the dynamics of the microbial community under different fungicide treatments may advise the best timing to apply treatments to the plants, toward the realization of more sustainable agricultural practices.
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Affiliation(s)
- Alex Gobbi
- Environmental Microbial Genomics (EMG), Plant and Environmental Microbiology, Copenhagen University, Copenhagen, DK, Denmark
- Aarhus University, Department of Environmental Science, Roskilde, DK, Denmark
| | - Ifigeneia Kyrkou
- Aarhus University, Department of Environmental Science, Roskilde, DK, Denmark
| | - Elisa Filippi
- Aarhus University, Department of Environmental Science, Roskilde, DK, Denmark
| | | | - Lars Hestbjerg Hansen
- Environmental Microbial Genomics (EMG), Plant and Environmental Microbiology, Copenhagen University, Copenhagen, DK, Denmark.
- Aarhus University, Department of Environmental Science, Roskilde, DK, Denmark.
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García-Girón J, Fernández-Aláez C, Fernández-Aláez M, Alahuhta J. Untangling the assembly of macrophyte metacommunities by means of taxonomic, functional and phylogenetic beta diversity patterns. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 693:133616. [PMID: 31377370 DOI: 10.1016/j.scitotenv.2019.133616] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 07/25/2019] [Accepted: 07/25/2019] [Indexed: 06/10/2023]
Abstract
Metacommunity ecology has broadened considerably with the recognition that measuring beta diversity beyond the purely taxonomic viewpoint may improve our understanding of the dispersal- and niche-based mechanisms across biological communities. In that perspective, we applied a novel multidimensional approach including taxonomic, functional and phylogenetic data to enhance our basic understanding of macrophyte metacommunity dynamics. For each beta diversity metric, we calculated the mean overall value and tested whether the mean value was different from that expected by chance using null models. We also employed evolutionary and spatially constrained models to first identify the degree to which the studied functional traits showed a phylogenetic signal, and then to estimate the relative importance of spatial and environmental effects on metacommunity structure. We first found that most individual ponds were inhabited by species that were merely random draws from the taxonomic and phylogenetic species pool available in the study region. Contrary to our expectations, not all measured traits were conserved along the phylogeny. We also showed that trait and phylogenetic dimensions strongly increased the amount of variation in beta diversity that can be explained by degree of environmental filtering and dispersal limitation. This suggests that accounting for functional traits and phylogeny in metacommunity ecology helps to explain idiosyncratic patterns of variation in macrophyte species distribution. Importantly, phylogenetic and functional analyses identified the influence of underlying mechanisms that would otherwise be missed in an analysis of taxonomic turnover. Together, these results let us conclude that macrophyte species have labile functional traits adapted to dispersal-based processes and some evolutionary trade-offs that drive community assembly via species sorting. Overall, our exploration of different facets of beta diversity showed how functional and phylogenetic information may be used with species-level data to test community assembly hypotheses that are more ecologically meaningful than assessments of environmental patterns based on the purely taxonomic viewpoint.
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Affiliation(s)
- Jorge García-Girón
- Group for Limnology and Environmental Biotechnology, Area of Ecology, Universidad de León, Campus de Vegazana, León, Spain.
| | - Camino Fernández-Aláez
- Group for Limnology and Environmental Biotechnology, Area of Ecology, Universidad de León, Campus de Vegazana, León, Spain.
| | - Margarita Fernández-Aláez
- Group for Limnology and Environmental Biotechnology, Area of Ecology, Universidad de León, Campus de Vegazana, León, Spain.
| | - Janne Alahuhta
- Geography Research Unit, University of Oulu, P.O. Box 3000, FI-90140 University of Oulu, Finland.
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Welsh HH, Cummings AK, Hodgson GR. Metrics of disturbance in a redwood forest ecosystem: responses of stream amphibians to repeated sediment infusions. Ecosphere 2019. [DOI: 10.1002/ecs2.2886] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Hartwell H. Welsh
- Pacific Southwest Research Station Redwood Sciences Laboratory USDA Forest Service 1700 Bayview Drive Arcata California 95521 USA
| | - Adam K. Cummings
- Pacific Southwest Research Station Redwood Sciences Laboratory USDA Forest Service 1700 Bayview Drive Arcata California 95521 USA
| | - Garth R. Hodgson
- Pacific Southwest Research Station Redwood Sciences Laboratory USDA Forest Service 1700 Bayview Drive Arcata California 95521 USA
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Véron S, Saito V, Padilla-García N, Forest F, Bertheau Y. The Use of Phylogenetic Diversity in Conservation Biology and Community Ecology: A Common Base but Different Approaches. QUARTERLY REVIEW OF BIOLOGY 2019. [DOI: 10.1086/703580] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Tucker CM, Davies TJ, Cadotte MW, Pearse WD. On the relationship between phylogenetic diversity and trait diversity. Ecology 2018; 99:1473-1479. [DOI: 10.1002/ecy.2349] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 02/26/2018] [Accepted: 03/21/2018] [Indexed: 01/08/2023]
Affiliation(s)
- Caroline M. Tucker
- Department of Biology University of North Carolina at Chapel Hill Coker Hall, CB #3280 120 South Road Chapel Hill North Carolina 27599‐3280 USA
- Centre d'Ecologie Fonctionnelle et Evolutive CNRS 1919, Route de Mende Montpellier Cedex 5 34293 France
| | - T. Jonathan Davies
- Department of Biology McGill University 1205 Avenue Docteur Penfield Montreal Quebec QC H3A 0G4 Canada
- African Centre for DNA Barcoding University of Johannesburg PO Box 524, Auckland Park Johannesburg 2006 South Africa
- Departments of Botany, Forest & Conservation Sciences University of British Columbia 6270 University Blvd. Vancouver British Columbia V6T 1Z4 Canada
| | - Marc W. Cadotte
- Department of Biological Sciences University of Toronto‐Scarborough 1265 Military Trail Toronto Ontario M1C 1A4 Canada
- Ecology and Evolutionary Biology University of Toronto 25 Willcocks St Toronto Ontario M5S 3B2 Canada
| | - William D. Pearse
- Department of Biology & Ecology Center Utah State University Logan Utah 84322 USA
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26
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Tetrapods on the EDGE: Overcoming data limitations to identify phylogenetic conservation priorities. PLoS One 2018; 13:e0194680. [PMID: 29641585 PMCID: PMC5894989 DOI: 10.1371/journal.pone.0194680] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 03/07/2018] [Indexed: 12/02/2022] Open
Abstract
The scale of the ongoing biodiversity crisis requires both effective conservation prioritisation and urgent action. As extinction is non-random across the tree of life, it is important to prioritise threatened species which represent large amounts of evolutionary history. The EDGE metric prioritises species based on their Evolutionary Distinctiveness (ED), which measures the relative contribution of a species to the total evolutionary history of their taxonomic group, and Global Endangerment (GE), or extinction risk. EDGE prioritisations rely on adequate phylogenetic and extinction risk data to generate meaningful priorities for conservation. However, comprehensive phylogenetic trees of large taxonomic groups are extremely rare and, even when available, become quickly out-of-date due to the rapid rate of species descriptions and taxonomic revisions. Thus, it is important that conservationists can use the available data to incorporate evolutionary history into conservation prioritisation. We compared published and new methods to estimate missing ED scores for species absent from a phylogenetic tree whilst simultaneously correcting the ED scores of their close taxonomic relatives. We found that following artificial removal of species from a phylogenetic tree, the new method provided the closest estimates of their “true” ED score, differing from the true ED score by an average of less than 1%, compared to the 31% and 38% difference of the previous methods. The previous methods also substantially under- and over-estimated scores as more species were artificially removed from a phylogenetic tree. We therefore used the new method to estimate ED scores for all tetrapods. From these scores we updated EDGE prioritisation rankings for all tetrapod species with IUCN Red List assessments, including the first EDGE prioritisation for reptiles. Further, we identified criteria to identify robust priority species in an effort to further inform conservation action whilst limiting uncertainty and anticipating future phylogenetic advances.
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27
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Jaffé R, Prous X, Calux A, Gastauer M, Nicacio G, Zampaulo R, Souza-Filho PWM, Oliveira G, Brandi IV, Siqueira JO. Conserving relics from ancient underground worlds: assessing the influence of cave and landscape features on obligate iron cave dwellers from the Eastern Amazon. PeerJ 2018; 6:e4531. [PMID: 29576987 PMCID: PMC5865468 DOI: 10.7717/peerj.4531] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 03/03/2018] [Indexed: 11/24/2022] Open
Abstract
The degradation of subterranean habitats is believed to represent a serious threat for the conservation of obligate subterranean dwellers (troglobites), many of which are short-range endemics. However, while the factors influencing cave biodiversity remain largely unknown, the influence of the surrounding landscape and patterns of subterranean connectivity of terrestrial troglobitic communities have never been systematically assessed. Using spatial statistics to analyze the most comprehensive speleological database yet available for tropical caves, we first assess the influence of iron cave characteristics and the surrounding landscape on troglobitic communities from the Eastern Amazon. We then determine the spatial pattern of troglobitic community composition, species richness, phylogenetic diversity, and the occurrence of frequent troglobitic species, and finally quantify how different landscape features influence the connectivity between caves. Our results reveal the key importance of habitat amount, guano, water, lithology, geomorphology, and elevation in shaping iron cave troglobitic communities. While mining within 250 m from the caves influenced species composition, increasing agricultural land cover within 50 m from the caves reduced species richness and phylogenetic diversity. Troglobitic species composition, species richness, phylogenetic diversity, and the occurrence of frequent troglobites showed spatial autocorrelation for up to 40 km. Finally, our results suggest that the conservation of cave clusters should be prioritized, as geographic distance was the main factor determining connectivity between troglobitic communities. Overall, our work sheds important light onto one of the most overlooked terrestrial ecosystems, and highlights the need to shift conservation efforts from individual caves to subterranean habitats as a whole.
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Affiliation(s)
- Rodolfo Jaffé
- Instituto Tecnológico Vale, Belém, PA, Brazil.,Ecology, Universidade de São Paulo, São Paulo, Brazil.,Ecology, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Xavier Prous
- Environmental Licensing and Speleology, Vale, Nova Lima, Minas Gerais, Brazil
| | - Allan Calux
- Environmental Licensing and Speleology, Vale, Nova Lima, Minas Gerais, Brazil
| | | | | | - Robson Zampaulo
- Environmental Licensing and Speleology, Vale, Nova Lima, Minas Gerais, Brazil
| | - Pedro W M Souza-Filho
- Instituto Tecnológico Vale, Belém, PA, Brazil.,Geoscience, Universidade Federal do Pará, Belém, Pará, Brazil
| | | | - Iuri V Brandi
- Environmental Licensing and Speleology, Vale, Nova Lima, Minas Gerais, Brazil
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Morelli F, Benedetti Y, Møller AP, Liang W, Carrascal LM. Cuckoos host range is associated positively with distribution range and negatively with evolutionary uniqueness. J Anim Ecol 2018; 87:765-773. [PMID: 29355941 DOI: 10.1111/1365-2656.12797] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 12/12/2017] [Indexed: 11/30/2022]
Abstract
The evolutionary distinctiveness (ED) score is a measure of phylogenetic isolation that quantifies the evolutionary uniqueness of a species. Here, we compared the ED score of parasitic and non-parasitic cuckoo species world-wide, to understand whether parental care or parasitism represents the largest amount of phylogenetic uniqueness. Next, we focused only on 46 cuckoo species characterized by brood parasitism with a known number of host species, and we explored the associations among ED score, number of host species and breeding range size for these species. We assessed these associations using phylogenetic generalized least squares (PGLS) models, taking into account the phylogenetic signal. Parasitic cuckoo species were not more unique in terms of ED than non-parasitic species. However, we found a significant negative association between the evolutionary uniqueness and host range and a positive correlation between the number of host species and range size of parasitic cuckoos, probably suggesting a passive sampling of hosts by parasitic species as the breeding range broadens. The findings of this study showed that more generalist brood parasites occupied very different positions in a phylogenetic tree, suggesting that they have evolved independently within the Cuculiformes order. Finally, we demonstrated that specialist cuckoo species also represent the most evolutionarily unique species in the order of Cuculiformes.
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Affiliation(s)
- Federico Morelli
- Faculty of Environmental Sciences, Department of Applied Geoinformatics and Spatial Planning, Czech University of Life Sciences Prague, Prague 6, Czech Republic
| | - Yanina Benedetti
- Faculty of Environmental Sciences, Department of Applied Geoinformatics and Spatial Planning, Czech University of Life Sciences Prague, Prague 6, Czech Republic
| | - Anders Pape Møller
- Ecologie Systématique Evolution, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Orsay Cedex, France
| | - Wei Liang
- College of Life Sciences, Ministry of Education Key Laboratory for Ecology of Tropical Islands, Hainan Normal University, Haikou, China
| | - Luis M Carrascal
- Department of Biogeography and Global Change, Museo Nacional de Ciencias Naturales-CSIC, Madrid, Spain
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29
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Khanna S, Vazquez-Baeza Y, González A, Weiss S, Schmidt B, Muñiz-Pedrogo DA, Rainey JF, Kammer P, Nelson H, Sadowsky M, Khoruts A, Farrugia SL, Knight R, Pardi DS, Kashyap PC. Changes in microbial ecology after fecal microbiota transplantation for recurrent C. difficile infection affected by underlying inflammatory bowel disease. MICROBIOME 2017; 5:55. [PMID: 28506317 PMCID: PMC5433077 DOI: 10.1186/s40168-017-0269-3] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 04/23/2017] [Indexed: 05/05/2023]
Abstract
BACKGROUND Gut microbiota play a key role in maintaining homeostasis in the human gut. Alterations in the gut microbial ecosystem predispose to Clostridium difficile infection (CDI) and gut inflammatory disorders such as inflammatory bowel disease (IBD). Fecal microbiota transplantation (FMT) from a healthy donor can restore gut microbial diversity and pathogen colonization resistance; consequently, it is now being investigated for its ability to improve inflammatory gut conditions such as IBD. In this study, we investigated changes in gut microbiota following FMT in 38 patients with CDI with or without underlying IBD. RESULTS There was a significant change in gut microbial composition towards the donor microbiota and an overall increase in microbial diversity consistent with previous studies after FMT. FMT was successful in treating CDI using a diverse set of donors, and varying degrees of donor stool engraftment suggesting that donor type and degree of engraftment are not drivers of a successful FMT treatment of CDI. However, patients with underlying IBD experienced an increased number of CDI relapses (during a 24-month follow-up) and a decreased growth of new taxa, as compared to the subjects without IBD. Moreover, the need for IBD therapy did not change following FMT. These results underscore the importance of the existing gut microbial landscape as a decisive factor to successfully treat CDI and potentially for improvement of the underlying pathophysiology in IBD. CONCLUSIONS FMT leads to a significant change in microbial diversity in patients with recurrent CDI and complete resolution of symptoms. Stool donor type (related or unrelated) and degree of engraftment are not the key for successful treatment of CDI by FMT. However, CDI patients with IBD have higher proportion of the original community after FMT and lack of improvement of their IBD symptoms and increased episodes of CDI on long-term follow-up.
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Affiliation(s)
- Sahil Khanna
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Yoshiki Vazquez-Baeza
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Antonio González
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Sophie Weiss
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO, USA
| | - Bradley Schmidt
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, 55905, USA
| | | | - John F Rainey
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Patricia Kammer
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Heidi Nelson
- Division of Colorectal Surgery, Mayo Clinic, Rochester, MN, USA
| | - Michael Sadowsky
- BioTechnology Institute, University of Minnesota, Minneapolis, MN, USA
| | - Alexander Khoruts
- Division of Gastroenterology, University of Minnesota, Minneapolis, MN, USA
| | - Stefan L Farrugia
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Rob Knight
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Darrell S Pardi
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, 55905, USA.
| | - Purna C Kashyap
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, 55905, USA.
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30
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Cavender-Bares J, Ackerly DD, Hobbie SE, Townsend PA. Evolutionary Legacy Effects on Ecosystems: Biogeographic Origins, Plant Traits, and Implications for Management in the Era of Global Change. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2016. [DOI: 10.1146/annurev-ecolsys-121415-032229] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jeannine Cavender-Bares
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, Minnesota 55108; ,
| | - David D. Ackerly
- Department of Integrative Biology and Jepson Herbarium, University of California, Berkeley, California 94720;
| | - Sarah E. Hobbie
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, Minnesota 55108; ,
| | - Philip A. Townsend
- Department of Forest and Wildlife Ecology, University of Wisconsin, Madison, Wisconsin 53706;
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Villalobos S, Vamosi JC. Increasing land use drives changes in plant phylogenetic diversity and prevalence of specialists. PeerJ 2016; 4:e1740. [PMID: 26966669 PMCID: PMC4782714 DOI: 10.7717/peerj.1740] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 02/05/2016] [Indexed: 11/20/2022] Open
Abstract
Increased human land use has resulted in the increased homogenization of biodiversity between sites, yet we lack sufficient indicators to predict which species decline and the consequence of their potential loss on ecosystem services. We used comparative phylogenetic analysis to (1) characterize how increasing conversion of forest and grasslands to grazing pasturelands changes plant diversity and composition; (2) examine how changes in land use relate to declines in functional trait diversity; and (3) specifically investigate how these changes in plant composition affect the prevalence of zygomorphy and the possible consequences that these changes may have on pollinator functional groups. As predicted, we found that the conversion to grazing pasturelands negatively impacted species richness and phylogenetic composition. Clades with significantly more represented taxa in grasslands (GL) were genera with a high representation of agricultural weeds, while the composition was biased towards clades of subalpine herbaceous wildflowers in Mixed Forest (MF). Changes in community composition and structure had strong effects on the prevalence of zygomorphic species likely driven by nitrogen-fixing abilities of certain clades with zygomorphic flowers (e.g., Fabaceae). Land conversion can thus have unexpected impacts on trait distributions relevant for the functioning of the community in other capacities (e.g., cascading effects to other trophic levels (i.e., pollinators). Finally, the combination of traits represented by the current composition of species in GL and MF might enhance the diagnostic value of productivity and ecosystem processes in the most eroded ecosystems.
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Affiliation(s)
- Soraya Villalobos
- Department of Biological Sciences, University of Calgary , Calgary, Alberta , Canada
| | - Jana C Vamosi
- Department of Biological Sciences, University of Calgary , Calgary, Alberta , Canada
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32
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Faith DP. The PD Phylogenetic Diversity Framework: Linking Evolutionary History to Feature Diversity for Biodiversity Conservation. BIODIVERSITY CONSERVATION AND PHYLOGENETIC SYSTEMATICS 2016. [DOI: 10.1007/978-3-319-22461-9_3] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Veresoglou SD, Halley JM, Rillig MC. Extinction risk of soil biota. Nat Commun 2015; 6:8862. [PMID: 26593272 PMCID: PMC4673489 DOI: 10.1038/ncomms9862] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2015] [Accepted: 10/09/2015] [Indexed: 01/01/2023] Open
Abstract
No species lives on earth forever. Knowing when and why species go extinct is crucial for a complete understanding of the consequences of anthropogenic activity, and its impact on ecosystem functioning. Even though soil biota play a key role in maintaining the functioning of ecosystems, the vast majority of existing studies focus on aboveground organisms. Many questions about the fate of belowground organisms remain open, so the combined effort of theorists and applied ecologists is needed in the ongoing development of soil extinction ecology.
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Affiliation(s)
- Stavros D. Veresoglou
- Freie Universität Berlin, Institut für Biologie, Plant Ecology, Altensteinstrasse 6, D-14195 Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), D-14195 Berlin, Germany
| | - John M. Halley
- Department of Biological Applications and Technology, University of Ioannina, 45110 Ioannina, Greece
| | - Matthias C. Rillig
- Freie Universität Berlin, Institut für Biologie, Plant Ecology, Altensteinstrasse 6, D-14195 Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), D-14195 Berlin, Germany
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34
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Brooks TM, Cuttelod A, Faith DP, Garcia-Moreno J, Langhammer P, Pérez-Espona S. Why and how might genetic and phylogenetic diversity be reflected in the identification of key biodiversity areas? Philos Trans R Soc Lond B Biol Sci 2015; 370:20140019. [PMID: 25561678 PMCID: PMC4290431 DOI: 10.1098/rstb.2014.0019] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
‘Key biodiversity areas' are defined as sites contributing significantly to the global persistence of biodiversity. The identification of these sites builds from existing approaches based on measures of species and ecosystem diversity and process. Here, we therefore build from the work of Sgró et al. (2011 Evol. Appl.4, 326–337. (doi:10.1111/j.1752-4571.2010.00157.x)) to extend a framework for how components of genetic diversity might be considered in the identification of key biodiversity areas. We make three recommendations to inform the ongoing process of consolidating a key biodiversity areas standard: (i) thresholds for the threatened species criterion currently consider a site's share of a threatened species' population; expand these to include the proportion of the species' genetic diversity unique to a site; (ii) expand criterion for ‘threatened species' to consider ‘threatened taxa’ and (iii) expand the centre of endemism criterion to identify as key biodiversity areas those sites holding a threshold proportion of the compositional or phylogenetic diversity of species (within a taxonomic group) whose restricted ranges collectively define a centre of endemism. We also recommend consideration of occurrence of EDGE species (i.e. threatened phylogenetic diversity) in key biodiversity areas to prioritize species-specific conservation actions among sites.
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Affiliation(s)
- T M Brooks
- IUCN, 28 rue Mauverney, Gland 1196, Switzerland
| | - A Cuttelod
- IUCN, 219c Huntingdon Road, Cambridge CB3 0DL, UK
| | - D P Faith
- Australian Museum, 6 College St., Sydney, New South Wales 2010, Australia
| | | | - P Langhammer
- School of Life Sciences, Arizona State University, PO Box 874601, Tempe, AZ 85287-4601, USA
| | - S Pérez-Espona
- Department of Life Sciences, Anglia Ruskin University, East Road, Cambridge CB1 1PT, UK
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35
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Narwani A, Alexandrou MA, Herrin J, Vouaux A, Zhou C, Oakley TH, Cardinale BJ. Common Ancestry Is a Poor Predictor of Competitive Traits in Freshwater Green Algae. PLoS One 2015; 10:e0137085. [PMID: 26348482 PMCID: PMC4562640 DOI: 10.1371/journal.pone.0137085] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 08/13/2015] [Indexed: 11/25/2022] Open
Abstract
Phytoplankton species traits have been used to successfully predict the outcome of competition, but these traits are notoriously laborious to measure. If these traits display a phylogenetic signal, phylogenetic distance (PD) can be used as a proxy for trait variation. We provide the first investigation of the degree of phylogenetic signal in traits related to competition in freshwater green phytoplankton. We measured 17 traits related to competition and tested whether they displayed a phylogenetic signal across a molecular phylogeny of 59 species of green algae. We also assessed the fit of five models of trait evolution to trait variation across the phylogeny. There was no significant phylogenetic signal for 13 out of 17 ecological traits. For 7 traits, a non-phylogenetic model provided the best fit. For another 7 traits, a phylogenetic model was selected, but parameter values indicated that trait variation evolved recently, diminishing the importance of common ancestry. This study suggests that traits related to competition in freshwater green algae are not generally well-predicted by patterns of common ancestry. We discuss the mechanisms by which the link between phylogenetic distance and phenotypic differentiation may be broken.
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Affiliation(s)
- Anita Narwani
- BU-G11 Überlandstrasse 133, Department of Aquatic Ecology, Eawag (Swiss Federal Institute of Aquatic Science and Technology), 8600, Dübendorf, Switzerland
- 1556 Dana Building, 440 Church Street, School of Natural Resources and Environment, University of Michigan, Ann Arbor, MI, 48109–1041, United States of America
| | - Markos A. Alexandrou
- 4101 Life Sciences Building, UCEN Road, Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, CA, 93106, United States of America
| | - James Herrin
- 1556 Dana Building, 440 Church Street, School of Natural Resources and Environment, University of Michigan, Ann Arbor, MI, 48109–1041, United States of America
| | - Alaina Vouaux
- 1556 Dana Building, 440 Church Street, School of Natural Resources and Environment, University of Michigan, Ann Arbor, MI, 48109–1041, United States of America
| | - Charles Zhou
- 1556 Dana Building, 440 Church Street, School of Natural Resources and Environment, University of Michigan, Ann Arbor, MI, 48109–1041, United States of America
| | - Todd H. Oakley
- 4101 Life Sciences Building, UCEN Road, Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, CA, 93106, United States of America
| | - Bradley J. Cardinale
- 1556 Dana Building, 440 Church Street, School of Natural Resources and Environment, University of Michigan, Ann Arbor, MI, 48109–1041, United States of America
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36
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Forest F, Crandall KA, Chase MW, Faith DP. Phylogeny, extinction and conservation: embracing uncertainties in a time of urgency. Philos Trans R Soc Lond B Biol Sci 2015; 370:20140002. [PMID: 25561663 PMCID: PMC4290416 DOI: 10.1098/rstb.2014.0002] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Evolutionary studies have played a fundamental role in our understanding of life, but until recently, they had only a relatively modest involvement in addressing conservation issues. The main goal of the present discussion meeting issue is to offer a platform to present the available methods allowing the integration of phylogenetic and extinction risk data in conservation planning. Here, we identify the main knowledge gaps in biodiversity science, which include incomplete sampling, reconstruction biases in phylogenetic analyses, partly known species distribution ranges, and the difficulty in producing conservation assessments for all known species, not to mention that much of the effective biological diversity remains to be discovered. Given the impact that human activities have on biodiversity and the urgency with which we need to address these issues, imperfect assumptions need to be sanctioned and surrogates used in the race to salvage as much as possible of our natural and evolutionary heritage. We discuss some aspects of the uncertainties found in biodiversity science, such as the ideal surrogates for biodiversity, the gaps in our knowledge and the numerous available phylogenetic diversity-based methods. We also introduce a series of cases studies that demonstrate how evolutionary biology can effectively contribute to biodiversity conservation science.
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Affiliation(s)
- Félix Forest
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond TW9 3DS, UK
| | - Keith A Crandall
- Computational Biology Institute, George Washington University, Ashburn, VA 20147, USA Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA
| | - Mark W Chase
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond TW9 3DS, UK School of Plant Biology, The University of Western Australia, Crawley, WA, Australia
| | - Daniel P Faith
- The Australian Museum, College Street, Sydney, New South Wales 2010, Australia
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