1
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Turley NE, Biddinger DJ, Joshi NK, López‐Uribe MM. Six years of wild bee monitoring shows changes in biodiversity within and across years and declines in abundance. Ecol Evol 2022; 12:e9190. [PMID: 35983174 PMCID: PMC9374588 DOI: 10.1002/ece3.9190] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 07/15/2022] [Accepted: 07/19/2022] [Indexed: 11/26/2022] Open
Abstract
Wild bees form diverse communities that pollinate plants in both native and agricultural ecosystems making them both ecologically and economically important. The growing evidence of bee declines has sparked increased interest in monitoring bee community and population dynamics using standardized methods. Here, we studied the dynamics of bee biodiversity within and across years by monitoring wild bees adjacent to four apple orchard locations in Southern Pennsylvania, USA. We collected bees using passive Blue Vane traps continuously from April to October for 6 years (2014-2019) amassing over 26,000 bees representing 144 species. We quantified total abundance, richness, diversity, composition, and phylogenetic structure. There were large seasonal changes in all measures of biodiversity with month explaining an average of 72% of the variation in our models. Changes over time were less dramatic with years explaining an average of 44% of the variation in biodiversity metrics. We found declines in all measures of biodiversity especially in the last 3 years, though additional years of sampling are needed to say if changes over time are part of a larger trend. Analyses of population dynamics over time for the 40 most abundant species indicate that about one third of species showed at least some evidence for declines in abundance. Bee family explained variation in species-level seasonal patterns but we found no consistent family-level patterns in declines, though bumble bees and sweat bees were groups that declined the most. Overall, our results show that season-wide standardized sampling across multiple years can reveal nuanced patterns in bee biodiversity, phenological patterns of bees, and population trends over time of many co-occurring species. These datasets could be used to quantify the relative effects that different aspects of environmental change have on bee communities and to help identify species of conservation concern.
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Affiliation(s)
- Nash E. Turley
- Department of Entomology, Center for Pollinator ResearchThe Pennsylvania State UniversityPennsylvaniaUSA
- Intercollege Graduate Degree Program in EcologyThe Pennsylvania State UniversityPennsylvaniaUSA
| | - David J. Biddinger
- Intercollege Graduate Degree Program in EcologyThe Pennsylvania State UniversityPennsylvaniaUSA
| | - Neelendra K. Joshi
- Department of Entomology and Plant PathologyUniversity of ArkansasFayettevilleArkansasUSA
| | - Margarita M. López‐Uribe
- Department of Entomology, Center for Pollinator ResearchThe Pennsylvania State UniversityPennsylvaniaUSA
- Intercollege Graduate Degree Program in EcologyThe Pennsylvania State UniversityPennsylvaniaUSA
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2
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New directions in tropical phenology. Trends Ecol Evol 2022; 37:683-693. [PMID: 35680467 DOI: 10.1016/j.tree.2022.05.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 03/08/2022] [Accepted: 05/04/2022] [Indexed: 11/21/2022]
Abstract
Earth's most speciose biomes are in the tropics, yet tropical plant phenology remains poorly understood. Tropical phenological data are comparatively scarce and viewed through the lens of a 'temperate phenological paradigm' expecting phenological traits to respond to strong, predictably annual shifts in climate (e.g., between subfreezing and frost-free periods). Digitized herbarium data greatly expand existing phenological data for tropical plants; and circular data, statistics, and models are more appropriate for analyzing tropical (and temperate) phenological datasets. Phylogenetic information, which remains seldom applied in phenological investigations, provides new insights into phenological responses of large groups of related species to climate. Consistent combined use of herbarium data, circular statistical distributions, and robust phylogenies will rapidly advance our understanding of tropical - and temperate - phenology.
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3
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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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4
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Burbrink FT, Bernstein JM, Kuhn A, Gehara M, Ruane S. Ecological Divergence and the History of Gene Flow in the Nearctic Milksnakes (Lampropeltis triangulum Complex). Syst Biol 2021; 71:839-858. [PMID: 35043210 DOI: 10.1093/sysbio/syab093] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 11/11/2021] [Accepted: 11/15/2021] [Indexed: 11/13/2022] Open
Abstract
Many phylogeographic studies on species with large ranges have found genetic-geographic structure associated with changes in habitat and physical barriers preventing or reducing gene flow. These interactions with geographic space, contemporary and historical climate, and biogeographic barriers have complex effects on contemporary population genetic structure and processes of speciation. While allopatric speciation at biogeographic barriers is considered the primary mechanism for generating species, more recently it has been shown that parapatric modes of divergence may be equally or even more common. With genomic data and better modeling capabilities, we can more clearly define causes of speciation in relation to biogeography and migration between lineages, the location of hybrid zones with respect to the ecology of parental lineages, and differential introgression of genes between taxa. Here, we examine the origins of three Nearctic milksnakes (Lampropeltis elapsoides, Lampropeltis triangulum and Lampropeltis gentilis) using genome-scale data to better understand species diversification. Results from artificial neural networks show that a mix of a strong biogeographic barrier, environmental changes, and physical space has affected genetic structure in these taxa. These results underscore conspicuous environmental changes that occur as the sister taxa L. triangulum and L. gentilis diverged near the Great Plains into the forested regions of the Eastern Nearctic. This area has been recognized as a region for turnover for many vertebrate species, but as we show here the contemporary boundary does not isolate these sister species. These two species likely formed in the mid-Pleistocene and have remained partially reproductively isolated over much of this time, showing differential introgression of loci. We also demonstrate that when L. triangulum and L. gentilis are each in contact with the much older L. elapsoides, some limited gene flow has occurred. Given the strong agreement between nuclear and mtDNA genomes, along with estimates of ecological niche, we suggest that all three lineages should continue to be recognized as unique species. Furthermore, this work emphasizes the importance of considering complex modes of divergence and differential allelic introgression over a complex landscape when testing mechanisms of speciation. [Cline; delimitation; Eastern Nearctic; Great Plains; hybrids; introgression; speciation.].
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Affiliation(s)
- Frank T Burbrink
- Department of Herpetology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
| | - Justin M Bernstein
- Department of Biological Sciences, Rutgers University Newark, 195 University Ave, Newark, NJ 07102, USA
| | - Arianna Kuhn
- Department of Herpetology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
| | - Marcelo Gehara
- Department of Earth and Environmental Sciences, Rutgers University Newark, 195 University Ave, Newark, NJ 07102, USA
| | - Sara Ruane
- Department of Earth and Environmental Sciences, Rutgers University Newark, 195 University Ave, Newark, NJ 07102, USA.,Amphibian and Reptile Collection, Negaunee Integrative Research Center, Field Museum of Natural History, 1400 S Lake Shore Dr, Chicago, IL 60605, USA
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5
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Jin L, Liu JJ, Xiao TW, Li QM, Lin LX, Shao XN, Ma CX, Li BH, Mi XC, Ren HB, Qiao XJ, Lian JY, Hao G, Ge XJ. Plastome-based phylogeny improves community phylogenetics of subtropical forests in China. Mol Ecol Resour 2021; 22:319-333. [PMID: 34233085 DOI: 10.1111/1755-0998.13462] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 06/22/2021] [Accepted: 07/01/2021] [Indexed: 11/30/2022]
Abstract
Phylogenetic trees have been extensively used in community ecology. However, how the phylogeny construction affects ecological inferences is poorly understood. In this study, we constructed three different types of phylogenetic trees (a synthetic-tree generated using V.PhyloMaker, a barcode-tree generated using rbcL+matK+trnH-psbA, and a plastome-tree generated from plastid genomes) that represented an increasing level of phylogenetic resolution among 580 woody plant species from six forest dynamic plots in subtropical evergreen broadleaved forests of China. We then evaluated the performance of each phylogeny in estimations of community phylogenetic structure, turnover and phylogenetic signal in functional traits. As expected, the plastome-tree was most resolved and most supported for relationships among species. For local phylogenetic structure, the three trees showed consistent results with Faith's PD and MPD; however, only the synthetic-tree produced significant clustering patterns using MNTD for some plots. For phylogenetic turnover, contrasting results between the molecular trees and the synthetic-tree occurred only with nearest neighbor distance. The barcode-tree agreed more with the plastome-tree than the synthetic-tree for both phylogenetic structure and turnover. For functional traits, both the barcode-tree and plastome-tree detected phylogenetic signal in maximum height, but only the plastome-tree detected signal in leaf width. This is the first study that uses plastid genomes in large-scale community phylogenetics. Our results highlight the improvement of plastome-trees over barcode-trees and synthetic-trees for the analyses studied here. Our results also point to the possibility of type I and II errors in estimation of phylogenetic structure and turnover and detection of phylogenetic signal when using synthetic-trees.
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Affiliation(s)
- Lu Jin
- College of Life Sciences, South China Agricultural University, Guangzhou, China.,Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Jia-Jia Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Tian-Wen Xiao
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Qiao-Ming Li
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
| | - Lu-Xiang Lin
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
| | - Xiao-Na Shao
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Chen-Xin Ma
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Bu-Hang Li
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Xiang-Cheng Mi
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Hai-Bao Ren
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Xiu-Juan Qiao
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| | - Ju-Yu Lian
- Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
| | - Gang Hao
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
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6
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Using phylogenetic information to impute missing functional trait values in ecological databases. ECOL INFORM 2021. [DOI: 10.1016/j.ecoinf.2021.101315] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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7
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Phylogenetic uncertainty and the inference of patterns in community ecology and comparative studies. Oecologia 2021; 196:633-647. [PMID: 34146131 DOI: 10.1007/s00442-021-04972-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 06/12/2021] [Indexed: 10/21/2022]
Abstract
Progress in phylogenetic community ecology is often limited by the availability of phylogenetic information and the lack of appropriate methods and solutions to deal with this problem. We estimate the effect of the lack of phylogenetic information on the relations among taxa measured by commonly used phylogenetic metrics in comparative studies and community ecology, namely: Blomberg's K phylogenetic signal, Faith's Phylogenetic Diversity (PD), Mean Phylogenetic Distance (MPD) and Mean Nearest Taxon Distance (MNTD). To overcome this problem, we tested two possible solutions: Polytomic trees and Operational trees. Our results show that the effects on K values strongly depended on the level of phylogenetic signal. In the case of the community metrics, the effects were insensitive to the patterns of species distribution in the communities. Community metrics tended to be overestimated with both Polytomic and Operational trees, but the overestimation was higher with Polytomic trees. PD and MPD metrics were less biased than MNTD metric. We show that the lack of phylogenetic resolution is not necessarily problematic for all analyses and that its effect will depend on the chosen metric and on the solutions used to deal with the problem. Based on our results, we suggest that ecologists should prefer the Operational tree solution to remove polytomies in the phylogenetic tree and take careful consideration while designing experiments, and analyzing and interpreting the results of phylogenetic metrics.
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8
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Monnet AC, Cilleros K, Médail F, Albassatneh MC, Arroyo J, Bacchetta G, Bagnoli F, Barina Z, Cartereau M, Casajus N, Dimopoulos P, Domina G, Doxa A, Escudero M, Fady B, Hampe A, Matevski V, Misfud S, Nikolic T, Pavon D, Roig A, Barea ES, Spanu I, Strid A, Vendramin GG, Leriche A. WOODIV, a database of occurrences, functional traits, and phylogenetic data for all Euro-Mediterranean trees. Sci Data 2021; 8:89. [PMID: 33758194 PMCID: PMC7988049 DOI: 10.1038/s41597-021-00873-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 02/17/2021] [Indexed: 01/31/2023] Open
Abstract
Trees play a key role in the structure and function of many ecosystems worldwide. In the Mediterranean Basin, forests cover approximately 22% of the total land area hosting a large number of endemics (46 species). Despite its particularities and vulnerability, the biodiversity of Mediterranean trees is not well known at the taxonomic, spatial, functional, and genetic levels required for conservation applications. The WOODIV database fills this gap by providing reliable occurrences, four functional traits (plant height, seed mass, wood density, and specific leaf area), and sequences from three DNA-regions (rbcL, matK, and trnH-psbA), together with modelled occurrences and a phylogeny for all 210 Euro-Mediterranean tree species. We compiled, homogenized, and verified occurrence data from sparse datasets and collated them on an INSPIRE-compliant 10 × 10 km grid. We also gathered functional trait and genetic data, filling existing gaps where possible. The WOODIV database can benefit macroecological studies in the fields of conservation, biogeography, and community ecology.
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Affiliation(s)
- Anne-Christine Monnet
- Aix Marseille Univ, Avignon Univ, CNRS, IRD, IMBE. Technopôle de l'Arbois-Méditerranée, cedex 4, BP 80, 13 545, Aix-en-Provence, France.
| | - Kévin Cilleros
- Aix Marseille Univ, Avignon Univ, CNRS, IRD, IMBE. Technopôle de l'Arbois-Méditerranée, cedex 4, BP 80, 13 545, Aix-en-Provence, France
| | - Frédéric Médail
- Aix Marseille Univ, Avignon Univ, CNRS, IRD, IMBE. Technopôle de l'Arbois-Méditerranée, cedex 4, BP 80, 13 545, Aix-en-Provence, France
| | - Marwan Cheikh Albassatneh
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle (MNHN), CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Juan Arroyo
- Department of Plant Biology and Ecology, University of Seville, Seville, Spain
| | - Gianluigi Bacchetta
- Department of Life and Environmental Sciences, University of Cagliari, Viale Sant'Ignazio da Laconi 13, Cagliari, Italy
| | - Francesca Bagnoli
- National Research Council, Institute of Biosciences and Bioresources, 50019, Sesto Fiorentino, (FI), Italy
| | - Zoltán Barina
- Department of Botany, Hungarian Natural History Museum, Pf. 137, Budapest, 1431, Hungary
| | - Manuel Cartereau
- Aix Marseille Univ, Avignon Univ, CNRS, IRD, IMBE. Technopôle de l'Arbois-Méditerranée, cedex 4, BP 80, 13 545, Aix-en-Provence, France
| | - Nicolas Casajus
- FRB-CESAB, 5 rue de l'Ecole de Médecine, 34000, Montpellier, France
| | - Panayotis Dimopoulos
- Department of Biology, Laboratory of Botany, University of Patras, 26504, Patras, Greece
| | - Gianniantonio Domina
- Department of Agriculture, Food and Forest Sciences, University of Palermo, Viale delle Scienze bldg. 4, 90128, Palermo, Italy
| | - Aggeliki Doxa
- Aix Marseille Univ, Avignon Univ, CNRS, IRD, IMBE. Technopôle de l'Arbois-Méditerranée, cedex 4, BP 80, 13 545, Aix-en-Provence, France
- Statistical Learning Lab, Institute of Applied and Computational Mathematics, Foundation for Research and Technology-Hellas (FORTH), Ν. Plastira 100, Vassilika Vouton, GR - 700 13, Heraklion, Crete, Greece
| | - Marcial Escudero
- Department of Plant Biology and Ecology, University of Seville, Seville, Spain
| | - Bruno Fady
- INRAE, UR629, Ecologie des forêts méditerranéennes, Avignon, France
| | - Arndt Hampe
- INRAE, Univ. Bordeaux, BIOGECO, F-33610, Cestas, France
| | - Vlado Matevski
- Macedonian Academy of Sciences and Arts, Krste Misirkov 2, 1000, Skopje, Republic of Macedonia
| | - Stephen Misfud
- EcoGozo, Regional Development Directorate - Ministry for Gozo, Flat 6, Sunset Court B, Triq Marsalforn, Xaghra, Gozo, Malta
| | - Toni Nikolic
- Department of Botany, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Daniel Pavon
- Aix Marseille Univ, Avignon Univ, CNRS, IRD, IMBE. Technopôle de l'Arbois-Méditerranée, cedex 4, BP 80, 13 545, Aix-en-Provence, France
| | - Anne Roig
- INRAE, UR629, Ecologie des forêts méditerranéennes, Avignon, France
| | | | - Ilaria Spanu
- National Research Council, Institute of Biosciences and Bioresources, 50019, Sesto Fiorentino, (FI), Italy
| | | | | | - Agathe Leriche
- Aix Marseille Univ, Avignon Univ, CNRS, IRD, IMBE. Technopôle de l'Arbois-Méditerranée, cedex 4, BP 80, 13 545, Aix-en-Provence, France.
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9
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Odom KJ, Araya-Salas M, Morano JL, Ligon RA, Leighton GM, Taff CC, Dalziell AH, Billings AC, Germain RR, Pardo M, de Andrade LG, Hedwig D, Keen SC, Shiu Y, Charif RA, Webster MS, Rice AN. Comparative bioacoustics: a roadmap for quantifying and comparing animal sounds across diverse taxa. Biol Rev Camb Philos Soc 2021; 96:1135-1159. [PMID: 33652499 DOI: 10.1111/brv.12695] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 02/03/2021] [Accepted: 02/05/2021] [Indexed: 12/12/2022]
Abstract
Animals produce a wide array of sounds with highly variable acoustic structures. It is possible to understand the causes and consequences of this variation across taxa with phylogenetic comparative analyses. Acoustic and evolutionary analyses are rapidly increasing in sophistication such that choosing appropriate acoustic and evolutionary approaches is increasingly difficult. However, the correct choice of analysis can have profound effects on output and evolutionary inferences. Here, we identify and address some of the challenges for this growing field by providing a roadmap for quantifying and comparing sound in a phylogenetic context for researchers with a broad range of scientific backgrounds. Sound, as a continuous, multidimensional trait can be particularly challenging to measure because it can be hard to identify variables that can be compared across taxa and it is also no small feat to process and analyse the resulting high-dimensional acoustic data using approaches that are appropriate for subsequent evolutionary analysis. Additionally, terminological inconsistencies and the role of learning in the development of acoustic traits need to be considered. Phylogenetic comparative analyses also have their own sets of caveats to consider. We provide a set of recommendations for delimiting acoustic signals into discrete, comparable acoustic units. We also present a three-stage workflow for extracting relevant acoustic data, including options for multivariate analyses and dimensionality reduction that is compatible with phylogenetic comparative analysis. We then summarize available phylogenetic comparative approaches and how they have been used in comparative bioacoustics, and address the limitations of comparative analyses with behavioural data. Lastly, we recommend how to apply these methods to acoustic data across a range of study systems. In this way, we provide an integrated framework to aid in quantitative analysis of cross-taxa variation in animal sounds for comparative phylogenetic analysis. In addition, we advocate the standardization of acoustic terminology across disciplines and taxa, adoption of automated methods for acoustic feature extraction, and establishment of strong data archival practices for acoustic recordings and data analyses. Combining such practices with our proposed workflow will greatly advance the reproducibility, biological interpretation, and longevity of comparative bioacoustic studies.
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Affiliation(s)
- Karan J Odom
- Cornell Lab of Ornithology, Cornell University, Ithaca, NY, 14850, U.S.A.,Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, U.S.A
| | - Marcelo Araya-Salas
- Cornell Lab of Ornithology, Cornell University, Ithaca, NY, 14850, U.S.A.,Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, U.S.A.,Sede del Sur, Universidad de Costa Rica, Golfito, 60701, Costa Rica
| | - Janelle L Morano
- Macaulay Library, Cornell Lab of Ornithology, Cornell University, Ithaca, NY, 14850, U.S.A.,Department of Natural Resources and the Environment, Cornell University, Ithaca, NY, 14853, U.S.A
| | - Russell A Ligon
- Cornell Lab of Ornithology, Cornell University, Ithaca, NY, 14850, U.S.A.,Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, U.S.A
| | - Gavin M Leighton
- Cornell Lab of Ornithology, Cornell University, Ithaca, NY, 14850, U.S.A.,Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, U.S.A.,Department of Biology, SUNY Buffalo State, Buffalo, NY, 14222, U.S.A
| | - Conor C Taff
- Cornell Lab of Ornithology, Cornell University, Ithaca, NY, 14850, U.S.A.,Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853, U.S.A
| | - Anastasia H Dalziell
- Cornell Lab of Ornithology, Cornell University, Ithaca, NY, 14850, U.S.A.,Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, U.S.A.,Centre for Sustainable Ecosystem Solutions, University of Wollongong, Northfields Ave, Wollongong, NSW, 2522, Australia
| | - Alexis C Billings
- Division of Biological Sciences, University of Montana, Missoula, MT, 59812, U.S.A.,Department of Environmental, Science, Policy and Management, University of California, Berkeley, Berkeley, CA, 94709, U.S.A
| | - Ryan R Germain
- Cornell Lab of Ornithology, Cornell University, Ithaca, NY, 14850, U.S.A.,Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, U.S.A.,Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, DK-2100, Denmark
| | - Michael Pardo
- Cornell Lab of Ornithology, Cornell University, Ithaca, NY, 14850, U.S.A.,Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, U.S.A.,Department of Fish, Wildlife, and Conservation Biology, Colorado State University, Fort Collins, CO, 80523, U.S.A
| | - Luciana Guimarães de Andrade
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853, U.S.A.,Center for Conservation Bioacoustics, Cornell Lab of Ornithology, Cornell University, Ithaca, NY, 14850, U.S.A
| | - Daniela Hedwig
- Center for Conservation Bioacoustics, Cornell Lab of Ornithology, Cornell University, Ithaca, NY, 14850, U.S.A
| | - Sara C Keen
- Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, U.S.A.,Center for Conservation Bioacoustics, Cornell Lab of Ornithology, Cornell University, Ithaca, NY, 14850, U.S.A.,Department of Geological Sciences, Stanford University, Stanford, CA, 94305, U.S.A
| | - Yu Shiu
- Center for Conservation Bioacoustics, Cornell Lab of Ornithology, Cornell University, Ithaca, NY, 14850, U.S.A
| | - Russell A Charif
- Center for Conservation Bioacoustics, Cornell Lab of Ornithology, Cornell University, Ithaca, NY, 14850, U.S.A
| | - Michael S Webster
- Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, U.S.A.,Macaulay Library, Cornell Lab of Ornithology, Cornell University, Ithaca, NY, 14850, U.S.A
| | - Aaron N Rice
- Center for Conservation Bioacoustics, Cornell Lab of Ornithology, Cornell University, Ithaca, NY, 14850, U.S.A
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10
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Kougioumoutzis K, Kokkoris IP, Panitsa M, Kallimanis A, Strid A, Dimopoulos P. Plant Endemism Centres and Biodiversity Hotspots in Greece. BIOLOGY 2021; 10:72. [PMID: 33498512 PMCID: PMC7909545 DOI: 10.3390/biology10020072] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 01/11/2021] [Accepted: 01/17/2021] [Indexed: 12/21/2022]
Abstract
Biodiversity hotspots (BH) cover a small fraction of the Earth's surface, yet host numerous endemics. Human-induced biodiversity loss has been increasing worldwide, despite attempts to halt the extinction crisis. There is thus an urgent need to efficiently allocate the available conservation funds in an optimised conservation prioritization scheme. Identifying BH and endemism centres (EC) is therefore a valuable tool in conservation prioritization and planning. Even though Greece is one of the most plant species-rich European countries, few studies have dealt with the identification of BH or EC and none has ever incorporated phylogenetic information or extended to the national scale. Consequently, we are unaware of the extent that Special Areas of Conservation (SAC) of the Natura 2000 network efficiently protect Greek plant diversity. Here, we located for the first time at a national scale and in a phylogenetic framework, the areas serving as BH and EC, and assessed the effectiveness of the Greek SAC in safeguarding them. BH and EC are mainly located near mountainous areas, and in areas supposedly floristically impoverished, such as the central Aegean islands. A critical re-assessment of the Greek SAC might be needed to minimize the extinction risk of the Greek endemics, by focusing the conservation efforts also on the BH and EC that fall outside the established Greek SAC.
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Affiliation(s)
- Konstantinos Kougioumoutzis
- Division of Plant Biology, Laboratory of Botany, Department of Biology, University of Patras, 26504 Patras, Greece; (I.P.K.); (M.P.); (P.D.)
- Department of Ecology and Systematics, Faculty of Biology, National and Kapodistrian University of Athens, Panepistimiopolis, 15701 Athens, Greece
- Department of Ecology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
| | - Ioannis P. Kokkoris
- Division of Plant Biology, Laboratory of Botany, Department of Biology, University of Patras, 26504 Patras, Greece; (I.P.K.); (M.P.); (P.D.)
| | - Maria Panitsa
- Division of Plant Biology, Laboratory of Botany, Department of Biology, University of Patras, 26504 Patras, Greece; (I.P.K.); (M.P.); (P.D.)
| | - Athanasios Kallimanis
- Department of Ecology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
| | | | - Panayotis Dimopoulos
- Division of Plant Biology, Laboratory of Botany, Department of Biology, University of Patras, 26504 Patras, Greece; (I.P.K.); (M.P.); (P.D.)
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11
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Plant Diversity Patterns and Conservation Implications under Climate-Change Scenarios in the Mediterranean: The Case of Crete (Aegean, Greece). DIVERSITY 2020. [DOI: 10.3390/d12070270] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Climate change poses a great challenge for biodiversity conservation. Several studies exist regarding climate change’s impacts on European plants, yet none has investigated how climate change will affect the extinction risk of the entire endemic flora of an island biodiversity hotspot, with intense human disturbance. Our aim is to assess climate change’s impacts on the biodiversity patterns of the endemic plants of Crete (S Aegean) and provide a case-study upon which a climate-smart conservation planning strategy might be set. We employed a variety of macroecological analyses and estimated the current and future biodiversity, conservation and extinction hotspots in Crete. We evaluated the effectiveness of climatic refugia and the Natura 2000 network of protected areas (PAs) for protecting the most vulnerable species and identified the taxa of conservation priority based on the Evolutionary Distinct and Globally Endangered (EDGE) index. The results revealed that high altitude areas of Cretan mountains constitute biodiversity hotspots and areas of high conservation and evolutionary value. Due to the “escalator to extinction” phenomenon, these areas are projected to become diversity “death-zones” and should thus be prioritised. Conservation efforts should be targeted at areas with overlaps among PAs and climatic refugia, characterised by high diversity and EDGE scores. This conservation-prioritisation planning will allow the preservation of evolutionary heritage, trait diversity and future ecosystem services for human well-being and acts as a pilot for similar regions worldwide.
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12
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Pischl PH, Burke SV, Bach EM, Duvall MR. Plastome phylogenomics and phylogenetic diversity of endangered and threatened grassland species (Poaceae) in a North American tallgrass prairie. Ecol Evol 2020; 10:7602-7615. [PMID: 32760551 PMCID: PMC7391303 DOI: 10.1002/ece3.6484] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 05/13/2020] [Accepted: 05/20/2020] [Indexed: 11/09/2022] Open
Abstract
Native grasslands are one of the most endangered ecosystems in North America. In this study, we examined the ecological and evolutionary roles of endangered and threatened (e/t) grasses by establishing robust evolutionary relationships with other nonthreatened native and introduced grass species of the community. We hypothesized that the phylogenomic distribution of e/t species of grasses in Illinois would be phylogenetically clustered because closely related species would be vulnerable to the same threats and have similar requirements for survival. This study presents the first time a phylogeny based on complete plastome DNA of Poaceae was analyzed by phylogenetic diversity analysis. To avoid the disturbance of e/t populations, DNA was extracted from herbarium specimens. Next-generation sequencing (NGS) techniques were used to sequence DNA of plastid genomes (plastomes). The resulting phylogenomic tree was analyzed by phylogenetic diversity metrics. The extracted DNA successfully produced complete plastomes demonstrating that herbarium material is a practical source of DNA for genomic studies. The phylogenomic tree was strongly supported and defined Dichanthelium as a separate clade from Panicum. The phylogenetic metrics revealed phylogenetic clustering of e/t species, confirming our hypothesis.
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Affiliation(s)
- Phyllis H. Pischl
- Department of Biological SciencesNorthern Illinois UniversityDeKalbIllinoisUSA
| | - Sean V. Burke
- Center for Translational Data ScienceUniversity of ChicagoChicagoIllinoisUSA
| | | | - Melvin R. Duvall
- Department of Biological SciencesNorthern Illinois UniversityDeKalbIllinoisUSA
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13
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Li D, Trotta L, Marx HE, Allen JM, Sun M, Soltis DE, Soltis PS, Guralnick RP, Baiser B. For common community phylogenetic analyses, go ahead and use synthesis phylogenies. Ecology 2019; 100:e02788. [PMID: 31225900 PMCID: PMC7079099 DOI: 10.1002/ecy.2788] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 04/15/2019] [Accepted: 05/29/2019] [Indexed: 12/21/2022]
Abstract
Should we build our own phylogenetic trees based on gene sequence data, or can we simply use available synthesis phylogenies? This is a fundamental question that any study involving a phylogenetic framework must face at the beginning of the project. Building a phylogeny from gene sequence data (purpose-built phylogeny) requires more effort, expertise, and cost than subsetting an already available phylogeny (synthesis-based phylogeny). However, we still lack a comparison of how these two approaches to building phylogenetic trees influence common community phylogenetic analyses such as comparing community phylogenetic diversity and estimating trait phylogenetic signal. Here, we generated three purpose-built phylogenies and their corresponding synthesis-based trees (two from Phylomatic and one from the Open Tree of Life, OTL). We simulated 1,000 communities and 12,000 continuous traits along each purpose-built phylogeny. We then compared the effects of different trees on estimates of phylogenetic diversity (alpha and beta) and phylogenetic signal (Pagel's λ and Blomberg's K). Synthesis-based phylogenies generally yielded higher estimates of phylogenetic diversity when compared to purpose-built phylogenies. However, resulting measures of phylogenetic diversity from both types of phylogenies were highly correlated (Spearman's ρ > 0.8 in most cases). Mean pairwise distance (both alpha and beta) is the index that is most robust to the differences in tree construction that we tested. Measures of phylogenetic diversity based on the OTL showed the highest correlation with measures based on the purpose-built phylogenies. Trait phylogenetic signal estimated with synthesis-based phylogenies, especially from the OTL, was also highly correlated with estimates of Blomberg's K or close to Pagel's λ from purpose-built phylogenies when traits were simulated under Brownian motion. For commonly employed community phylogenetic analyses, our results justify taking advantage of recently developed and continuously improving synthesis trees, especially the Open Tree of Life.
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Affiliation(s)
- Daijiang Li
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, Florida, 32611 , USA
| | - Lauren Trotta
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, Florida, 32611 , USA
| | - Hannah E Marx
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Julie M Allen
- Biology Department, University of Nevada Reno, Reno, Nevada, 89557, USA
| | - Miao Sun
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, 32611, USA
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, 32611, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, 32611, USA
| | - Robert P Guralnick
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, 32611, USA
| | - Benjamin Baiser
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, Florida, 32611 , USA
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14
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Bravo GA, Antonelli A, Bacon CD, Bartoszek K, Blom MPK, Huynh S, Jones G, Knowles LL, Lamichhaney S, Marcussen T, Morlon H, Nakhleh LK, Oxelman B, Pfeil B, Schliep A, Wahlberg N, Werneck FP, Wiedenhoeft J, Willows-Munro S, Edwards SV. Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics. PeerJ 2019; 7:e6399. [PMID: 30783571 PMCID: PMC6378093 DOI: 10.7717/peerj.6399] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 01/07/2019] [Indexed: 12/23/2022] Open
Abstract
Building the Tree of Life (ToL) is a major challenge of modern biology, requiring advances in cyberinfrastructure, data collection, theory, and more. Here, we argue that phylogenomics stands to benefit by embracing the many heterogeneous genomic signals emerging from the first decade of large-scale phylogenetic analysis spawned by high-throughput sequencing (HTS). Such signals include those most commonly encountered in phylogenomic datasets, such as incomplete lineage sorting, but also those reticulate processes emerging with greater frequency, such as recombination and introgression. Here we focus specifically on how phylogenetic methods can accommodate the heterogeneity incurred by such population genetic processes; we do not discuss phylogenetic methods that ignore such processes, such as concatenation or supermatrix approaches or supertrees. We suggest that methods of data acquisition and the types of markers used in phylogenomics will remain restricted until a posteriori methods of marker choice are made possible with routine whole-genome sequencing of taxa of interest. We discuss limitations and potential extensions of a model supporting innovation in phylogenomics today, the multispecies coalescent model (MSC). Macroevolutionary models that use phylogenies, such as character mapping, often ignore the heterogeneity on which building phylogenies increasingly rely and suggest that assimilating such heterogeneity is an important goal moving forward. Finally, we argue that an integrative cyberinfrastructure linking all steps of the process of building the ToL, from specimen acquisition in the field to publication and tracking of phylogenomic data, as well as a culture that values contributors at each step, are essential for progress.
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Affiliation(s)
- Gustavo A. Bravo
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Alexandre Antonelli
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
- Gothenburg Global Biodiversity Centre, Göteborg, Sweden
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
- Gothenburg Botanical Garden, Göteborg, Sweden
| | - Christine D. Bacon
- Gothenburg Global Biodiversity Centre, Göteborg, Sweden
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
| | - Krzysztof Bartoszek
- Department of Computer and Information Science, Linköping University, Linköping, Sweden
| | - Mozes P. K. Blom
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Stella Huynh
- Institut de Biologie, Université de Neuchâtel, Neuchâtel, Switzerland
| | - Graham Jones
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
| | - L. Lacey Knowles
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Sangeet Lamichhaney
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Thomas Marcussen
- Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway
| | - Hélène Morlon
- Institut de Biologie, Ecole Normale Supérieure de Paris, Paris, France
| | - Luay K. Nakhleh
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Bengt Oxelman
- Gothenburg Global Biodiversity Centre, Göteborg, Sweden
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
| | - Bernard Pfeil
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
| | - Alexander Schliep
- Department of Computer Science and Engineering, Chalmers University of Technology and University of Gothenburg, Göteborg, Sweden
| | | | - Fernanda P. Werneck
- Coordenação de Biodiversidade, Programa de Coleções Científicas Biológicas, Instituto Nacional de Pesquisa da Amazônia, Manaus, AM, Brazil
| | - John Wiedenhoeft
- Department of Computer Science and Engineering, Chalmers University of Technology and University of Gothenburg, Göteborg, Sweden
- Department of Computer Science, Rutgers University, Piscataway, NJ, USA
| | - Sandi Willows-Munro
- School of Life Sciences, University of Kwazulu-Natal, Pietermaritzburg, South Africa
| | - Scott V. Edwards
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
- Gothenburg Centre for Advanced Studies in Science and Technology, Chalmers University of Technology and University of Gothenburg, Göteborg, Sweden
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15
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Kubota Y, Kusumoto B, Shiono T, Ulrich W. Multiple filters affect tree species assembly in mid-latitude forest communities. Oecologia 2018; 187:245-253. [DOI: 10.1007/s00442-018-4122-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 03/17/2018] [Indexed: 10/17/2022]
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16
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Evolutionary Mechanisms of Varying Chromosome Numbers in the Radiation of Erebia Butterflies. Genes (Basel) 2018; 9:genes9030166. [PMID: 29547586 PMCID: PMC5867887 DOI: 10.3390/genes9030166] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Revised: 03/14/2018] [Accepted: 03/14/2018] [Indexed: 02/03/2023] Open
Abstract
The evolution of intrinsic barriers to gene flow is a crucial step in the process of speciation. Chromosomal changes caused by fusion and fission events are one such barrier and are common in several groups of Lepidoptera. However, it remains unclear if and how chromosomal changes have contributed to speciation in this group. I tested for a phylogenetic signal of varying chromosome numbers in Erebia butterflies by combining existing sequence data with karyological information. I also compared different models of trait evolution in order to infer the underlying evolutionary mechanisms. Overall, I found significant phylogenetic signals that are consistent with non-neutral trait evolution only when parts of the mitochondrial genome were included, suggesting cytonuclear discordances. The adaptive evolutionary model tested in this study consistently outperformed the neutral model of trait evolution. Taken together, these results suggest that, unlike other Lepidoptera groups, changes in chromosome numbers may have played a role in the diversification of Erebia butterflies.
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17
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Liu XA, Peng Y, Li JJ, Peng PH. Enhanced shoot investment makes invasive plants exhibit growth advantages in high nitrogen conditions. BRAZ J BIOL 2018. [PMID: 29538482 DOI: 10.1590/1519-6984.169578] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Resource amendments commonly promote plant invasions, raising concerns over the potential consequences of nitrogen (N) deposition; however, it is unclear whether invaders will benefit from N deposition more than natives. Growth is among the most fundamental inherent traits of plants and thus good invaders may have superior growth advantages in response to resource amendments. We compared the growth and allocation between invasive and native plants in different N regimes including controls (ambient N concentrations). We found that invasive plants always grew much larger than native plants in varying N conditions, regardless of growth- or phylogeny-based analyses, and that the former allocated more biomass to shoots than the latter. Although N addition enhanced the growth of invasive plants, this enhancement did not increase with increasing N addition. Across invasive and native species, changes in shoot biomass allocation were positively correlated with changes in whole-plant biomass; and the slope of this relationship was greater in invasive plants than native plants. These findings suggest that enhanced shoot investment makes invasive plants retain a growth advantage in high N conditions relative to natives, and also highlight that future N deposition may increase the risks of plant invasions.
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Affiliation(s)
- X A Liu
- Ecological Resources and Landscape Research Institute, Chengdu University of Technology, Chengdu 610059, CHN, China
| | - Y Peng
- Ecological Resources and Landscape Research Institute, Chengdu University of Technology, Chengdu 610059, CHN, China
| | - J J Li
- Ecological Resources and Landscape Research Institute, Chengdu University of Technology, Chengdu 610059, CHN, China
| | - P H Peng
- Ecological Resources and Landscape Research Institute, Chengdu University of Technology, Chengdu 610059, CHN, China
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18
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Park DS, Worthington S, Xi Z. Taxon sampling effects on the quantification and comparison of community phylogenetic diversity. Mol Ecol 2018; 27:1296-1308. [PMID: 29423927 DOI: 10.1111/mec.14520] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 12/12/2017] [Accepted: 01/02/2018] [Indexed: 11/26/2022]
Abstract
Ecologists are increasingly making use of molecular phylogenies, especially in the fields of community ecology and conservation. However, these phylogenies are often used without full appreciation of their underlying assumptions and uncertainties. A frequent practice in ecological studies is inferring a phylogeny with molecular data from taxa only within the community of interest. These "inferred community phylogenies" are inherently biased in their taxon sampling. Despite the importance of comprehensive sampling in constructing phylogenies, the implications of using inferred community phylogenies in ecological studies have not been examined. Here, we evaluate how taxon sampling affects the quantification and comparison of community phylogenetic diversity using both simulated and empirical data sets. We demonstrate that inferred community trees greatly underestimate phylogenetic diversity and that the probability of incorrectly ranking community diversity can reach up to 25%, depending on the dating methods employed. We argue that to reach reliable conclusions, ecological studies must improve their taxon sampling and generate the best phylogeny possible.
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Affiliation(s)
- Daniel S Park
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Steven Worthington
- Institute for Quantitative Social Science, Harvard University, Cambridge, MA, USA
| | - Zhenxiang Xi
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
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19
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Daru BH, Park DS, Primack RB, Willis CG, Barrington DS, Whitfeld TJS, Seidler TG, Sweeney PW, Foster DR, Ellison AM, Davis CC. Widespread sampling biases in herbaria revealed from large-scale digitization. THE NEW PHYTOLOGIST 2018; 217:939-955. [PMID: 29083043 DOI: 10.1111/nph.14855] [Citation(s) in RCA: 132] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 09/18/2017] [Indexed: 05/19/2023]
Abstract
Nonrandom collecting practices may bias conclusions drawn from analyses of herbarium records. Recent efforts to fully digitize and mobilize regional floras online offer a timely opportunity to assess commonalities and differences in herbarium sampling biases. We determined spatial, temporal, trait, phylogenetic, and collector biases in c. 5 million herbarium records, representing three of the most complete digitized floras of the world: Australia (AU), South Africa (SA), and New England, USA (NE). We identified numerous shared and unique biases among these regions. Shared biases included specimens collected close to roads and herbaria; specimens collected more frequently during biological spring and summer; specimens of threatened species collected less frequently; and specimens of close relatives collected in similar numbers. Regional differences included overrepresentation of graminoids in SA and AU and of annuals in AU; and peak collection during the 1910s in NE, 1980s in SA, and 1990s in AU. Finally, in all regions, a disproportionately large percentage of specimens were collected by very few individuals. We hypothesize that these mega-collectors, with their associated preferences and idiosyncrasies, shaped patterns of collection bias via 'founder effects'. Studies using herbarium collections should account for sampling biases, and future collecting efforts should avoid compounding these biases to the extent possible.
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Affiliation(s)
- Barnabas H Daru
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, Harvard University, Cambridge, MA, 02138, USA
| | - Daniel S Park
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, Harvard University, Cambridge, MA, 02138, USA
| | | | - Charles G Willis
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, Harvard University, Cambridge, MA, 02138, USA
| | - David S Barrington
- Pringle Herbarium, Plant Biology Department, University of Vermont, Torrey Hall, 27 Colchester Ave, Burlington, VT, 05405, USA
| | - Timothy J S Whitfeld
- Brown University Herbarium, Department of Ecology and Evolutionary Biology, Brown University, 34 Olive Street, Box G-B225, Providence, RI, 02912, USA
| | - Tristram G Seidler
- Biology Department, University of Massachusetts, 611 North Pleasant Street, Amherst, MA, 01003, USA
| | - Patrick W Sweeney
- Division of Botany, Peabody Museum of Natural History, Yale University, New Haven, CT, 06511, USA
| | - David R Foster
- Harvard Forest, Harvard University, 324 North Main Street, Petersham, MA, 01366, USA
| | - Aaron M Ellison
- Harvard Forest, Harvard University, 324 North Main Street, Petersham, MA, 01366, USA
- Tropical Forests & People Research Centre, University of the Sunshine Coast, Maroochydore, Qld, 4558, Australia
| | - Charles C Davis
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, Harvard University, Cambridge, MA, 02138, USA
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20
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Coelho de Souza F, Dexter KG, Phillips OL, Brienen RJW, Chave J, Galbraith DR, Lopez Gonzalez G, Monteagudo Mendoza A, Pennington RT, Poorter L, Alexiades M, Álvarez-Dávila E, Andrade A, Aragão LEOC, Araujo-Murakami A, Arets EJMM, Aymard C GA, Baraloto C, Barroso JG, Bonal D, Boot RGA, Camargo JLC, Comiskey JA, Valverde FC, de Camargo PB, Di Fiore A, Elias F, Erwin TL, Feldpausch TR, Ferreira L, Fyllas NM, Gloor E, Herault B, Herrera R, Higuchi N, Honorio Coronado EN, Killeen TJ, Laurance WF, Laurance S, Lloyd J, Lovejoy TE, Malhi Y, Maracahipes L, Marimon BS, Marimon-Junior BH, Mendoza C, Morandi P, Neill DA, Vargas PN, Oliveira EA, Lenza E, Palacios WA, Peñuela-Mora MC, Pipoly JJ, Pitman NCA, Prieto A, Quesada CA, Ramirez-Angulo H, Rudas A, Ruokolainen K, Salomão RP, Silveira M, Stropp J, Ter Steege H, Thomas-Caesar R, van der Hout P, van der Heijden GMF, van der Meer PJ, Vasquez RV, Vieira SA, Vilanova E, Vos VA, Wang O, Young KR, Zagt RJ, Baker TR. Evolutionary heritage influences Amazon tree ecology. Proc Biol Sci 2017; 283:rspb.2016.1587. [PMID: 27974517 PMCID: PMC5204144 DOI: 10.1098/rspb.2016.1587] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 11/03/2016] [Indexed: 12/03/2022] Open
Abstract
Lineages tend to retain ecological characteristics of their ancestors through time. However, for some traits, selection during evolutionary history may have also played a role in determining trait values. To address the relative importance of these processes requires large-scale quantification of traits and evolutionary relationships among species. The Amazonian tree flora comprises a high diversity of angiosperm lineages and species with widely differing life-history characteristics, providing an excellent system to investigate the combined influences of evolutionary heritage and selection in determining trait variation. We used trait data related to the major axes of life-history variation among tropical trees (e.g. growth and mortality rates) from 577 inventory plots in closed-canopy forest, mapped onto a phylogenetic hypothesis spanning more than 300 genera including all major angiosperm clades to test for evolutionary constraints on traits. We found significant phylogenetic signal (PS) for all traits, consistent with evolutionarily related genera having more similar characteristics than expected by chance. Although there is also evidence for repeated evolution of pioneer and shade tolerant life-history strategies within independent lineages, the existence of significant PS allows clearer predictions of the links between evolutionary diversity, ecosystem function and the response of tropical forests to global change.
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Affiliation(s)
| | - Kyle G Dexter
- School of Geosciences, University of Edinburgh, 201 Crew Building, King's Buildings, Edinburgh EH9 3FF, UK.,Royal Botanic Garden Edinburgh, 20a Inverleith Row, Edinburgh EH3 5LR, UK
| | | | | | - Jerome Chave
- Université Paul Sabatier CNRS, UMR 5174 Evolution et Diversité Biologique, bâtiment 4R1, Toulouse 31062, France
| | | | | | - Abel Monteagudo Mendoza
- Jardín Botánico de Missouri, Prolongacion Bolognesi Mz. E, Lote 6, Oxapampa, Pasco, Peru.,Universidad Nacional de San Antonio Abad del Cusco, Av. de la Cultura N° 733, Cusco, Peru
| | - R Toby Pennington
- Royal Botanic Garden Edinburgh, 20a Inverleith Row, Edinburgh EH3 5LR, UK
| | - Lourens Poorter
- Forest Ecology and Forest Management Group, Wageningen University and Research, PO Box 47, 6700 AA Wageningen, The Netherlands
| | - Miguel Alexiades
- School of Anthropology and Conservation, University of Kent, Marlowe Building, Canterbury, Kent CT2 7NR, UK
| | | | - Ana Andrade
- Biological Dynamics of Forest Fragment Project (INPA & STRI), C.P. 478, Manaus, Amazonas 69.011-970, Brazil
| | - Luis E O C Aragão
- Geography, College of Life and Environmental Sciences, University of Exeter, Drive, Exeter, Rennes EX4 4RJ, UK.,National Institute for Space Research (INPE), São José dos Campos, São Paulo, Brazil
| | - Alejandro Araujo-Murakami
- Museo de Historia Natural Noel Kempff Mercado, Universidad Autonoma Gabriel Rene Moreno, Casilla 2489, Av. Irala 565, Santa Cruz, Bolivia
| | - Eric J M M Arets
- Alterra, Wageningen University and Research Centre, PO Box 47, Wageningen 6700 AA, The Netherlands
| | - Gerardo A Aymard C
- UNELLEZ-Guanare, Programa del Agro y del Mar, Herbario Universitario (PORT), Mesa de Cavacas, Estado Portuguesa 3350, Venezuela
| | - Christopher Baraloto
- International Center for Tropical Botany, Department of Biological Sciences, Florida International University, Miami, FL 33199, USA
| | - Jorcely G Barroso
- Universidade Federal do Acre, Campus de Cruzeiro do Sul, Acre, Brazil
| | - Damien Bonal
- INRA, UMR 1137 'Ecologie et Ecophysiologie Forestiere', Champenoux 54280, France
| | - Rene G A Boot
- Tropenbos International, PO Box 232, Wageningen 6700 AE, The Netherlands
| | - José L C Camargo
- Biological Dynamics of Forest Fragment Project (INPA & STRI), C.P. 478, Manaus, Amazonas 69.011-970, Brazil
| | - James A Comiskey
- National Park Service, 120 Chatham Lane, Fredericksburg, VA 22405, USA.,Smithsonian Institution, 1100 Jefferson Dr, SW, Washington, DC 20560, USA
| | | | - Plínio B de Camargo
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, São Paulo, Sao Paulo, Brazil
| | - Anthony Di Fiore
- Department of Anthropology, University of Texas at Austin, SAC Room 5.150, 2201 Speedway Stop C3200, Austin, TX 78712, USA
| | - Fernando Elias
- Universidade do Estado de Mato Grosso, Campus de Nova Xavantina, Caixa Postal 08, 78.690-000, Nova Xavantina, Mato Grosso, Brazil
| | - Terry L Erwin
- Department of Entomology, Smithsonian Institution, PO Box 37012, MRC 187, Washington, DC 20013-7012, USA
| | - Ted R Feldpausch
- Geography, College of Life and Environmental Sciences, University of Exeter, Drive, Exeter, Rennes EX4 4RJ, UK
| | - Leandro Ferreira
- Museu Paraense Emilio Goeldi, C.P. 399, 66.040-170, Belém, Pará, Brazil
| | | | - Emanuel Gloor
- School of Geography, University of Leeds, Leeds LS2 9JT, UK
| | - Bruno Herault
- Cirad, UMR EcoFoG (AgroParisTech, CNRS, Inra, U Antilles, U Guyane), Campus Agronomique, Kourou 97310, French Guiana
| | - Rafael Herrera
- Centro de Ecología IVIC, Caracas, Venezuela.,Institut für Geographie und Regionalforschung, University of Vienna, Wien, Austria
| | - Niro Higuchi
- INPA, Av. André Araújo, 2.936 - Petrópolis - 69.067-375, Manaus, Amazonas, Brazil
| | | | | | - William F Laurance
- Centre for Tropical Environmental and Sustainability Science (TESS) and College of Science and Engineering, James Cook University, Cairns, Queensland 4878, Australia
| | - Susan Laurance
- Centre for Tropical Environmental and Sustainability Science (TESS) and College of Science and Engineering, James Cook University, Cairns, Queensland 4878, Australia
| | - Jon Lloyd
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Buckhurst, Road, Ascot, Berkshire SL5 7PY, UK
| | - Thomas E Lovejoy
- Environmental Science and Policy, and the Department of Public and International Affairs, George Mason University (GMU), Washington, DC, USA
| | - Yadvinder Malhi
- Environmental Change Institute, School of Geography and the Environment, University of Oxford, Oxford, UK
| | - Leandro Maracahipes
- Programa de Pós-graduação em Ecologia e Evolução, Universidade Federal de Goias, Goiânia, Goias, Brazil
| | - Beatriz S Marimon
- Universidade do Estado de Mato Grosso, Campus de Nova Xavantina, Caixa Postal 08, 78.690-000, Nova Xavantina, Mato Grosso, Brazil
| | - Ben H Marimon-Junior
- Universidade do Estado de Mato Grosso, Campus de Nova Xavantina, Caixa Postal 08, 78.690-000, Nova Xavantina, Mato Grosso, Brazil
| | - Casimiro Mendoza
- Escuela de Ciencias Forestales, Unidad Académica del Trópico, Universidad Mayor de San Simón, Sacta, Bolivia
| | - Paulo Morandi
- Universidade do Estado de Mato Grosso, Campus de Nova Xavantina, Caixa Postal 08, 78.690-000, Nova Xavantina, Mato Grosso, Brazil
| | - David A Neill
- Universidad Estatal Amazónica, Puyo, Pastaza, Ecuador
| | - Percy Núñez Vargas
- Universidad Nacional de San Antonio Abad del Cusco, Av. de la Cultura N° 733, Cusco, Peru
| | - Edmar A Oliveira
- Universidade do Estado de Mato Grosso, Campus de Nova Xavantina, Caixa Postal 08, 78.690-000, Nova Xavantina, Mato Grosso, Brazil
| | - Eddie Lenza
- Universidade do Estado de Mato Grosso, Campus de Nova Xavantina, Caixa Postal 08, 78.690-000, Nova Xavantina, Mato Grosso, Brazil
| | - Walter A Palacios
- Universidad Técnica del Norte and Herbario Nacional del Ecuador, Casilla 17-21-1787, Av. Río Coca E6-115, Quito, Ecuador
| | | | - John J Pipoly
- Broward County Parks and Recreation Division, 950 NW 38th St., Oakland Park, FL 33309, USA
| | - Nigel C A Pitman
- Center for Tropical Conservation, Duke University, PO Box 90381, Durham, NC 27708, USA
| | - Adriana Prieto
- Doctorado Instituto de Ciencias Naturales, Universidad ciol de Colombia, Colombia
| | - Carlos A Quesada
- INPA, Av. André Araújo, 2.936 - Petrópolis - 69.067-375, Manaus, Amazonas, Brazil
| | - Hirma Ramirez-Angulo
- Instituto de Investigaciones para el Desarrollo Forestal (INDEFOR), Facultad de Ciencias Forestales y Ambientales, Universidad de Los Andes, Conjunto Forestal, C.P. 5101, Mérida, Venezuela
| | - Agustin Rudas
- Doctorado Instituto de Ciencias Naturales, Universidad ciol de Colombia, Colombia
| | - Kalle Ruokolainen
- Department of Geography and Geology, University of Turku, 20014 Turku, Finland
| | - Rafael P Salomão
- Museu Paraense Emilio Goeldi, C.P. 399, 66.040-170, Belém, Pará, Brazil
| | - Marcos Silveira
- Museu Universitário, Universidade Federal do Acre, Rio Branco, AC 69910-900, Brazil
| | - Juliana Stropp
- Institute of Biological and Health Sciences (ICBS), Federal University of Alagoas, Maceió, AL, Brazil
| | - Hans Ter Steege
- Naturalis Biodiversity Center, Vondellaan 55, Postbus 9517, Leiden 2300 RA, The Netherlands
| | - Raquel Thomas-Caesar
- Iwokrama Intertiol Centre for Rainforest Conservation and Development, 77 High Street Kingston, Georgetown, Guyana
| | - Peter van der Hout
- Van der Hout Forestry Consulting, Jan Trooststraat 6, Rotterdam 3078 HP, The Netherlands
| | | | - Peter J van der Meer
- Van Hall Larenstein University of Applied Sciences, PO Box 9001, 6880 GB Velp, The Netherlands
| | - Rodolfo V Vasquez
- Jardín Botánico de Missouri, Prolongacion Bolognesi Mz. E, Lote 6, Oxapampa, Pasco, Peru
| | - Simone A Vieira
- Universidade Estadual de Campinas, Núcleo de Estudos e Pesquisas Ambientais - NEPAM, Campinas, São Paulo, Brazil
| | - Emilio Vilanova
- Facultad de Ciencias Forestales y Ambientales, Universidad de Los Andes, Mérida, Venezuela
| | - Vincent A Vos
- Centro de Investigación y Promoción del Campesinado - regional Norte Amazónico, C/ Nicanor Gonzalo Salvatierra N° 362, Casilla 16, Riberalta, Bolivia.,Universidad Autónoma del Beni, Campus Universitario, Riberalta, Bolivia
| | - Ophelia Wang
- Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Kenneth R Young
- Department of Geography and the Environment, University of Texas at Austin, Austin, TX 78712, USA
| | - Roderick J Zagt
- Tropenbos International, PO Box 232, Wageningen 6700 AE, The Netherlands
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Understanding the Processes Underpinning Patterns of Phylogenetic Regionalization. Trends Ecol Evol 2017; 32:845-860. [PMID: 28919204 DOI: 10.1016/j.tree.2017.08.013] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Revised: 07/04/2017] [Accepted: 08/22/2017] [Indexed: 12/16/2022]
Abstract
A key step in understanding the distribution of biodiversity is the grouping of regions based on their shared elements. Historically, regionalization schemes have been largely species centric. Recently, there has been interest in incorporating phylogenetic information into regionalization schemes. Phylogenetic regionalization can provide novel insights into the mechanisms that generate, distribute, and maintain biodiversity. We argue that four processes (dispersal limitation, extinction, speciation, and niche conservatism) underlie the formation of species assemblages into phylogenetically distinct biogeographic units. We outline how it can be possible to distinguish among these processes, and identify centers of evolutionary radiation, museums of diversity, and extinction hotspots. We suggest that phylogenetic regionalization provides a rigorous and objective classification of regional diversity and enhances our knowledge of biodiversity patterns.
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Dolan RW, Aronson MFJ, Hipp AL. Floristic response to urbanization: Filtering of the bioregional flora in Indianapolis, Indiana, USA. AMERICAN JOURNAL OF BOTANY 2017; 104:1179-1187. [PMID: 28794058 DOI: 10.3732/ajb.1700136] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 06/23/2017] [Indexed: 06/07/2023]
Abstract
PREMISE OF THE STUDY Globally, urban plant populations are becoming increasingly important, as these plants play a vital role in ameliorating effects of ecosystem disturbance and climate change. Urban environments act as filters to bioregional flora, presenting survival challenges to spontaneous plants. Yet, because of the paucity of inventory data on plants in landscapes both before and after urbanization, few studies have directly investigated this effect of urbanization. METHODS We used historical, contemporary, and regional plant species inventories for Indianapolis, Indiana USA to evaluate how urbanization filters the bioregional flora based on species diversity, functional traits, and phylogenetic community structure. KEY RESULTS Approximately 60% of the current regional flora was represented in the Indianapolis flora, both historically and presently. Native species that survived over time were significantly different in growth form, life form, and dispersal and pollination modes than those that were extirpated. Phylogenetically, the historical flora represented a random sample of the regional flora, while the current urban flora represented a nonrandom sample. Both graminoid habit and abiotic pollination are significantly more phylogenetically conserved than expected. CONCLUSIONS Our results likely reflect the shift from agricultural cover to built environment, coupled with the influence of human preference, in shaping the current urban flora of Indianapolis. Based on our analyses, the urban environment of Indianapolis does filter the bioregional species pool. To the extent that these filters are shared by other cities and operate similarly, we may see increasingly homogenized urban floras across regions, with concurrent loss of evolutionary information.
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Affiliation(s)
- Rebecca W Dolan
- Friesner Herbarium and Center for Urban Ecology, Butler University, Indianapolis, Indiana 46208
| | - Myla F J Aronson
- Department of Ecology, Evolution and Natural Resources, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901
| | - Andrew L Hipp
- The Morton Arboretum, Lisle, Illinois 60523
- The Field Museum, Chicago, Illinois 60605
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23
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Vamosi JC, Gong YB, Adamowicz SJ, Packer L. Forecasting pollination declines through DNA barcoding: the potential contributions of macroecological and macroevolutionary scales of inquiry. THE NEW PHYTOLOGIST 2017; 214:11-18. [PMID: 27901268 DOI: 10.1111/nph.14356] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
While pollinators are widely acknowledged as important contributors to seed production in plant communities, we do not yet have a good understanding of the importance of pollinator specialists for this ecosystem service. Determination of the prevalence of pollinator specialists is often hindered by the occurrence of cryptic species and the limitations of observational data on pollinator visitation rates, two areas where DNA barcoding of pollinators and pollen can be useful. Further, the demonstrated adequacy of pollen DNA barcoding from historical records offers opportunities to observe the effects of pollinator loss over longer timescales, and phylogenetic approaches can elucidate the historical rates of extinction of specialist lineages. In this Viewpoint article, we review how advances in DNA barcoding and metabarcoding of plants and pollinators have brought important developments to our understanding of specialization in plant-pollinator interactions. We then put forth several lines of inquiry that we feel are especially promising for providing insight on changes in plant-pollinator interactions over space and time. Obtaining estimates of the effects of reductions in specialists will contribute to forecasting the loss of ecosystem services that will accompany the erosion of plant and pollinator diversity.
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Affiliation(s)
- Jana C Vamosi
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB, T2N 1N4, Canada
| | - Yan-Bing Gong
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Sarah J Adamowicz
- Biodiversity Institute of Ontario & Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
| | - Laurence Packer
- Department of Biology, York University, Toronto, ON, M3J 1P3, Canada
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24
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Molina-Venegas R, Rodríguez MÁ. Revisiting phylogenetic signal; strong or negligible impacts of polytomies and branch length information? BMC Evol Biol 2017; 17:53. [PMID: 28201989 PMCID: PMC5312541 DOI: 10.1186/s12862-017-0898-y] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 01/30/2017] [Indexed: 11/10/2022] Open
Abstract
Background Inaccurate estimates of phylogenetic signal may mislead interpretations of many ecological and evolutionary processes, and hence understanding where potential sources of uncertainty may lay has become a priority for comparative studies. Importantly, the sensitivity of phylogenetic signal indices and their associated statistical tests to incompletely resolved phylogenies and suboptimal branch-length information has been only partially investigated. Methods Here, we use simulations of trait evolution along phylogenetic trees to assess whether incompletely resolved phylogenies (polytomic chronograms) and phylogenies with suboptimal branch-length information (pseudo-chronograms) could produce directional biases in significance tests (p-values) associated with Blomberg et al.’s K and Pagel’s lambda (λ) statistics, two of the most widely used indices to measure and test phylogenetic signal. Specifically, we conducted pairwise comparisons between the p-values resulted from the use of “true” chronograms and their degraded counterparts (i.e. polytomic chronograms and pseudo-chronograms), and computed the frequency with which the null hypothesis of no phylogenetic signal was accepted using “true” chronograms but rejected when using their degraded counterparts (type I bias) and vice versa (type II bias). Results We found that the use of polytomic chronograms in combination with Blomberg et al.’s K resulted in both, clearly inflated estimates of phylogenetic signal and moderate levels of type I and II biases. More importantly, pseudo-chronograms led to high rates of type I biases. In contrast, Pagel’s λ was strongly robust to either incompletely resolved phylogenies and suboptimal branch-length information. Conclusions Our results suggest that pseudo-chronograms can lead to strong overestimation of phylogenetic signal when using Blomberg et al.’s K (i.e. high rates of type I biases), while polytomies may be a minor concern given other sources of uncertainty. In contrast, Pagel’s λ seems strongly robust to either incompletely resolved phylogenies and suboptimal branch-length information. Hence, Pagel’s λ may be a more appropriate alternative over Blomberg et al.’s K to measure and test phylogenetic signal in most ecologically relevant traits when phylogenetic information is incomplete. Electronic supplementary material The online version of this article (doi:10.1186/s12862-017-0898-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rafael Molina-Venegas
- Departamento de Ciencias de la Vida, Universidad de Alcalá, 28805, Alcalá de Henares, Madrid, Spain.
| | - Miguel Á Rodríguez
- Departamento de Ciencias de la Vida, Universidad de Alcalá, 28805, Alcalá de Henares, Madrid, Spain
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25
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Daru BH, van der Bank M, Bello A, Yessoufou K. Testing the reliability of standard and complementary DNA barcodes for the monocot subfamily Alooideae from South Africa. Genome 2016; 60:337-347. [PMID: 28177838 DOI: 10.1139/gen-2015-0183] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Although a standard DNA barcode has been identified for plants, it does not always provide species-level specimen identifications for investigating important ecological questions. In this study, we assessed the species-level discriminatory power of standard (rbcLa + matK) and complementary barcodes (ITS1 and trnH-psbA) within the subfamily Alooideae (Asphodelaceae), a large and recent plant radiation, whose species are important in horticulture yet are threatened. Alooideae has its centre of endemism in southern Africa, with some outlier species occurring elsewhere in Africa and Madagascar. We sampled 360 specimens representing 235 species within all 11 genera of the subfamily. With three distance-based methods, all markers performed poorly for our combined data set, with the highest proportion of correct species-level specimen identifications (30%) found for ITS1. However, when performance was assessed across genera, the discriminatory power varied from 0% for all single markers and combinations in Gasteria to 63% in Haworthiopsis, again for ITS1, suggesting that DNA barcoding success may be related to the evolutionary history of the lineage considered. Although ITS1 could be a good barcode for Haworthiopsis, the generally poor performance of all markers suggests that Alooideae remains a challenge. As species boundaries within Alooideae remain controversial, we call for continued search for suitable markers or the use of genomics approaches to further explore species discrimination in the group.
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Affiliation(s)
- Barnabas H Daru
- a Department of Organismic and Evolutionary Biology and Harvard University Herbaria, Harvard University, Cambridge, MA 02138, USA.,b Department of Plant Science, University of Pretoria, Private Bag X20, 0028 Hatfield, Pretoria, South Africa
| | - Michelle van der Bank
- c African Centre for DNA Barcoding, University of Johannesburg, APK Campus, PO Box 524, Auckland Park 2006, Johannesburg, South Africa
| | - Abubakar Bello
- d Bolus Herbarium, Biological Sciences Department, University of Cape Town, Private Bag X3, Rondebosch 7700, South Africa; Department of Biology, Umaru Musa Yarádua University, Katsina, Nigeria
| | - Kowiyou Yessoufou
- e Department of Geography, Environmental Management and Energy Studies, University of Johannesburg, APK Campus, PO Box 524, Auckland Park 2006, Johannesburg, South Africa
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26
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Larkin DJ, Jacobi SK, Hipp AL, Kramer AT. Keeping All the PIECES: Phylogenetically Informed Ex Situ Conservation of Endangered Species. PLoS One 2016; 11:e0156973. [PMID: 27257671 PMCID: PMC4892560 DOI: 10.1371/journal.pone.0156973] [Citation(s) in RCA: 12] [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: 02/07/2016] [Accepted: 05/23/2016] [Indexed: 11/19/2022] Open
Abstract
Ex situ conservation in germplasm and living collections is a major focus of global plant conservation strategies. Prioritizing species for ex situ collection is a necessary component of this effort for which sound strategies are needed. Phylogenetic considerations can play an important role in prioritization. Collections that are more phylogenetically diverse are likely to encompass more ecological and trait variation, and thus provide stronger conservation insurance and richer resources for future restoration efforts. However, phylogenetic criteria need to be weighed against other, potentially competing objectives. We used ex situ collection and threat rank data for North American angiosperms to investigate gaps in ex situ coverage and phylogenetic diversity of collections and to develop a flexible framework for prioritizing species across multiple objectives. We found that ex situ coverage of 18,766 North American angiosperm taxa was low with respect to the most vulnerable taxa: just 43% of vulnerable to critically imperiled taxa were in ex situ collections, far short of a year-2020 goal of 75%. In addition, species held in ex situ collections were phylogenetically clustered (P < 0.001), i.e., collections comprised less phylogenetic diversity than would be expected had species been drawn at random. These patterns support incorporating phylogenetic considerations into ex situ prioritization in a manner balanced with other criteria, such as vulnerability. To meet this need, we present the ‘PIECES’ index (Phylogenetically Informed Ex situ Conservation of Endangered Species). PIECES integrates phylogenetic considerations into a flexible framework for prioritizing species across competing objectives using multi-criteria decision analysis. Applying PIECES to prioritizing ex situ conservation of North American angiosperms, we show strong return on investment across multiple objectives, some of which are negatively correlated with each other. A spreadsheet-based decision support tool for North American angiosperms is provided; this tool can be customized to align with different conservation objectives.
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Affiliation(s)
- Daniel J. Larkin
- Department of Fisheries, Wildlife, and Conservation Biology, University of Minnesota, St. Paul, Minnesota, United States of America
- Plant Science and Conservation, Chicago Botanic Garden, Glencoe, Illinois, United States of America
- * E-mail:
| | - Sarah K. Jacobi
- Plant Science and Conservation, Chicago Botanic Garden, Glencoe, Illinois, United States of America
| | - Andrew L. Hipp
- Herbarium, The Morton Arboretum, Lisle, Illinois, United States of America
- Department of Botany, The Field Museum, Chicago, Illinois, United States of America
| | - Andrea T. Kramer
- Plant Science and Conservation, Chicago Botanic Garden, Glencoe, Illinois, United States of America
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27
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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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28
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He WM, Sun ZK. Convergent production and tolerance among 107 woody species and divergent production between shrubs and trees. Sci Rep 2016; 6:20485. [PMID: 26854019 PMCID: PMC4745073 DOI: 10.1038/srep20485] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 01/05/2016] [Indexed: 11/09/2022] Open
Abstract
Green leaves face two fundamental challenges (i.e., carbon fixation and stress tolerance) during their lifespan. However, the relationships between leaf production potential and leaf tolerance potential have not been explicitly tested with a broad range of plant species in the same environment. To do so, we conducted a field investigation based on 107 woody plants grown in a common garden and complementary laboratory measurements. The values, as measured by a chlorophyll meter, were significantly related to the direct measurements of chlorophyll content on a leaf area basis. Area-based chlorophyll content was positively correlated with root surface area, whole-plant biomass, leaf mass per area (LMA), and force to punch. Additionally, LMA had a positive correlation with force to punch. Shrubs had a higher leaf chlorophyll content than trees; however, shrubs and trees exhibited a similar leaf lifespan, force to punch, and LMA. These findings suggest that the production potential of leaves and their tolerance to stresses may be convergent in woody species and that the leaf production potential may differ between shrubs and trees. This study highlights the possibility that functional convergence and divergence might be linked to long-term selection pressures and genetic constraints.
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Affiliation(s)
- Wei-Ming He
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Haidian District, Beijing 100093, China
| | - Zhen-Kai Sun
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Haidian District, Beijing 100093, China
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29
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Mouillot D, Parravicini V, Bellwood DR, Leprieur F, Huang D, Cowman PF, Albouy C, Hughes TP, Thuiller W, Guilhaumon F. Global marine protected areas do not secure the evolutionary history of tropical corals and fishes. Nat Commun 2016; 7:10359. [PMID: 26756609 PMCID: PMC4729959 DOI: 10.1038/ncomms10359] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 12/03/2015] [Indexed: 11/25/2022] Open
Abstract
Although coral reefs support the largest concentrations of marine biodiversity worldwide, the extent to which the global system of marine-protected areas (MPAs) represents individual species and the breadth of evolutionary history across the Tree of Life has never been quantified. Here we show that only 5.7% of scleractinian coral species and 21.7% of labrid fish species reach the minimum protection target of 10% of their geographic ranges within MPAs. We also estimate that the current global MPA system secures only 1.7% of the Tree of Life for corals, and 17.6% for fishes. Regionally, the Atlantic and Eastern Pacific show the greatest deficit of protection for corals while for fishes this deficit is located primarily in the Western Indian Ocean and in the Central Pacific. Our results call for a global coordinated expansion of current conservation efforts to fully secure the Tree of Life on coral reefs. Marine protected areas (MPAs) are established to conserve species, but the extent to which they also conserve evolutionary history is not clear. Here, Mouillot et al. show that for tropical corals and fish, the current global MPA network secures only 1.7 and 17.6% of phylogenetic diversity, respectively.
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Affiliation(s)
- D Mouillot
- UMR 9190 MARBEC, IRD-CNRS-IFREMER-UM, Université de Montpellier, Montpellier 34095, France.,Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland 4811, Australia
| | - V Parravicini
- CRIOBE, USR 3278 CNRS-EPHE-UPVD, Labex 'Corail', University of Perpignan, Perpignan 66860, France
| | - D R Bellwood
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland 4811, Australia
| | - F Leprieur
- UMR 9190 MARBEC, IRD-CNRS-IFREMER-UM, Université de Montpellier, Montpellier 34095, France
| | - D Huang
- Department of Biological Sciences and Tropical Marine Science Institute, National University of Singapore, Singapore 117543, Singapore
| | - P F Cowman
- Department of Ecology &Evolutionary Biology, Yale University, 21 Sachem St, New Haven, Connecticut 06511 USA
| | - C Albouy
- Département de biologie, chimie et géographie, Université du Québec à Rimouski, 300 Allée des Ursulines, Rimouski, Canada G5L 3A1
| | - T P Hughes
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland 4811, Australia
| | - W Thuiller
- Laboratoire d'Écologie Alpine (LECA), Univ. Grenoble Alpes, Grenoble F-38000, France.,Laboratoire d'Écologie Alpine (LECA), CNRS, Grenoble F-38000, France
| | - F Guilhaumon
- UMR 9190 MARBEC, IRD-CNRS-IFREMER-UM, Université de Montpellier, Montpellier 34095, France
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30
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Pennell MW, FitzJohn RG, Cornwell WK. A simple approach for maximizing the overlap of phylogenetic and comparative data. Methods Ecol Evol 2016. [DOI: 10.1111/2041-210x.12517] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Matthew W. Pennell
- Institute for Bioinformatics and Evolutionary Studies; University of Idaho; Moscow ID 83844 USA
- Department of Zoology; Biodiversity Research Centre; University of British Columbia; Vancouver BC V6T 1Z4 Canada
| | - Richard G. FitzJohn
- Department of Biological Sciences; Macquarie University; Sydney NSW 2109 Australia
| | - William K. Cornwell
- Ecology and Evolution Research Centre; School of Biological, Earth and Environmental Sciences; University of New South Wales; Sydney NSW 2052 Australia
- Centre for Ecosystem Science; School of Biological, Earth and Environmental Sciences; University of New South Wales; Sydney NSW 2052 Australia
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31
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Pan X, Song YB, Jiang C, Liu GF, Ye XH, Xie XF, Hu YK, Zhao WW, Cui L, Cornelissen JHC, Dong M, Prinzing A. Evolutionary Position and Leaf Toughness Control Chemical Transformation of Litter, and Drought Reinforces This Control: Evidence from a Common Garden Experiment across 48 Species. PLoS One 2015; 10:e0143140. [PMID: 26575641 PMCID: PMC4648592 DOI: 10.1371/journal.pone.0143140] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 10/30/2015] [Indexed: 11/18/2022] Open
Abstract
Plant leaf litter is an important source of soil chemicals that are essential for the ecosystem and changes in leaf litter chemical traits during decomposition will determine the availability of multiple chemical elements recycling in the ecosystem. However, it is unclear whether the changes in litter chemical traits during decomposition and their similarities across species can be predicted, respectively, using other leaf traits or using the phylogenetic relatedness of the litter species. Here we examined the fragmentation levels, mass losses, and the changes of 10 litter chemical traits during 1-yr decomposition under different environmental conditions (within/above surrounding litter layer) for 48 temperate tree species and related them to an important leaf functional trait, i.e. leaf toughness. Leaf toughness could predict the changes well in terms of amounts, but poorly in terms of concentrations. Changes of 7 out of 10 litter chemical traits during decomposition showed a significant phylogenetic signal notably when litter was exposed above surrounding litter. These phylogenetic signals in element dynamics were stronger than those of initial elementary composition. Overall, relatively hard-to-measure ecosystem processes like element dynamics during decomposition could be partly predicted simply from phylogenies and leaf toughness measures. We suggest that the strong phylogenetic signals in chemical ecosystem functioning of species may reflect the concerted control by multiple moderately conserved traits, notably if interacting biota suffer microclimatic stress and spatial isolation from ambient litter.
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Affiliation(s)
- Xu Pan
- Key Laboratory of Hangzhou City for Ecosystem Protection and Restoration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Institute of Wetland Research, Chinese Academy of Forestry, Beijing, China
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Yao-Bin Song
- Key Laboratory of Hangzhou City for Ecosystem Protection and Restoration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Can Jiang
- Key Laboratory of Hangzhou City for Ecosystem Protection and Restoration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Guo-Fang Liu
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Xue-Hua Ye
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Xiu-Fang Xie
- Key Laboratory of Hangzhou City for Ecosystem Protection and Restoration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Yu-Kun Hu
- Key Laboratory of Hangzhou City for Ecosystem Protection and Restoration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Wei-Wei Zhao
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- Systems Ecology, Department of Ecological Science, Faculty of Earth and Life Sciences, VU University Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Lijuan Cui
- Institute of Wetland Research, Chinese Academy of Forestry, Beijing, China
| | - Johannes H. C. Cornelissen
- Systems Ecology, Department of Ecological Science, Faculty of Earth and Life Sciences, VU University Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Ming Dong
- Key Laboratory of Hangzhou City for Ecosystem Protection and Restoration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Andreas Prinzing
- Université de Rennes 1, Centre National de la Recherche Scientifique Campus de Beaulieu, Research Unit Ecobio, Bâtiment 14 A, 35042 Rennes, France
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Rangel TF, Colwell RK, Graves GR, Fučíková K, Rahbek C, Diniz-Filho JAF. Phylogenetic uncertainty revisited: Implications for ecological analyses. Evolution 2015; 69:1301-12. [PMID: 25800868 DOI: 10.1111/evo.12644] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 03/11/2015] [Indexed: 11/30/2022]
Abstract
Ecologists and biogeographers usually rely on a single phylogenetic tree to study evolutionary processes that affect macroecological patterns. This approach ignores the fact that each phylogenetic tree is a hypothesis about the evolutionary history of a clade, and cannot be directly observed in nature. Also, trees often leave out many extant species, or include missing species as polytomies because of a lack of information on the relationship among taxa. Still, researchers usually do not quantify the effects of phylogenetic uncertainty in ecological analyses. We propose here a novel analytical strategy to maximize the use of incomplete phylogenetic information, while simultaneously accounting for several sources of phylogenetic uncertainty that may distort statistical inferences about evolutionary processes. We illustrate the approach using a clade-wide analysis of the hummingbirds, evaluating how different sources of uncertainty affect several phylogenetic comparative analyses of trait evolution and biogeographic patterns. Although no statistical approximation can fully substitute for a complete and robust phylogeny, the method we describe and illustrate enables researchers to broaden the number of clades for which studies informed by evolutionary relationships are possible, while allowing the estimation and control of statistical error that arises from phylogenetic uncertainty. Software tools to carry out the necessary computations are offered.
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Affiliation(s)
- Thiago F Rangel
- Departmento de Ecologia, Universidade Federal de Goiás, CP 131, Goiânia, GO, Brasil, 74.001-970.
| | - Robert K Colwell
- Departmento de Ecologia, Universidade Federal de Goiás, CP 131, Goiânia, GO, Brasil, 74.001-970.,Department of Ecology and Evolutionary Biology, University of Connecticut, 75 North Eagleville Road, Unit 3043, Storrs, Connecticut, 06269-3043.,Museum of Natural History, University of Colorado, Boulder, Colorado, 80309
| | - Gary R Graves
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20013.,Department of Biology, Center for Macroecology, Evolution and Climate, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen O, Denmark
| | - Karolina Fučíková
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 North Eagleville Road, Unit 3043, Storrs, Connecticut, 06269-3043
| | - Carsten Rahbek
- Department of Biology, Center for Macroecology, Evolution and Climate, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen O, Denmark
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Soul LC, Friedman M. Taxonomy and Phylogeny Can Yield Comparable Results in Comparative Paleontological Analyses. Syst Biol 2015; 64:608-20. [PMID: 25805045 DOI: 10.1093/sysbio/syv015] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 03/18/2015] [Indexed: 11/14/2022] Open
Abstract
Many extinct taxa with extensive fossil records and mature taxonomic classifications have not yet been the subject of formal phylogenetic analysis. Here, we test whether the taxonomies available for such groups represent useful (i.e., non-misleading) substitutes for trees derived from matrix-based phylogenetic analyses. We collected data for 52 animal clades that included fossil representatives, and for which a recent cladogram and pre-cladistic taxonomy were available. We quantified the difference between the time-scaled phylogenies implied by taxonomies and cladograms using the matching cluster distance metric. We simulated phenotypic trait values and used them to estimate a series of commonly used, phylogenetically explicit measures (phylogenetic signal [Blomberg's [Formula: see text]], phylogenetic generalized least squares [PGLS], mode of evolution [Brownian vs. Ornstein-Uhlenbeck], and phylogenetic clustering of extinction [Fritz and Purvis' [Formula: see text]]) in order to determine the degree to which they co-varied on taxonomic and cladistic trees. With respect to topology taxonomies are good approximations of the underlying evolutionary relationships as recorded in inferred cladograms. Detection of phylogenetic clustering of extinction could not be properly assessed. For all other evolutionary analyses, results from taxonomy-based phylogenies (TBPs) co-varied with those from cladogram-based phylogenies (CBPs), but individual comparisons could be misleading. The relative length of terminal branches (influenced by stratigraphy and sampling rate) is a key control on the shared information between, and therefore the relative performance of, TBP and CBP. Collectively these results suggest that under particular circumstances and after careful consideration some taxonomies, or composite trees that incorporate taxonomic information, could be used in place of a formal analytical solution, but workers must be cautious. This opens certain parts of a previously inaccessible section of the fossil record to interrogation within an explicit comparative framework, which will help to test many classical macroevolutionary hypotheses formulated for groups that currently lack formal phylogenetic estimates.
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Affiliation(s)
- Laura C Soul
- Department of Earth Sciences, University of Oxford, South Parks Road, Oxford OX1 3AN, UK
| | - Matt Friedman
- Department of Earth Sciences, University of Oxford, South Parks Road, Oxford OX1 3AN, UK
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Funk JL, Rakovski CS, Macpherson JM. On the analysis of phylogenetically paired designs. Ecol Evol 2015; 5:940-7. [PMID: 25750719 PMCID: PMC4338975 DOI: 10.1002/ece3.1406] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 12/19/2014] [Accepted: 12/22/2014] [Indexed: 11/08/2022] Open
Abstract
As phylogenetically controlled experimental designs become increasingly common in ecology, the need arises for a standardized statistical treatment of these datasets. Phylogenetically paired designs circumvent the need for resolved phylogenies and have been used to compare species groups, particularly in the areas of invasion biology and adaptation. Despite the widespread use of this approach, the statistical analysis of paired designs has not been critically evaluated. We propose a mixed model approach that includes random effects for pair and species. These random effects introduce a "two-layer" compound symmetry variance structure that captures both the correlations between observations on related species within a pair as well as the correlations between the repeated measurements within species. We conducted a simulation study to assess the effect of model misspecification on Type I and II error rates. We also provide an illustrative example with data containing taxonomically similar species and several outcome variables of interest. We found that a mixed model with species and pair as random effects performed better in these phylogenetically explicit simulations than two commonly used reference models (no or single random effect) by optimizing Type I error rates and power. The proposed mixed model produces acceptable Type I and II error rates despite the absence of a phylogenetic tree. This design can be generalized to a variety of datasets to analyze repeated measurements in clusters of related subjects/species.
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Affiliation(s)
- Jennifer L Funk
- Schmid College of Science and Technology, Chapman University Orange, California, 92866
| | - Cyril S Rakovski
- Schmid College of Science and Technology, Chapman University Orange, California, 92866
| | - J Michael Macpherson
- Schmid College of Science and Technology, Chapman University Orange, California, 92866
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Kantar MB, Sosa CC, Khoury CK, Castañeda-Álvarez NP, Achicanoy HA, Bernau V, Kane NC, Marek L, Seiler G, Rieseberg LH. Ecogeography and utility to plant breeding of the crop wild relatives of sunflower (Helianthus annuus L.). FRONTIERS IN PLANT SCIENCE 2015; 6:841. [PMID: 26500675 PMCID: PMC4597133 DOI: 10.3389/fpls.2015.00841] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Accepted: 09/24/2015] [Indexed: 05/22/2023]
Abstract
Crop wild relatives (CWR) are a rich source of genetic diversity for crop improvement. Combining ecogeographic and phylogenetic techniques can inform both conservation and breeding. Geographic occurrence, bioclimatic, and biophysical data were used to predict species distributions, range overlap and niche occupancy in 36 taxa closely related to sunflower (Helianthus annuus L.). Taxa lacking comprehensive ex situ conservation were identified. The predicted distributions for 36 Helianthus taxa identified substantial range overlap, range asymmetry and niche conservatism. Specific taxa (e.g., Helianthus deblis Nutt., Helianthus anomalus Blake, and Helianthus divaricatus L.) were identified as targets for traits of interest, particularly for abiotic stress tolerance, and adaptation to extreme soil properties. The combination of techniques demonstrates the potential for publicly available ecogeographic and phylogenetic data to facilitate the identification of possible sources of abiotic stress traits for plant breeding programs. Much of the primary genepool (wild H. annuus) occurs in extreme environments indicating that introgression of targeted traits may be relatively straightforward. Sister taxa in Helianthus have greater range overlap than more distantly related taxa within the genus. This adds to a growing body of literature suggesting that in plants (unlike some animal groups), geographic isolation may not be necessary for speciation.
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Affiliation(s)
- Michael B. Kantar
- Biodiversity Research Centre and Department of Botany, University of British ColumbiaVancouver, BC, Canada
- Department of Agronomy and Plant Genetics, University of MinnesotaSt. Paul, MN, USA
- *Correspondence: Michael B. Kantar
| | | | - Colin K. Khoury
- International Center for Tropical AgricultureCali, Colombia
- Centre for Crop Systems Analysis, Wageningen UniversityWageningen, Netherlands
| | - Nora P. Castañeda-Álvarez
- International Center for Tropical AgricultureCali, Colombia
- School of Biosciences, University of BirminghamBirmingham, UK
| | | | - Vivian Bernau
- International Center for Tropical AgricultureCali, Colombia
- Department of Horticulture and Crop Science, The Ohio State UniversityColumbus, OH, USA
| | - Nolan C. Kane
- Department of Ecology and Evolutionary Biology, University of Colorado at BoulderBoulder, CO, USA
| | - Laura Marek
- Agronomy Department, North Central Regional Plant Introduction Station, Iowa State University and United States Department of Agriculture Agricultural Research ServiceAmes, IA, USA
| | - Gerald Seiler
- Northern Crop Science Laboratory, United States Department of Agriculture Agricultural Research ServiceFargo, ND, USA
| | - Loren H. Rieseberg
- Biodiversity Research Centre and Department of Botany, University of British ColumbiaVancouver, BC, Canada
- Department of Biology, Indiana UniversityBloomington, IN, USA
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Muscarella R, Uriarte M, Erickson DL, Swenson NG, Zimmerman JK, Kress WJ. A well-resolved phylogeny of the trees of Puerto Rico based on DNA barcode sequence data. PLoS One 2014; 9:e112843. [PMID: 25386879 PMCID: PMC4227909 DOI: 10.1371/journal.pone.0112843] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 10/17/2014] [Indexed: 11/23/2022] Open
Abstract
Background The use of phylogenetic information in community ecology and conservation has grown in recent years. Two key issues for community phylogenetics studies, however, are (i) low terminal phylogenetic resolution and (ii) arbitrarily defined species pools. Methodology/principal findings We used three DNA barcodes (plastid DNA regions rbcL, matK, and trnH-psbA) to infer a phylogeny for 527 native and naturalized trees of Puerto Rico, representing the vast majority of the entire tree flora of the island (89%). We used a maximum likelihood (ML) approach with and without a constraint tree that enforced monophyly of recognized plant orders. Based on 50% consensus trees, the ML analyses improved phylogenetic resolution relative to a comparable phylogeny generated with Phylomatic (proportion of internal nodes resolved: constrained ML = 74%, unconstrained ML = 68%, Phylomatic = 52%). We quantified the phylogenetic composition of 15 protected forests in Puerto Rico using the constrained ML and Phylomatic phylogenies. We found some evidence that tree communities in areas of high water stress were relatively phylogenetically clustered. Reducing the scale at which the species pool was defined (from island to soil types) changed some of our results depending on which phylogeny (ML vs. Phylomatic) was used. Overall, the increased terminal resolution provided by the ML phylogeny revealed additional patterns that were not observed with a less-resolved phylogeny. Conclusions/significance With the DNA barcode phylogeny presented here (based on an island-wide species pool), we show that a more fully resolved phylogeny increases power to detect nonrandom patterns of community composition in several Puerto Rican tree communities. Especially if combined with additional information on species functional traits and geographic distributions, this phylogeny will (i) facilitate stronger inferences about the role of historical processes in governing the assembly and composition of Puerto Rican forests, (ii) provide insight into Caribbean biogeography, and (iii) aid in incorporating evolutionary history into conservation planning.
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Affiliation(s)
- Robert Muscarella
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, New York 10027, United States of America
| | - María Uriarte
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, New York 10027, United States of America
| | - David L Erickson
- Department of Botany, MRC-166, National Museum of Natural History Smithsonian Institution, P.O. Box 37012, Washington, D. C., 20013, United States of America
| | - Nathan G Swenson
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824, United States of America
| | - Jess K Zimmerman
- Department of Environmental Science, University of Puerto Rico, San Juan, Puerto Rico 00925, United States of America
| | - W John Kress
- Department of Botany, MRC-166, National Museum of Natural History Smithsonian Institution, P.O. Box 37012, Washington, D. C., 20013, United States of America
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Erickson DL, Jones FA, Swenson NG, Pei N, Bourg NA, Chen W, Davies SJ, Ge XJ, Hao Z, Howe RW, Huang CL, Larson AJ, Lum SKY, Lutz JA, Ma K, Meegaskumbura M, Mi X, Parker JD, Fang-Sun I, Wright SJ, Wolf AT, Ye W, Xing D, Zimmerman JK, Kress WJ. Comparative evolutionary diversity and phylogenetic structure across multiple forest dynamics plots: a mega-phylogeny approach. Front Genet 2014; 5:358. [PMID: 25414723 PMCID: PMC4220724 DOI: 10.3389/fgene.2014.00358] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 09/26/2014] [Indexed: 11/13/2022] Open
Abstract
Forest dynamics plots, which now span longitudes, latitudes, and habitat types across the globe, offer unparalleled insights into the ecological and evolutionary processes that determine how species are assembled into communities. Understanding phylogenetic relationships among species in a community has become an important component of assessing assembly processes. However, the application of evolutionary information to questions in community ecology has been limited in large part by the lack of accurate estimates of phylogenetic relationships among individual species found within communities, and is particularly limiting in comparisons between communities. Therefore, streamlining and maximizing the information content of these community phylogenies is a priority. To test the viability and advantage of a multi-community phylogeny, we constructed a multi-plot mega-phylogeny of 1347 species of trees across 15 forest dynamics plots in the ForestGEO network using DNA barcode sequence data (rbcL, matK, and psbA-trnH) and compared community phylogenies for each individual plot with respect to support for topology and branch lengths, which affect evolutionary inference of community processes. The levels of taxonomic differentiation across the phylogeny were examined by quantifying the frequency of resolved nodes throughout. In addition, three phylogenetic distance (PD) metrics that are commonly used to infer assembly processes were estimated for each plot [PD, Mean Phylogenetic Distance (MPD), and Mean Nearest Taxon Distance (MNTD)]. Lastly, we examine the partitioning of phylogenetic diversity among community plots through quantification of inter-community MPD and MNTD. Overall, evolutionary relationships were highly resolved across the DNA barcode-based mega-phylogeny, and phylogenetic resolution for each community plot was improved when estimated within the context of the mega-phylogeny. Likewise, when compared with phylogenies for individual plots, estimates of phylogenetic diversity in the mega-phylogeny were more consistent, thereby removing a potential source of bias at the plot-level, and demonstrating the value of assessing phylogenetic relationships simultaneously within a mega-phylogeny. An unexpected result of the comparisons among plots based on the mega-phylogeny was that the communities in the ForestGEO plots in general appear to be assemblages of more closely related species than expected by chance, and that differentiation among communities is very low, suggesting deep floristic connections among communities and new avenues for future analyses in community ecology.
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Affiliation(s)
- David L. Erickson
- Department of Botany, Museum Routing Code-166, National Museum of Natural History, Smithsonian InstitutionWashington, DC, USA
| | - Frank A. Jones
- Department of Botany and Plant Pathology, Oregon State UniversityCorvallis, OR, USA
- Smithsonian Tropical Research Institute, PanamáPanamá
| | - Nathan G. Swenson
- Department of Plant Biology, Michigan State UniversityEast Lansing, MI, USA
| | - Nancai Pei
- Forest Ecosystem Station of the Pearl River Delta, State Forestry Administration, Research Institute of Tropical Forestry, Chinese Academy of ForestryGuangzhou, China
| | - Norman A. Bourg
- Conservation Ecology Center, Smithsonian Conservation Biology Institute, Smithsonian InstitutionFront Royal, VA, USA
| | - Wenna Chen
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, The Chinese Academy of SciencesGuangzhou, China
| | - Stuart J. Davies
- Center for Tropical Forest Science-Forest Global Earth Observatory, Smithsonian Tropical Research InstituteWashington, DC, USA
| | - Xue-jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, The Chinese Academy of SciencesGuangzhou, China
| | - Zhanqing Hao
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of ScienceShenyang, China
| | - Robert W. Howe
- Department of Natural and Applied Sciences, Biology Program, University of Wisconsin-Green BayGreen Bay, WI, USA
| | - Chun-Lin Huang
- Laboratory of Molecular Phylogenetics, Department of Biology, National Museum of Natural ScienceTaichung, Taiwan
| | - Andrew J. Larson
- Department of Forest Management, The University of MontanaMissoula, MT, USA
| | - Shawn K. Y. Lum
- National Institute of Education, Nanyang Technological University, SingaporeSingapore
| | - James A. Lutz
- Wildland Resources, Utah State UniversityLogan, UT, USA
| | - Keping Ma
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of SciencesBeijing, China
| | - Madhava Meegaskumbura
- Department of Zoology, Faculty of Science, University of PeradeniyaPeradeniya, Sri Lanka
| | - Xiangcheng Mi
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of SciencesBeijing, China
| | - John D. Parker
- Smithsonian Environmental Research Center, Smithsonian InstitutionEdgewater, MD, USA
| | - I. Fang-Sun
- Department of Natural Resources and Environmental Studies, National Dong Hwa UniversityHualien, Taiwan
| | | | - Amy T. Wolf
- Department of Natural and Applied Sciences, Biology Program, University of Wisconsin-Green BayGreen Bay, WI, USA
| | - W. Ye
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, The Chinese Academy of SciencesGuangzhou, China
| | - Dingliang Xing
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of ScienceShenyang, China
| | - Jess K. Zimmerman
- Institute for Tropical Ecosystem Studies, University of Puerto RicoSan Juan, PR, USA
| | - W. John Kress
- Department of Botany, Museum Routing Code-166, National Museum of Natural History, Smithsonian InstitutionWashington, DC, USA
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Leão TCC, Fonseca CR, Peres CA, Tabarelli M. Predicting extinction risk of Brazilian Atlantic forest angiosperms. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2014; 28:1349-1359. [PMID: 24665927 DOI: 10.1111/cobi.12286] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Accepted: 12/24/2013] [Indexed: 06/03/2023]
Abstract
Understanding how plant life history affects species vulnerability to anthropogenic disturbances and environmental change is a major ecological challenge. We examined how vegetation type, growth form, and geographic range size relate to extinction risk throughout the Brazilian Atlantic Forest domain. We used a database containing species-level information of 6,929 angiosperms within 112 families and a molecular-based working phylogeny. We used decision trees, standard regression, and phylogenetic regression to explore the relationships between species attributes and extinction risk. We found a significant phylogenetic signal in extinction risk. Vegetation type, growth form, and geographic range size were related to species extinction risk, but the effect of growth form was not evident after phylogeny was controlled for. Species restricted to either rocky outcrops or scrub vegetation on sandy coastal plains exhibited the highest extinction risk among vegetation types, a finding that supports the hypothesis that species adapted to resource-limited environments are more vulnerable to extinction. Among growth forms, epiphytes were associated with the highest extinction risk in non-phylogenetic regression models, followed by trees, whereas shrubs and climbers were associated with lower extinction risk. However, the higher extinction risk of epiphytes was not significant after correcting for phylogenetic relatedness. Our findings provide new indicators of extinction risk and insights into the mechanisms governing plant vulnerability to extinction in a highly diverse flora where human disturbances are both frequent and widespread.
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Affiliation(s)
- Tarciso C C Leão
- Departamento de Botânica, Universidade Federal de Pernambuco, Recife, PE, 50670-901, Brazil; Department of Forest Resources, University of Minnesota, St. Paul, MN, 55108, U.S.A
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Pan X, Cornelissen JHC, Zhao WW, Liu GF, Hu YK, Prinzing A, Dong M, Cornwell WK. Experimental evidence that the Ornstein-Uhlenbeck model best describes the evolution of leaf litter decomposability. Ecol Evol 2014; 4:3339-49. [PMID: 25535551 PMCID: PMC4228609 DOI: 10.1002/ece3.1115] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Revised: 04/18/2014] [Accepted: 04/28/2014] [Indexed: 11/23/2022] Open
Abstract
Leaf litter decomposability is an important effect trait for ecosystem functioning. However, it is unknown how this effect trait evolved through plant history as a leaf 'afterlife' integrator of the evolution of multiple underlying traits upon which adaptive selection must have acted. Did decomposability evolve in a Brownian fashion without any constraints? Was evolution rapid at first and then slowed? Or was there an underlying mean-reverting process that makes the evolution of extreme trait values unlikely? Here, we test the hypothesis that the evolution of decomposability has undergone certain mean-reverting forces due to strong constraints and trade-offs in the leaf traits that have afterlife effects on litter quality to decomposers. In order to test this, we examined the leaf litter decomposability and seven key leaf traits of 48 tree species in the temperate area of China and fitted them to three evolutionary models: Brownian motion model (BM), Early burst model (EB), and Ornstein-Uhlenbeck model (OU). The OU model, which does not allow unlimited trait divergence through time, was the best fit model for leaf litter decomposability and all seven leaf traits. These results support the hypothesis that neither decomposability nor the underlying traits has been able to diverge toward progressively extreme values through evolutionary time. These results have reinforced our understanding of the relationships between leaf litter decomposability and leaf traits in an evolutionary perspective and may be a helpful step toward reconstructing deep-time carbon cycling based on taxonomic composition with more confidence.
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Affiliation(s)
- Xu Pan
- Key Laboratory of Hangzhou City for Ecosystem Protection and Restoration, College of Life and Environmental Sciences, Hangzhou Normal UniversityHangzhou, China
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of SciencesBeijing, China
| | | | - Wei-Wei Zhao
- Department of Ecological Science, VU UniversityAmsterdam, the Netherlands
| | - Guo-Fang Liu
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of SciencesBeijing, China
| | - Yu-Kun Hu
- Key Laboratory of Hangzhou City for Ecosystem Protection and Restoration, College of Life and Environmental Sciences, Hangzhou Normal UniversityHangzhou, China
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of SciencesBeijing, China
| | - Andreas Prinzing
- Université de Rennes 1, Centre National de la Recherche Scientifique Campus de BeaulieuBâtiment 14 A, 35042, Rennes, France
| | - Ming Dong
- Key Laboratory of Hangzhou City for Ecosystem Protection and Restoration, College of Life and Environmental Sciences, Hangzhou Normal UniversityHangzhou, China
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of SciencesBeijing, China
| | - William K Cornwell
- Department of Ecological Science, VU UniversityAmsterdam, the Netherlands
- School of Biological, Earth and Environmental Sciences, University of New South WalesSydney, NSW, Australia
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Molina-Venegas R, Roquet C. Directional biases in phylogenetic structure quantification: a Mediterranean case study. ECOGRAPHY 2014; 37:572-580. [PMID: 25076812 PMCID: PMC4112217 DOI: 10.1111/j.1600-0587.2013.00442.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Recent years have seen an increasing effort to incorporate phylogenetic hypotheses to the study of community assembly processes. The incorporation of such evolutionary information has been eased by the emergence of specialized software for the automatic estimation of partially resolved supertrees based on published phylogenies. Despite this growing interest in the use of phylogenies in ecological research, very few studies have attempted to quantify the potential biases related to the use of partially resolved phylogenies and to branch length accuracy, and no work has examined how tree shape may affect inference of community phylogenetic metrics. In this study, using a large plant community and elevational dataset, we tested the influence of phylogenetic resolution and branch length information on the quantification of phylogenetic structure; and also explored the impact of tree shape (stemminess) on the loss of accuracy in phylogenetic structure quantification due to phylogenetic resolution. For this purpose, we used 9 sets of phylogenetic hypotheses of varying resolution and branch lengths to calculate three indices of phylogenetic structure: the mean phylogenetic distance (NRI), the mean nearest taxon distance (NTI) and phylogenetic diversity (stdPD) metrics. The NRI metric was the less sensitive to phylogenetic resolution, stdPD showed an intermediate sensitivity, and NTI was the most sensitive one; NRI was also less sensitive to branch length accuracy than NTI and stdPD, the degree of sensitivity being strongly dependent on the dating method and the sample size. Directional biases were generally towards type II errors. Interestingly, we detected that tree shape influenced the accuracy loss derived from the lack of phylogenetic resolution, particularly for NRI and stdPD. We conclude that well-resolved molecular phylogenies with accurate branch length information are needed to identify the underlying phylogenetic structure of communities, and also that sensitivity of phylogenetic structure measures to low phylogenetic resolution can strongly differ depending on phylogenetic tree shape.
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Affiliation(s)
- Rafael Molina-Venegas
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, Apartado 1095, E-41080 Sevilla, Spain
| | - Cristina Roquet
- Laboratoire d’Écologie Alpine, UMR-CNRS 5553, Université Joseph Fourier, Grenoble 1, BP 53, 38041 Grenoble Cedex 9, France
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Lasky JR, Yang J, Zhang G, Cao M, Tang Y, Keitt TH. The role of functional traits and individual variation in the co-occurrence ofFicusspecies. Ecology 2014; 95:978-90. [DOI: 10.1890/13-0437.1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Broadbent EN, Almeyda Zambrano AM, Asner GP, Soriano M, Field CB, de Souza HR, Peña-Claros M, Adams RI, Dirzo R, Giles L. Integrating stand and soil properties to understand foliar nutrient dynamics during forest succession following slash-and-burn agriculture in the Bolivian Amazon. PLoS One 2014; 9:e86042. [PMID: 24516525 PMCID: PMC3917844 DOI: 10.1371/journal.pone.0086042] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 12/04/2013] [Indexed: 11/19/2022] Open
Abstract
Secondary forests cover large areas of the tropics and play an important role in the global carbon cycle. During secondary forest succession, simultaneous changes occur among stand structural attributes, soil properties, and species composition. Most studies classify tree species into categories based on their regeneration requirements. We use a high-resolution secondary forest chronosequence to assign trees to a continuous gradient in species successional status assigned according to their distribution across the chronosequence. Species successional status, not stand age or differences in stand structure or soil properties, was found to be the best predictor of leaf trait variation. Foliar δ(13)C had a significant positive relationship with species successional status, indicating changes in foliar physiology related to growth and competitive strategy, but was not correlated with stand age, whereas soil δ(13)C dynamics were largely constrained by plant species composition. Foliar δ(15)N had a significant negative correlation with both stand age and species successional status, - most likely resulting from a large initial biomass-burning enrichment in soil (15)N and (13)C and not closure of the nitrogen cycle. Foliar %C was neither correlated with stand age nor species successional status but was found to display significant phylogenetic signal. Results from this study are relevant to understanding the dynamics of tree species growth and competition during forest succession and highlight possibilities of, and potentially confounding signals affecting, the utility of leaf traits to understand community and species dynamics during secondary forest succession.
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Affiliation(s)
- Eben N. Broadbent
- Department of Global Ecology, Carnegie Institution for Science, Stanford, California, United States of America
- Department of Biology, Stanford University, Stanford, California, United States of America
- Sustainability Science Program, Kennedy School of Government, Harvard University, Cambridge, Massachusetts, United States of America
| | - Angélica M. Almeyda Zambrano
- Department of Global Ecology, Carnegie Institution for Science, Stanford, California, United States of America
- Sustainability Science Program, Kennedy School of Government, Harvard University, Cambridge, Massachusetts, United States of America
- Department of Anthropology, Stanford University, Stanford, California, United States of America
| | - Gregory P. Asner
- Department of Global Ecology, Carnegie Institution for Science, Stanford, California, United States of America
| | - Marlene Soriano
- Instituto Boliviano de Investigación Forestal, Santa Cruz de la Sierra, Bolivia
| | - Christopher B. Field
- Department of Global Ecology, Carnegie Institution for Science, Stanford, California, United States of America
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Harrison Ramos de Souza
- Centro de Investigación y Preservación de la Amazonia, Universidad Amazónica de Pando, Cobija, Bolivia
| | - Marielos Peña-Claros
- Instituto Boliviano de Investigación Forestal, Santa Cruz de la Sierra, Bolivia
- Forest Ecology and Forest Management Group, Wageningen University, Wageningen, the Netherlands
| | - Rachel I. Adams
- Plant and Microbial Biology, University of California, Berkeley, California, United States of America
| | - Rodolfo Dirzo
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Larry Giles
- Department of Global Ecology, Carnegie Institution for Science, Stanford, California, United States of America
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Lefcheck JS, Buchheister A, Laumann KM, Stratton MA, Sobocinski KL, Chak STC, Clardy TR, Reynolds PL, Latour RJ, Duffy JE. Dimensions of biodiversity in Chesapeake Bay demersal fishes: patterns and drivers through space and time. Ecosphere 2014. [DOI: 10.1890/es13-00284.1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Fowler D, Lessard JP, Sanders NJ. Niche filtering rather than partitioning shapes the structure of temperate forest ant communities. J Anim Ecol 2014; 83:943-52. [PMID: 24289457 DOI: 10.1111/1365-2656.12188] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 11/25/2013] [Indexed: 11/29/2022]
Abstract
An ever-increasing number of studies use tools from community phylogenetics to infer the processes underlying the assembly of communities. However, very few studies simultaneously use experimental approaches to characterize the ecological niches of species and directly assess the importance of these structuring processes. In this study, we developed an experimental approach for quantifying the use of four types of food resources and three habitat templets in temperate forest ant assemblages. We then used null models to assess whether niches overlapped more or less than expected by chance. Finally, we integrated comparative phylogenetic methods with experimental data on niche use to assess the degree of phylogenetic signal in several key components of the niche. We found that niche filtering, rather than partitioning, was the predominant structuring force. Niche filtering resulted from conservatism in habitat niches in evolutionary time and limitations in the availability of food resources in ecological time. Our study thus supports the idea that similarities in niches among species, rather than the differences, drive the assembly of ant communities.
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Affiliation(s)
- David Fowler
- Department of Ecology and Evolutionary Biology, University of Tennessee, 569 Dabney Hall, Knoxville, TN, 37996, USA
| | - Jean-Philippe Lessard
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, DK-2100, Denmark.,Department of Biology, Quebec Centre for Biodiversity Science, McGill University, Montreal, QC, H3A-1B1, Canada
| | - Nathan J Sanders
- Department of Ecology and Evolutionary Biology, University of Tennessee, 569 Dabney Hall, Knoxville, TN, 37996, USA.,Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, DK-2100, Denmark
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Seger GDS, Duarte LDS, Debastiani VJ, Kindel A, Jarenkow JA. Discriminating the effects of phylogenetic hypothesis, tree resolution and clade age estimates on phylogenetic signal measurements. PLANT BIOLOGY (STUTTGART, GERMANY) 2013; 15:858-867. [PMID: 23368095 DOI: 10.1111/j.1438-8677.2012.00699.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2012] [Accepted: 10/10/2012] [Indexed: 06/01/2023]
Abstract
Understanding how species traits evolved over time is the central question to comprehend assembly rules that govern the phylogenetic structure of communities. The measurement of phylogenetic signal (PS) in ecologically relevant traits is a first step to understand phylogenetically structured community patterns. The different methods available to estimate PS make it difficult to choose which is most appropriate. Furthermore, alternative phylogenetic tree hypotheses, node resolution and clade age estimates might influence PS measurements. In this study, we evaluated to what extent these parameters affect different methods of PS analysis, and discuss advantages and disadvantages when selecting which method to use. We measured fruit/seed traits and flowering/fruiting phenology of endozoochoric species occurring in Southern Brazilian Araucaria forests and evaluated their PS using Mantel regressions, phylogenetic eigenvector regressions (PVR) and K statistic. Mantel regressions always gave less significant results compared to PVR and K statistic in all combinations of phylogenetic trees constructed. Moreover, a better phylogenetic resolution affected PS, independently of the method used to estimate it. Morphological seed traits tended to show higher PS than diaspores traits, while PS in flowering/fruiting phenology depended mostly on the method used to estimate it. This study demonstrates that different PS estimates are obtained depending on the chosen method and the phylogenetic tree resolution. This finding has implications for inferences on phylogenetic niche conservatism or ecological processes determining phylogenetic community structure.
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Affiliation(s)
- G D S Seger
- Laboratório de Fitoecologia e Fitogeografia, Departamento de Botânica, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.
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Wolkovich EM, Davies TJ, Schaefer H, Cleland EE, Cook BI, Travers SE, Willis CG, Davis CC. Temperature-dependent shifts in phenology contribute to the success of exotic species with climate change. AMERICAN JOURNAL OF BOTANY 2013; 100:1407-21. [PMID: 23797366 DOI: 10.3732/ajb.1200478] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
PREMISE OF THE STUDY The study of how phenology may contribute to the assembly of plant communities has a long history in ecology. Climate change has brought renewed interest in this area, with many studies examining how phenology may contribute to the success of exotic species. In particular, there is increasing evidence that exotic species occupy unique phenological niches and track climate change more closely than native species. METHODS Here, we use long-term records of species’ first flowering dates from fi ve northern hemisphere temperate sites (Chinnor, UK and in the United States, Concord, Massachusetts; Fargo, North Dakota; Konza Prairie, Kansas; and Washington,D.C.) to examine whether invaders have distinct phenologies. Using a broad phylogenetic framework, we tested for differences between exotic and native species in mean annual flowering time, phenological changes in response to temperature and precipitation,and longer-term shifts in first flowering dates during recent pronounced climate change (“flowering time shifts”). KEY RESULTS Across North American sites, exotic species have shifted flowering with climate change while native species, on average, have not. In the three mesic systems, exotic species exhibited higher tracking of interannual variation in temperature,such that flowering advances more with warming, than native species. Across the two grassland systems, however, exotic species differed from native species primarily in responses to precipitation and soil moisture, not temperature. CONCLUSIONS Our findings provide cross-site support for the role of phenology and climate change in explaining species’ invasions.Further, they support recent evidence that exotic species may be important drivers of extended growing seasons observed with climate change in North America.
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Affiliation(s)
- Elizabeth M Wolkovich
- Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada.
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Best RJ, Stachowicz JJ. Phylogeny as a proxy for ecology in seagrass amphipods: which traits are most conserved? PLoS One 2013; 8:e57550. [PMID: 23505433 PMCID: PMC3591422 DOI: 10.1371/journal.pone.0057550] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Accepted: 01/25/2013] [Indexed: 11/24/2022] Open
Abstract
Increasingly, studies of community assembly and ecosystem function combine trait data and phylogenetic relationships to gain novel insight into the ecological and evolutionary constraints on community dynamics. However, the key to interpreting these two types of information is an understanding of the extent to which traits are phylogenetically conserved. In this study, we develop the necessary framework for community phylogenetics approaches in a system of marine crustacean herbivores that play an important role in the ecosystem functioning of seagrass systems worldwide. For 16 species of amphipods and isopods, we (1) reconstructed phylogenetic relationships using COI, 16S, and 18S sequences and Bayesian analyses, (2) measured traits that are potentially important for assembling species between and within habitats, and (3) compared the degree to which each of these traits are evolutionarily conserved. Despite poor phylogenetic resolution for the order Amphipoda as a whole, we resolved almost all of the topology for the species in our system, and used a sampling of ultrametric trees from the posterior distribution to account for remaining uncertainty in topology and branch lengths. We found that traits varied widely in their degree of phylogenetic signal. Body mass, fecundity, and tube building showed very strong phylogenetic signal, and temperature tolerance and feeding traits showed much less. As such, the degree of signal was not predictable based on whether the trait is related to environmental filtering or to resource partitioning. Further, we found that even with strong phylogenetic signal in body size, (which may have large impacts on ecosystem function), the predictive relationship between phylogenetic diversity and ecosystem function is not straightforward. We show that patterns of phylogenetic diversity in communities of seagrass mesograzers could lead to a variety of interpretations and predictions, and that detailed study of trait similarities and differences will be necessary to interpret these patterns.
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Affiliation(s)
- Rebecca J Best
- Department of Evolution and Ecology, University of California Davis, Davis, California, United States of America.
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Yessoufou K, Daru BH, Davies TJ. Phylogenetic patterns of extinction risk in the eastern arc ecosystems, an African biodiversity hotspot. PLoS One 2012; 7:e47082. [PMID: 23056587 PMCID: PMC3466253 DOI: 10.1371/journal.pone.0047082] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2012] [Accepted: 09/12/2012] [Indexed: 11/19/2022] Open
Abstract
There is an urgent need to reduce drastically the rate at which biodiversity is declining worldwide. Phylogenetic methods are increasingly being recognised as providing a useful framework for predicting future losses, and guiding efforts for pre-emptive conservation actions. In this study, we used a reconstructed phylogenetic tree of angiosperm species of the Eastern Arc Mountains - an important African biodiversity hotspot - and described the distribution of extinction risk across taxonomic ranks and phylogeny. We provide evidence for both taxonomic and phylogenetic selectivity in extinction risk. However, we found that selectivity varies with IUCN extinction risk category. Vulnerable species are more closely related than expected by chance, whereas endangered and critically endangered species are not significantly clustered on the phylogeny. We suggest that the general observation for taxonomic and phylogenetic selectivity (i.e. phylogenetic signal, the tendency of closely related species to share similar traits) in extinction risks is therefore largely driven by vulnerable species, and not necessarily the most highly threatened. We also used information on altitudinal distribution and climate to generate a predictive model of at-risk species richness, and found that greater threatened species richness is found at higher altitude, allowing for more informed conservation decision making. Our results indicate that evolutionary history can help predict plant susceptibility to extinction threats in the hyper-diverse but woefully-understudied Eastern Arc Mountains, and illustrate the contribution of phylogenetic approaches in conserving African floristic biodiversity where detailed ecological and evolutionary data are often lacking.
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Affiliation(s)
- Kowiyou Yessoufou
- African Centre for DNA Barcoding, University of Johannesburg, Gauteng, South Africa.
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