2701
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Quantification of the relative roles of niche and neutral processes in structuring gastrointestinal microbiomes. Proc Natl Acad Sci U S A 2012; 109:9692-8. [PMID: 22615407 DOI: 10.1073/pnas.1206721109] [Citation(s) in RCA: 123] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The theoretical description of the forces that shape ecological communities focuses around two classes of models. In niche theory, deterministic interactions between species, individuals, and the environment are considered the dominant factor, whereas in neutral theory, stochastic forces, such as demographic noise, speciation, and immigration, are dominant. Species abundance distributions predicted by the two classes of theory are difficult to distinguish empirically, making it problematic to deduce ecological dynamics from typical measures of diversity and community structure. Here, we show that the fusion of species abundance data with genome-derived measures of evolutionary distance can provide a clear indication of ecological dynamics, capable of quantifying the relative roles played by niche and neutral forces. We apply this technique to six gastrointestinal microbiomes drawn from three different domesticated vertebrates, using high-resolution surveys of microbial species abundance obtained from carefully curated deep 16S rRNA hypervariable tag sequencing data. Although the species abundance patterns are seemingly well fit by the neutral theory of metacommunity assembly, we show that this theory cannot account for the evolutionary patterns in the genomic data; moreover, our analyses strongly suggest that these microbiomes have, in fact, been assembled through processes that involve a significant nonneutral (niche) contribution. Our results demonstrate that high-resolution genomics can remove the ambiguities of process inference inherent in classic ecological measures and permits quantification of the forces shaping complex microbial communities.
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2702
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Streicker DG, Lemey P, Velasco-Villa A, Rupprecht CE. Rates of viral evolution are linked to host geography in bat rabies. PLoS Pathog 2012; 8:e1002720. [PMID: 22615575 PMCID: PMC3355098 DOI: 10.1371/journal.ppat.1002720] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2012] [Accepted: 04/10/2012] [Indexed: 02/03/2023] Open
Abstract
Rates of evolution span orders of magnitude among RNA viruses with important implications for viral transmission and emergence. Although the tempo of viral evolution is often ascribed to viral features such as mutation rates and transmission mode, these factors alone cannot explain variation among closely related viruses, where host biology might operate more strongly on viral evolution. Here, we analyzed sequence data from hundreds of rabies viruses collected from bats throughout the Americas to describe dramatic variation in the speed of rabies virus evolution when circulating in ecologically distinct reservoir species. Integration of ecological and genetic data through a comparative bayesian analysis revealed that viral evolutionary rates were labile following historical jumps between bat species and nearly four times faster in tropical and subtropical bats compared to temperate species. The association between geography and viral evolution could not be explained by host metabolism, phylogeny or variable selection pressures, and instead appeared to be a consequence of reduced seasonality in bat activity and virus transmission associated with climate. Our results demonstrate a key role for host ecology in shaping the tempo of evolution in multi-host viruses and highlight the power of comparative phylogenetic methods to identify the host and environmental features that influence transmission dynamics.
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Affiliation(s)
- Daniel G Streicker
- Odum School of Ecology, University of Georgia, Athens, Georgia, United States of America.
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2703
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Clavijo-Baque S, Bozinovic F. Testing the fitness consequences of the thermoregulatory and parental care models for the origin of endothermy. PLoS One 2012; 7:e37069. [PMID: 22606328 PMCID: PMC3351390 DOI: 10.1371/journal.pone.0037069] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2011] [Accepted: 04/15/2012] [Indexed: 11/18/2022] Open
Abstract
The origin of endothermy is a puzzling phenomenon in the evolution of vertebrates. To address this issue several explicative models have been proposed. The main models proposed for the origin of endothermy are the aerobic capacity, the thermoregulatory and the parental care models. Our main proposal is that to compare the alternative models, a critical aspect is to determine how strongly natural selection was influenced by body temperature, and basal and maximum metabolic rates during the evolution of endothermy. We evaluate these relationships in the context of three main hypotheses aimed at explaining the evolution of endothermy, namely the parental care hypothesis and two hypotheses related to the thermoregulatory model (thermogenic capacity and higher body temperature models). We used data on basal and maximum metabolic rates and body temperature from 17 rodent populations, and used intrinsic population growth rate (R(max)) as a global proxy of fitness. We found greater support for the thermogenic capacity model of the thermoregulatory model. In other words, greater thermogenic capacity is associated with increased fitness in rodent populations. To our knowledge, this is the first test of the fitness consequences of the thermoregulatory and parental care models for the origin of endothermy.
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Affiliation(s)
- Sabrina Clavijo-Baque
- Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile.
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2704
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Gilbert GS, Magarey R, Suiter K, Webb CO. Evolutionary tools for phytosanitary risk analysis: phylogenetic signal as a predictor of host range of plant pests and pathogens. Evol Appl 2012; 5:869-78. [PMID: 23346231 PMCID: PMC3552404 DOI: 10.1111/j.1752-4571.2012.00265.x] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Accepted: 03/28/2012] [Indexed: 11/28/2022] Open
Abstract
Assessing risk from a novel pest or pathogen requires knowing which local plant species are susceptible. Empirical data on the local host range of novel pests are usually lacking, but we know that some pests are more likely to attack closely related plant species than species separated by greater evolutionary distance. We use the Global Pest and Disease Database, an internal database maintained by the United States Department of Agriculture Animal and Plant Health Inspection Service - Plant Protection and Quarantine Division (USDA APHIS-PPQ), to evaluate the strength of the phylogenetic signal in host range for nine major groups of plant pests and pathogens. Eight of nine groups showed significant phylogenetic signal in host range. Additionally, pests and pathogens with more known hosts attacked a phylogenetically broader range of hosts. This suggests that easily obtained data - the number of known hosts and the phylogenetic distance between known hosts and other species of interest - can be used to predict which plant species are likely to be susceptible to a particular pest. This can facilitate rapid assessment of risk from novel pests and pathogens when empirical host range data are not yet available and guide efficient collection of empirical data for risk evaluation.
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Affiliation(s)
- Gregory S Gilbert
- Environmental Studies Department, University of California Santa Cruz, CA, USA ; Smithsonian Tropical Research Institute Balboa, Ancón, Panama
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2705
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Kennedy JD, Weir JT, Hooper DM, Tietze DT, Martens J, Price TD. ECOLOGICAL LIMITS ON DIVERSIFICATION OF THE HIMALAYAN CORE CORVOIDEA. Evolution 2012; 66:2599-613. [DOI: 10.1111/j.1558-5646.2012.01618.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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2706
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Hultgren KM, Duffy JE. Phylogenetic community ecology and the role of social dominance in sponge-dwelling shrimp. Ecol Lett 2012; 15:704-13. [DOI: 10.1111/j.1461-0248.2012.01788.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2011] [Revised: 01/19/2012] [Accepted: 03/26/2012] [Indexed: 11/30/2022]
Affiliation(s)
- Kristin M. Hultgren
- National Museum of Natural History; Smithsonian Institution; MRC 163, PO Box 37012; Washington; DC; 20013-7012; USA
| | - J. Emmett Duffy
- Virginia Institute of Marine Science; PO Box 1346; Gloucester Pt; VA; 23062-1346; USA
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2707
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Alvarez-Añorve MY, Quesada M, Sánchez-Azofeifa GA, Avila-Cabadilla LD, Gamon JA. Functional regeneration and spectral reflectance of trees during succession in a highly diverse tropical dry forest ecosystem. AMERICAN JOURNAL OF BOTANY 2012; 99:816-826. [PMID: 22523349 DOI: 10.3732/ajb.1100200] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
PREMISE OF THE STUDY The function of most ecosystems has been altered by human activities. To asses the recovery of plant communities, we must evaluate the recovery of plant functional traits. The seasonally dry tropical forest (SDTF), a highly threatened ecosystem, is assumed to recover relatively quickly from disturbance, but an integrated evaluation of recovery in floristic, structural, and functional terms has not been performed. In this study we aimed to (a) compare SDTF plant functional, floristic, and structural change along succession; (b) identify tree functional groups; and (c) explore the spectral properties of different successional stages. METHODS Across a SDTF successional gradient, we evaluated the change of species composition, vegetation structure, and leaf spectral reflectance and functional traits (related to water use, light acquisition, nutrient conservation, and CO(2) acquisition) of 25 abundant tree species. KEY RESULTS A complete recovery of SDTF takes longer than the time period inferred from floristic or structural data. Plant functional traits changed along succession from those that maximize photoprotection and heat dissipation in early succession, where temperature is an environmental constraint, to those that enhance light acquisition in late succession, where light may be limiting. A spectral indicator of plant photosynthetic performance (photochemical reflectance index) discriminated between early and late succession. This constitutes a foundation for further exploration of remote sensing technologies for studying tropical succession. CONCLUSIONS A functional approach should be incorporated as a regular descriptor of forest succession because it provides a richer understanding of vegetation dynamics than is offered by either the floristic or structural approach alone.
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Affiliation(s)
- Mariana Y Alvarez-Añorve
- Universidad Nacional Autónoma de México, Centro de Investigaciones en Ecosistemas, Apartado Postal 27-3 (Xangari), Morelia, Michoacan, Mexico
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2708
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Tan J, Pu Z, Ryberg WA, Jiang L. Species phylogenetic relatedness, priority effects, and ecosystem functioning. Ecology 2012; 93:1164-72. [DOI: 10.1890/11-1557.1] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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2709
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González-Caro S, Parra JL, Graham CH, McGuire JA, Cadena CD. Sensitivity of metrics of phylogenetic structure to scale, source of data and species pool of hummingbird assemblages along elevational gradients. PLoS One 2012; 7:e35472. [PMID: 22558157 PMCID: PMC3338702 DOI: 10.1371/journal.pone.0035472] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2011] [Accepted: 03/19/2012] [Indexed: 12/02/2022] Open
Abstract
Patterns of phylogenetic structure of assemblages are increasingly used to gain insight into the ecological and evolutionary processes involved in the assembly of co-occurring species. Metrics of phylogenetic structure can be sensitive to scaling issues and data availability. Here we empirically assess the sensitivity of four metrics of phylogenetic structure of assemblages to changes in (i) the source of data, (ii) the spatial grain at which assemblages are defined, and (iii) the definition of species pools using hummingbird (Trochilidae) assemblages along an elevational gradient in Colombia. We also discuss some of the implications in terms of the potential mechanisms driving these patterns. To explore how source of data influence phylogenetic structure we defined assemblages using three sources of data: field inventories, museum specimens, and range maps. Assemblages were defined at two spatial grains: coarse-grained (elevational bands of 800-m width) and fine-grained (1-km2 plots). We used three different species pools: all species contained in assemblages, all species within half-degree quadrats, and all species either above or below 2000 m elevation. Metrics considering phylogenetic relationships among all species within assemblages showed phylogenetic clustering at high elevations and phylogenetic evenness in the lowlands, whereas those metrics considering only the closest co-occurring relatives showed the opposite trend. This result suggests that using multiple metrics of phylogenetic structure should provide greater insight into the mechanisms shaping assemblage structure. The source and spatial grain of data had important influences on estimates of both richness and phylogenetic structure. Metrics considering the co-occurrence of close relatives were particularly sensitive to changes in the spatial grain. Assemblages based on range maps included more species and showed less phylogenetic structure than assemblages based on museum or field inventories. Coarse-grained assemblages included more distantly related species and thus showed a more even phylogenetic structure than fine-grained assemblages. Our results emphasize the importance of carefully selecting the scale, source of data and metric used in analysis of the phylogenetic structure of assemblages.
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Affiliation(s)
- Sebastián González-Caro
- Laboratorio de Biología Evolutiva de Vertebrados, Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, Colombia
| | - Juan L. Parra
- Instituto de Biología, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia, Medellín, Colombia
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, United States of America
- * E-mail:
| | - Catherine H. Graham
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, United States of America
| | - Jimmy A. McGuire
- Department of Integrative Biology, University of California, Berkeley, California, United States of America
| | - Carlos Daniel Cadena
- Laboratorio de Biología Evolutiva de Vertebrados, Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, Colombia
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2710
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Cenozoic imprints on the phylogenetic structure of palm species assemblages worldwide. Proc Natl Acad Sci U S A 2012; 109:7379-84. [PMID: 22529387 DOI: 10.1073/pnas.1120467109] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Despite long-standing interest in the origin and maintenance of species diversity, little is known about historical drivers of species assemblage structure at large spatiotemporal scales. Here, we use global species distribution data, a dated genus-level phylogeny, and paleo-reconstructions of biomes and climate to examine Cenozoic imprints on the phylogenetic structure of regional species assemblages of palms (Arecaceae), a species-rich plant family characteristic of tropical ecosystems. We find a strong imprint on phylogenetic clustering due to geographic isolation and in situ diversification, especially in the Neotropics and on islands with spectacular palm radiations (e.g., Madagascar, Hawaii, and Cuba). Phylogenetic overdispersion on mainlands and islands corresponds to biotic interchange areas. Differences in the degree of phylogenetic clustering among biogeographic realms are related to differential losses of tropical rainforests during the Cenozoic, but not to the cumulative area of tropical rainforest over geological time. A largely random phylogenetic assemblage structure in Africa coincides with severe losses of rainforest area, especially after the Miocene. More recent events also appear to be influential: phylogenetic clustering increases with increasing intensity of Quaternary glacial-interglacial climatic oscillations in South America and, to a lesser extent, Africa, indicating that specific clades perform better in climatically unstable regions. Our results suggest that continental isolation (in combination with limited long-distance dispersal) and changing climate and habitat loss throughout the Cenozoic have had strong impacts on the phylogenetic structure of regional species assemblages in the tropics.
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2711
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Münkemüller T, Lavergne S, Bzeznik B, Dray S, Jombart T, Schiffers K, Thuiller W. How to measure and test phylogenetic signal. Methods Ecol Evol 2012. [DOI: 10.1111/j.2041-210x.2012.00196.x] [Citation(s) in RCA: 613] [Impact Index Per Article: 51.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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2712
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Printzen C, Fernández-Mendoza F, Muggia L, Berg G, Grube M. Alphaproteobacterial communities in geographically distant populations of the lichen Cetraria aculeata. FEMS Microbiol Ecol 2012; 82:316-25. [PMID: 22469494 DOI: 10.1111/j.1574-6941.2012.01358.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Revised: 03/05/2012] [Accepted: 03/06/2012] [Indexed: 12/01/2022] Open
Abstract
Lichen symbioses were recently shown to include diverse bacterial communities. Although the biogeography of lichen species is fairly well known, the patterns of their bacterial associates are relatively poorly understood. Here we analyse the composition of Alphaproteobacteria in Cetraria aculeata, a common lichen species that occurs at high latitudes and various habitats. Using clone libraries we show that most of the associated Alphaproteobacteria belong to Acetobacteraceae, which have also been found previously in other lichen species of acidic soils and rocks in alpine habitats. The majority of alphaproteobacterial sequences from C. aculeata are very similar to each other and form a single clade. Data from C. aculeata reveal that alphaproteobacterial communities of high latitudes are depauperate and more closely related to each other than to those of extrapolar habitats. This agrees with previous findings for the fungal and algal symbiont in this lichen. Similar to the algal partner, the composition of lichen alphaproteobacterial communities is affected by environmental parameters.
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Affiliation(s)
- Christian Printzen
- Senckenberg Forschungsinstitut und Naturmuseum, Abt. Botanik und Molekulare Evolutionsforschung, Frankfurt am Main, Germany.
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2713
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Krasnov BR, Fortuna MA, Mouillot D, Khokhlova IS, Shenbrot GI, Poulin R. Phylogenetic Signal in Module Composition and Species Connectivity in Compartmentalized Host-Parasite Networks. Am Nat 2012; 179:501-11. [DOI: 10.1086/664612] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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2714
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Wang J, Soininen J, He J, Shen J. Phylogenetic clustering increases with elevation for microbes. ENVIRONMENTAL MICROBIOLOGY REPORTS 2012; 4:217-226. [PMID: 23757276 DOI: 10.1111/j.1758-2229.2011.00324.x] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Although phylogenetic approaches are useful for providing insights into the processes underlying biodiversity patterns, the studies of microbial phylogenetic relatedness are rare, especially for elevational gradients. Using high-throughput pyrosequencing, we examined the biodiversity patterns for biofilm bacterial communities that were scraped from stream stones along an elevational gradient from 1820 to 4050 m in China. The patterns of bacterial species richness and phylogenetic diversity were hollow towards higher elevations. The bacterial communities consisted of closer relatives than expected and displayed increasing terminal phylogenetic clustering towards mountain top. The increasing phylogenetic clustering with elevation contrasts reports for macroorganisms that revealed phylogenetic overdispersion at low or intermediate elevations. Because water temperature showed the strongest correlation with phylogenetic relatedness (r(2) = 0.516), the elevational pattern in the bacterial phylogenetic structure indicated that environmental filtering possibly due to lower temperature or more frequent temperature fluctuations increased towards higher elevations. Evidence supporting the environmental filtering on bacteria was also reflected by the orderly succession in the relative abundance of different bacterial phyla along the elevational gradient and in the high evenness of bacterial taxa at higher elevations. Overall, our results indicated that ecological processes possibly related to temperature may play a dominant role in structuring bacterial biodiversity along the elevational gradient.
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Affiliation(s)
- Jianjun Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008 China State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085 China Department of Environmental Sciences, PO Box 65, FIN-00014, University of Helsinki, Finland
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2715
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Boucher FC, Thuiller W, Roquet C, Douzet R, Aubert S, Alvarez N, Lavergne S. Reconstructing the origins of high-alpine niches and cushion life form in the genus Androsace S.L. (Primulaceae). Evolution 2012; 66:1255-68. [PMID: 22486702 PMCID: PMC3999638 DOI: 10.1111/j.1558-5646.2011.01483.x] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Relatively, few species have been able to colonize extremely cold alpine environments. We investigate the role played by the cushion life form in the evolution of climatic niches in the plant genus Androsace s.l., which spreads across the mountain ranges of the Northern Hemisphere. Using robust methods that account for phylogenetic uncertainty, intraspecific variability of climatic requirements and different life-history evolution scenarios, we show that climatic niches of Androsace s.l. exhibit low phylogenetic signal and that they evolved relatively recently and punctually. Models of niche evolution fitted onto phylogenies show that the cushion life form has been a key innovation providing the opportunity to occupy extremely cold environments, thus contributing to rapid climatic niche diversification in the genus Androsace s.l. We then propose a plausible scenario for the adaptation of plants to alpine habitats.
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2716
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Abstract
A substantial proportion of the world's living species, including one-third of the reef-building corals, are threatened with extinction and in pressing need of conservation action. In order to reduce biodiversity loss, it is important to consider species' contribution to evolutionary diversity along with their risk of extinction for the purpose of setting conservation priorities. Here I reconstruct the most comprehensive tree of life for the order Scleractinia (1,293 species) that includes all 837 living reef species, and employ a composite measure of phylogenetic distinctiveness and extinction risk to identify the most endangered lineages that would not be given top priority on the basis of risk alone. The preservation of these lineages, not just the threatened species, is vital for safeguarding evolutionary diversity. Tests for phylogeny-associated patterns show that corals facing elevated extinction risk are not clustered on the tree, but species that are susceptible, resistant or resilient to impacts such as bleaching and disease tend to be close relatives. Intensification of these threats or extirpation of the endangered lineages could therefore result in disproportionate pruning of the coral tree of life.
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Affiliation(s)
- Danwei Huang
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America.
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2717
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Erickson GM, Gignac PM, Steppan SJ, Lappin AK, Vliet KA, Brueggen JD, Inouye BD, Kledzik D, Webb GJW. Insights into the ecology and evolutionary success of crocodilians revealed through bite-force and tooth-pressure experimentation. PLoS One 2012; 7:e31781. [PMID: 22431965 PMCID: PMC3303775 DOI: 10.1371/journal.pone.0031781] [Citation(s) in RCA: 103] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2011] [Accepted: 01/19/2012] [Indexed: 12/14/2022] Open
Abstract
Background Crocodilians have dominated predatory niches at the water-land interface for over 85 million years. Like their ancestors, living species show substantial variation in their jaw proportions, dental form and body size. These differences are often assumed to reflect anatomical specialization related to feeding and niche occupation, but quantified data are scant. How these factors relate to biomechanical performance during feeding and their relevance to crocodilian evolutionary success are not known. Methodology/Principal Findings We measured adult bite forces and tooth pressures in all 23 extant crocodilian species and analyzed the results in ecological and phylogenetic contexts. We demonstrate that these reptiles generate the highest bite forces and tooth pressures known for any living animals. Bite forces strongly correlate with body size, and size changes are a major mechanism of feeding evolution in this group. Jaw shape demonstrates surprisingly little correlation to bite force and pressures. Bite forces can now be predicted in fossil crocodilians using the regression equations generated in this research. Conclusions/Significance Critical to crocodilian long-term success was the evolution of a high bite-force generating musculo-skeletal architecture. Once achieved, the relative force capacities of this system went essentially unmodified throughout subsequent diversification. Rampant changes in body size and concurrent changes in bite force served as a mechanism to allow access to differing prey types and sizes. Further access to the diversity of near-shore prey was gained primarily through changes in tooth pressure via the evolution of dental form and distributions of the teeth within the jaws. Rostral proportions changed substantially throughout crocodilian evolution, but not in correspondence with bite forces. The biomechanical and ecological ramifications of such changes need further examination.
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Affiliation(s)
- Gregory M Erickson
- Department of Biological Science, Florida State University, Tallahassee, Florida, United States of America.
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2718
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Kooyman R, Rossetto M, Allen C, Cornwell W. Australian Tropical and Subtropical Rain Forest Community Assembly: Phylogeny, Functional Biogeography, and Environmental Gradients. Biotropica 2012. [DOI: 10.1111/j.1744-7429.2012.00861.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
| | - Maurizio Rossetto
- National Herbarium of New South Wales; the Royal Botanic Gardens and Domain Trust; Mrs Macquaries Road; 2000; Sydney; NSW; Australia
| | - Chris Allen
- National Herbarium of New South Wales; the Royal Botanic Gardens and Domain Trust; Mrs Macquaries Road; 2000; Sydney; NSW; Australia
| | - William Cornwell
- Vrije Universiteit Amsterdam; Faculty of Earth and Life Sciences, Systems Ecology; De Boelelaan; 1085; 1081 HV Amsterdam; The Netherlands
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2719
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Hidasi-Neto J, Barlow J, Cianciaruso MV. Bird functional diversity and wildfires in the Amazon: the role of forest structure. Anim Conserv 2012. [DOI: 10.1111/j.1469-1795.2012.00528.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- J. Hidasi-Neto
- Departamento de Ecologia; Universidade Federal de Goiás; Goiânia; GO; Brazil
| | - J. Barlow
- Lancaster Environment Centre; Lancaster University; Lancaster; UK
| | - M. V. Cianciaruso
- Departamento de Ecologia; Universidade Federal de Goiás; Goiânia; GO; Brazil
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2720
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Reverchon F, Ortega-Larrocea M, Bonilla-Rosso G, Pérez-Moreno J. Structure and species composition of ectomycorrhizal fungal communities colonizing seedlings and adult trees of Pinus montezumae in Mexican neotropical forests. FEMS Microbiol Ecol 2012; 80:479-87. [DOI: 10.1111/j.1574-6941.2012.01314.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Revised: 01/15/2012] [Accepted: 01/16/2012] [Indexed: 11/28/2022] Open
Affiliation(s)
- Frédérique Reverchon
- Instituto de Geología; Universidad Nacional Autónoma de México (UNAM); México D.F; Mexico
| | - María Ortega-Larrocea
- Instituto de Geología; Universidad Nacional Autónoma de México (UNAM); México D.F; Mexico
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2721
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Saar L, Takkis K, Pärtel M, Helm A. Which plant traits predict species loss in calcareous grasslands with extinction debt? DIVERS DISTRIB 2012. [DOI: 10.1111/j.1472-4642.2012.00885.x] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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2722
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MERCKX VINCENTSFT, JANSSENS STEVENB, HYNSON NICOLEA, SPECHT CHELSEAD, BRUNS THOMASD, SMETS ERIKF. Mycoheterotrophic interactions are not limited to a narrow phylogenetic range of arbuscular mycorrhizal fungi. Mol Ecol 2012; 21:1524-32. [DOI: 10.1111/j.1365-294x.2012.05472.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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2723
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Gleason SM, Butler DW, Ziemińska K, Waryszak P, Westoby M. Stem xylem conductivity is key to plant water balance across Australian angiosperm species. Funct Ecol 2012. [DOI: 10.1111/j.1365-2435.2012.01962.x] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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2724
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Miller ZJ. Fungal Pathogen Species Richness: Why Do Some Plant Species Have More Pathogens than Others? Am Nat 2012; 179:282-92. [DOI: 10.1086/663676] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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2725
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Hammond JI, Jones DK, Stephens PR, Relyea RA. Phylogeny meets ecotoxicology: evolutionary patterns of sensitivity to a common insecticide. Evol Appl 2012; 5:593-606. [PMID: 23028400 PMCID: PMC3461142 DOI: 10.1111/j.1752-4571.2011.00237.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2011] [Accepted: 12/13/2011] [Indexed: 11/27/2022] Open
Abstract
Pesticides commonly occur in aquatic systems and pose a substantial challenge to the conservation of many taxa. Ecotoxicology has traditionally met this challenge by focusing on short-term, single-species tests and conducting risk assessments based on the most sensitive species tested. Rarely have ecotoxicology data been examined from an evolutionary perspective, and to our knowledge, there has never been a phylogenetic analysis of sensitivity, despite the fact that doing so would provide insights into patterns of sensitivity among species and identify which clades are the most sensitive to a particular pesticide. We examined phylogenetic patterns of pesticide sensitivity in amphibians, a group of conservation concern owing to global population declines. Using the insecticide endosulfan, we combined previously published results across seven species of tadpoles and added eight additional species from the families Bufonidae, Hylidae, and Ranidae. We found significant phylogenetic signal in the sensitivity to the insecticide and in the existence of time lag effects on tadpole mortality. Bufonids were less sensitive than hylids, which were less sensitive than the ranids. Moreover, mortality time lags were common in ranids, occasional in hylids, and rare in bufonids. These results highlight the importance of an evolutionary perspective and offer important insights for conservation.
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Affiliation(s)
- John I Hammond
- Department of Biological Sciences, University of Pittsburgh Pittsburgh, PA, USA
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2726
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Compositional and phylogenetic dissimilarity of host communities drives dissimilarity of ectoparasite assemblages: geographical variation and scale-dependence. Parasitology 2012; 139:338-47. [DOI: 10.1017/s0031182011002058] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
SUMMARYWe tested the hypothesis that compositional and/or phylogenetic dissimilarity of host assemblages affect compositional and/or phylogenetic dissimilarity of parasite assemblages, to different extents depending on scale, using regional surveys of fleas parasitic on small mammals from 4 biogeographical realms. Using phylogenetic community dissimilarity metric, we calculated the compositional and phylogenetic dissimilarity components between all pairs of host and parasite communities within realms and hemispheres. We then quantified the effect of compositional or phylogenetic dissimilarity in host regional assemblages, and geographical distance between assemblages, on the compositional or phylogenetic dissimilarity of flea regional assemblages within a realm, respectively. The compositional dissimilarity in host assemblages strongly affected compositional dissimilarity in flea assemblages within all realms and within both hemispheres. However, the effect of phylogenetic dissimilarity of host assemblages on that of flea assemblages was mostly confined to the Neotropics and Nearctic, but was detected in both the Old and New World at the higher scale, possibly because of phylogenetic heterogeneity in flea and host faunas between realms. The clearer effect of the compositional rather than the phylogenetic component of host community dissimilarity on flea community dissimilarity suggests important roles for host switching and ecological fitting during the assembly history of flea communities.
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2727
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Litsios G, Salamin N. Effects of Phylogenetic Signal on Ancestral State Reconstruction. Syst Biol 2012; 61:533-8. [DOI: 10.1093/sysbio/syr124] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Affiliation(s)
- Glenn Litsios
- Department of Ecology and Evolution, Biophore, University of Lausanne, 1015 Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland
| | - Nicolas Salamin
- Department of Ecology and Evolution, Biophore, University of Lausanne, 1015 Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland
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2728
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Abstract
Ecologists and conservation biologists are increasingly focusing on quantifying the phylogenetic component of biodiversity in order to inform basic and applied research. A major obstacle of this approach in tropical ecosystems has been the difficulty of generating high-quality phylogenetic trees for the vast numbers of species in these systems. Phylogenetic trees inferred from DNA barcodes hold the potential to overcome this obstacle. Here, I present a methodological framework for analyzing the phylogenetic alpha and beta diversity of ecological communities using a phylogenetic tree. The analytical approach is presented using the freely available and widely used software platform "R".
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Affiliation(s)
- Nathan G Swenson
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA.
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2729
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Cardillo M. Phylogenetic structure of mammal assemblages at large geographical scales: linking phylogenetic community ecology with macroecology. Philos Trans R Soc Lond B Biol Sci 2011; 366:2545-53. [PMID: 21807735 DOI: 10.1098/rstb.2011.0021] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Phylogenetic community ecology seeks to explain the processes involved in the formation of species assemblages by analysing their phylogenetic structure, and to date has focused primarily on local-scale communities. Macroecology, on the other hand, is concerned with the structure of assemblages at large geographical scales, but has remained largely non-phylogenetic. Analysing the phylogenetic structure of large-scale assemblages provides a link between these two research programmes. In this paper, I ask whether we should expect large-scale assemblages to show significant phylogenetic structure, by outlining some of the ecological and macroevolutionary processes that may play a role in assemblage formation. As a case study, I then explore the phylogenetic structure of carnivore assemblages within the terrestrial ecoregions of Africa. Many assemblages at these scales are indeed phylogenetically non-random (either clustered or overdispersed). One interpretation of the observed patterns of phylogenetic structure is that many clades underwent rapid biome-filling radiations, followed by diversification slowdown and competitive sorting as niche space became saturated.
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Affiliation(s)
- Marcel Cardillo
- Centre for Macroevolution and Macroecology, Research School of Biology, Australian National University, Canberra, Australian Capital Territory
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2730
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Abellán P, Ribera I. Geographic location and phylogeny are the main determinants of the size of the geographical range in aquatic beetles. BMC Evol Biol 2011; 11:344. [PMID: 22122885 PMCID: PMC3247920 DOI: 10.1186/1471-2148-11-344] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2011] [Accepted: 11/28/2011] [Indexed: 11/10/2022] Open
Abstract
Background Why some species are widespread while others are very restricted geographically is one of the most basic questions in biology, although it remains largely unanswered. This is particularly the case for groups of closely related species, which often display large differences in the size of the geographical range despite sharing many other factors due to their common phylogenetic inheritance. We used ten lineages of aquatic Coleoptera from the western Palearctic to test in a comparative framework a broad set of possible determinants of range size: species' age, differences in ecological tolerance, dispersal ability and geographic location. Results When all factors were combined in multiple regression models between 60-98% of the variance was explained by geographic location and phylogenetic signal. Maximum latitudinal and longitudinal limits were positively correlated with range size, with species at the most northern latitudes and eastern longitudes displaying the largest ranges. In lineages with lotic and lentic species, the lentic (better dispersers) display larger distributional ranges than the lotic species (worse dispersers). The size of the geographical range was also positively correlated with the extent of the biomes in which the species is found, but we did not find evidence of a clear relationship between range size and age of the species. Conclusions Our findings show that range size of a species is shaped by an interplay of geographic and ecological factors, with a phylogenetic component affecting both of them. The understanding of the factors that determine the size and geographical location of the distributional range of species is fundamental to the study of the origin and assemblage of the current biota. Our results show that for this purpose the most relevant data may be the phylogenetic history of the species and its geographical location.
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Affiliation(s)
- Pedro Abellán
- Institute of Evolutionary Biology, CSIC-UPF, Barcelona, Spain.
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2731
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Smith ND. BODY MASS AND FORAGING ECOLOGY PREDICT EVOLUTIONARY PATTERNS OF SKELETAL PNEUMATICITY IN THE DIVERSE “WATERBIRD” CLADE. Evolution 2011; 66:1059-78. [DOI: 10.1111/j.1558-5646.2011.01494.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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2732
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Liu X, Liang M, Etienne RS, Wang Y, Staehelin C, Yu S. Experimental evidence for a phylogenetic Janzen-Connell effect in a subtropical forest. Ecol Lett 2011; 15:111-8. [PMID: 22082078 DOI: 10.1111/j.1461-0248.2011.01715.x] [Citation(s) in RCA: 205] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xubing Liu
- Department of Ecology, School of Life Sciences/State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
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2733
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2734
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Analysis of the community structure of abyssal kinetoplastids revealed similar communities at larger spatial scales. ISME JOURNAL 2011; 6:713-23. [PMID: 22071346 DOI: 10.1038/ismej.2011.138] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Knowledge of the spatial scales of diversity is necessary to evaluate the mechanisms driving biodiversity and biogeography in the vast but poorly understood deep sea. The community structure of kinetoplastids, an important group of microbial eukaryotes belonging to the Euglenozoa, from all abyssal plains of the South Atlantic and two areas of the eastern Mediterranean was studied using partial small subunit ribosomal DNA gene clone libraries. A total of 1364 clones from 10 different regions were retrieved. The analysis revealed statistically not distinguishable communities from both the South-East Atlantic (Angola and Guinea Basin) and the South-West Atlantic (Angola and Brazil Basin) at spatial scales of 1000-3000 km, whereas all other communities were significantly differentiated from one another. It seems likely that multiple processes operate at the same time to shape communities of deep-sea kinetoplastids. Nevertheless, constant and homogenous environmental conditions over large spatial scales at abyssal depths, together with high dispersal capabilities of microbial eukaryotes, maintain best the results of statistically indistinguishable communities at larger spatial scales.
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2735
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Jenkins T, Thomas GH, Hellgren O, Owens IPF. Migratory behavior of birds affects their coevolutionary relationship with blood parasites. Evolution 2011; 66:740-751. [PMID: 22380437 DOI: 10.1111/j.1558-5646.2011.01470.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Host traits, such as migratory behavior, could facilitate the dispersal of disease-causing parasites, potentially leading to the transfer of infections both across geographic areas and between host species. There is, however, little quantitative information on whether variation in such host attributes does indeed affect the evolutionary outcome of host-parasite associations. Here, we employ Leucocytozoon blood parasites of birds, a group of parasites closely related to avian malaria, to study host-parasite coevolution in relation to host behavior using a phylogenetic comparative approach. We reconstruct the molecular phylogenies of both the hosts and parasites and use cophylogenetic tools to assess whether each host-parasite association contributes significantly to the overall congruence between the two phylogenies. We find evidence for a significant fit between host and parasite phylogenies in this system, but show that this is due only to associations between nonmigrant parasites and their hosts. We also show that migrant bird species harbor a greater genetic diversity of parasites compared with nonmigrant species. Taken together, these results suggest that the migratory habits of birds could influence their coevolutionary relationship with their parasites, and that consideration of host traits is important in predicting the outcome of coevolutionary interactions.
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Affiliation(s)
- Tania Jenkins
- NERC Centre for Population Biology & Division of Biology, Department of Life Sciences, Imperial College London, Silwood Park, Ascot, Berkshire SL5 7PY, United Kingdom E-mail: and Molecular Population Genetics, Institute for Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH-3012 Bern, SwitzerlandSchool of Biological Sciences, University of Bristol, Woodland Road, Bristol BS8 IUG, United KingdomDepartment of Animal Ecology Animal Ecology Building Lund University, SE-22362 Lund, Sweden
| | - Gavin H Thomas
- NERC Centre for Population Biology & Division of Biology, Department of Life Sciences, Imperial College London, Silwood Park, Ascot, Berkshire SL5 7PY, United Kingdom E-mail: and Molecular Population Genetics, Institute for Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH-3012 Bern, SwitzerlandSchool of Biological Sciences, University of Bristol, Woodland Road, Bristol BS8 IUG, United KingdomDepartment of Animal Ecology Animal Ecology Building Lund University, SE-22362 Lund, Sweden
| | - Olof Hellgren
- NERC Centre for Population Biology & Division of Biology, Department of Life Sciences, Imperial College London, Silwood Park, Ascot, Berkshire SL5 7PY, United Kingdom E-mail: and Molecular Population Genetics, Institute for Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH-3012 Bern, SwitzerlandSchool of Biological Sciences, University of Bristol, Woodland Road, Bristol BS8 IUG, United KingdomDepartment of Animal Ecology Animal Ecology Building Lund University, SE-22362 Lund, Sweden
| | - Ian P F Owens
- NERC Centre for Population Biology & Division of Biology, Department of Life Sciences, Imperial College London, Silwood Park, Ascot, Berkshire SL5 7PY, United Kingdom E-mail: and Molecular Population Genetics, Institute for Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH-3012 Bern, SwitzerlandSchool of Biological Sciences, University of Bristol, Woodland Road, Bristol BS8 IUG, United KingdomDepartment of Animal Ecology Animal Ecology Building Lund University, SE-22362 Lund, Sweden
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2736
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Couvreur TLP, Porter-Morgan H, Wieringa JJ, Chatrou LW. Little ecological divergence associated with speciation in two African rain forest tree genera. BMC Evol Biol 2011; 11:296. [PMID: 21985574 PMCID: PMC3203876 DOI: 10.1186/1471-2148-11-296] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2011] [Accepted: 10/11/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The tropical rain forests (TRF) of Africa are the second largest block of this biome after the Amazon and exhibit high levels of plant endemism and diversity. Two main hypotheses have been advanced to explain speciation processes that have led to this high level of biodiversity: allopatric speciation linked to geographic isolation and ecological speciation linked to ecological gradients. Both these hypotheses rely on ecology: in the former conservation of ecological niches through time is implied, while in the latter adaptation via selection to alternative ecological niches would be a prerequisite. Here, we investigate the role of ecology in explaining present day species diversity in African TRF using a species level phylogeny and ecological niche modeling of two predominantly restricted TRF tree genera, Isolona and Monodora (Annonaceae). Both these genera, with 20 and 14 species, respectively, are widely distributed in African TRFs, with a few species occurring in slightly less humid regions such as in East Africa. RESULTS A total of 11 sister species pairs were identified most of them occurring in allopatry or with little geographical overlap. Our results provide a mixed answer on the role of ecology in speciation. Although no sister species have identical niches, just under half of the tests suggest that sister species do have more similar niches than expected by chance. PCA analyses also support little ecological differences between sister species. Most speciation events within both genera predate the Pleistocene, occurring during the Late Miocene and Pliocene periods. CONCLUSIONS Ecology is almost always involved in speciation, however, it would seem to have had a little role in species generation within Isolona and Monodora at the scale analyzed here. This is consistent with the geographical speciation model for TRF diversification. These results contrast to other studies for non-TRF plant species where ecological speciation was found to be an important factor of diversification. The Pliocene period appears to be a vital time in the generation of African TRF diversity, whereas Pleistocene climatic fluctuations have had a smaller role on speciation than previously thought.Ecological niche modeling, species level phylogeny, ecological speciation, African tropics, Isolona, Monodora, Annonaceae.
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Affiliation(s)
- Thomas L P Couvreur
- Institut de Recherche pour le Développement (IRD), UMR DIA-DE, DYNADIV researche group, 911, avenue Agropolis, BP 64501, F-34394 Montpellier cedex 5, France.
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2737
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Flynn DFB, Mirotchnick N, Jain M, Palmer MI, Naeem S. Functional and phylogenetic diversity as predictors of biodiversity--ecosystem-function relationships. Ecology 2011; 92:1573-81. [PMID: 21905424 DOI: 10.1890/10-1245.1] [Citation(s) in RCA: 344] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
How closely does variability in ecologically important traits reflect evolutionary divergence? The use of phylogenetic diversity (PD) to predict biodiversity effects on ecosystem functioning, and more generally the use of phylogenetic information in community ecology, depends in part on the answer to this question. However, comparisons of the predictive power of phylogenetic diversity and functional diversity (FD) have not been conducted across a range of experiments. To address how phylogenetic diversity and functional trait variation control biodiversity effects on biomass production, we summarized the results of 29 grassland plant experiments where both the phylogeny of plant species used in the experiments is well described and where extensive trait data are available. Functional trait variation was only partially related to phylogenetic distances between species, and the resulting FD values therefore correlate only partially with PD. Despite these differences, FD and PD predicted biodiversity effects across all experiments with similar strength, including in subsets that excluded plots with legumes and that focused on fertilization experiments. Two- and three-trait combinations of the five traits used here (leaf nitrogen percentage, height, specific root length, leaf mass per unit area, and nitrogen fixation) resulted in the FD values with the greatest predictive power. Both PD and FD can be valuable predictors of the effect of biodiversity on ecosystem functioning, which suggests that a focus on both community trait diversity and evolutionary history can improve understanding of the consequences of biodiversity loss.
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Affiliation(s)
- Dan F B Flynn
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, 1200 Amsterdam Avenue, Schermerhorn Extension, New York, New York 10027, USA.
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2738
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Jacquemyn H, Merckx V, Brys R, Tyteca D, Cammue BPA, Honnay O, Lievens B. Analysis of network architecture reveals phylogenetic constraints on mycorrhizal specificity in the genus Orchis (Orchidaceae). THE NEW PHYTOLOGIST 2011; 192:518-28. [PMID: 21668874 DOI: 10.1111/j.1469-8137.2011.03796.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The specificity of orchids for their fungi can vary substantially, from highly specialist interactions to more generalist interactions, but little is known about the evolutionary history of the mycorrhizal specificity of orchids. Here, we used a network analysis approach to investigate orchid mycorrhizal associations in 16 species of the genus Orchis sampled across 11 different regions in Europe. We first examined in detail the structure of the network of associations and then tested for a phylogenetic signal in mycorrhizal specificity and identified the fungi with which the orchids associated. We found 20 different fungal lineages that associated with species of the genus Orchis, most of them being related to members of the Tulasnellaceae (84.33% of all identified associations) and a smaller proportion being related to members of the Ceratobasidiaceae (9.97%). Species associations formed a nested network that is built on asymmetric links among species. Evolution of mycorrhizal specificity in Orchis closely resembles a Brownian motion process, and the interaction between Orchis and Tulasnellaceae fungi is significantly influenced by the phylogenetic relationships between the Orchis species. Our results provide evidence of the presence of phylogenetic conservatism in mycorrhizal specificity in orchids and demonstrate that evolutionary processes may be an important factor in generating patterns of mycorrhizal associations.
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2739
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Zaneveld JRR, Parfrey LW, Van Treuren W, Lozupone C, Clemente JC, Knights D, Stombaugh J, Kuczynski J, Knight R. Combined phylogenetic and genomic approaches for the high-throughput study of microbial habitat adaptation. Trends Microbiol 2011; 19:472-82. [PMID: 21872475 PMCID: PMC3184378 DOI: 10.1016/j.tim.2011.07.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2011] [Revised: 07/22/2011] [Accepted: 07/25/2011] [Indexed: 01/21/2023]
Abstract
High-throughput sequencing technologies provide new opportunities to address longstanding questions about habitat adaptation in microbial organisms. How have microbes managed to adapt to such a wide range of environments, and what genomic features allow for such adaptation? We review recent large-scale studies of habitat adaptation, with emphasis on those that utilize phylogenetic techniques. On the basis of current trends, we summarize methodological challenges faced by investigators, and the tools, techniques and analytical approaches available to overcome them. Phylogenetic approaches and detailed information about each environmental sample will be crucial as the ability to collect genome sequences continues to expand.
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Affiliation(s)
- Jesse R R Zaneveld
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
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2740
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ÁLVAREZ A, PEREZ SI, VERZI DH. Early evolutionary differentiation of morphological variation in the mandible of South American caviomorph rodents (Rodentia, Caviomorpha). J Evol Biol 2011; 24:2687-95. [DOI: 10.1111/j.1420-9101.2011.02395.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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2741
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Rabosky DL, Cowan MA, Talaba AL, Lovette IJ. Species interactions mediate phylogenetic community structure in a hyperdiverse lizard assemblage from arid Australia. Am Nat 2011; 178:579-95. [PMID: 22030728 DOI: 10.1086/662162] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Evolutionary history can exert a profound influence on ecological communities, but few generalities have emerged concerning the relationships among phylogeny, community membership, and niche evolution. We compared phylogenetic community structure and niche evolution in three lizard clades (Ctenotus skinks, agamids, and diplodactyline geckos) from arid Australia. We surveyed lizard communities at 32 sites in the northwestern Great Victoria Desert and generated complete species-level molecular phylogenies for regional representatives of the three clades. We document a striking pattern of phylogenetic evenness within local communities for all groups: pairwise correlations in species abundance across sites are negatively related to phylogenetic similarity. By modeling site suitability on the basis of species' habitat preferences, we demonstrate that phylogenetic evenness generally persists even after controlling for habitat filtering among species. This phylogenetic evenness is coupled with evolutionary lability of habitat-associated traits, to the extent that closely related species are more divergent in habitat use than distantly related species. In contrast, lizard diets are phylogenetically conserved, and pairwise dietary overlap between species is negatively related to phylogenetic distance in two of the three clades. Our results suggest that contemporary and historical species interactions have led to similar patterns of community structure across multiple clades in one of the world's most diverse lizard communities.
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Affiliation(s)
- Daniel L Rabosky
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, USA.
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2742
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Huang J, Chen B, Liu C, Lai J, Zhang J, Ma K. Identifying hotspots of endemic woody seed plant diversity in China. DIVERS DISTRIB 2011. [DOI: 10.1111/j.1472-4642.2011.00845.x] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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2743
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Stevens RD, Gavilanez MM, Tello JS, Ray DA. Phylogenetic structure illuminates the mechanistic role of environmental heterogeneity in community organization. J Anim Ecol 2011; 81:455-62. [PMID: 21895648 DOI: 10.1111/j.1365-2656.2011.01900.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
1. Diversity begets diversity. Numerous published positive correlations between environmental heterogeneity and species diversity indicate ubiquity of this phenomenon. Nonetheless, most assessments of this relationship are phenomenological and provide little insight into the mechanism whereby such positive association results. 2. Two unresolved issues could better illuminate the mechanistic basis to diversity begets diversity. First, as environmental heterogeneity increases, both productivity and the species richness that contributes to that productivity often increase in a correlated fashion thus obscuring the primary driver. Second, it is unclear how species are added to communities as diversity increases and whether additions are trait based. 3. We examined these issues based on 31 rodent communities in the central Mojave Desert. At each site, we estimated rodent species richness and characterized environmental heterogeneity from the perspectives of standing primary productivity and number of seed resources. We further examined the phylogenetic structure of communities by estimating the mean phylogenetic distance (MPD) among species and by comparing empirical phylogenetic distances to those based on random assembly from a regional species pool. 4. The relationship between rodent species diversity and environmental heterogeneity was positive and significant. Moreover, diversity of resources accounted for more unique variation than did total productivity, suggesting that variety and not total amount of resource was the driver of increased rodent diversity. Relationships between environmental heterogeneity and phylogenetic distance were negative and significant; species were significantly phylogenetically over-dispersed in communities of low environmental heterogeneity and became more clumped as environmental heterogeneity increased. 5. Results suggest that species diversity increases with environmental heterogeneity because a wider variety of resources allow greater species packing within communities.
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Affiliation(s)
- Richard D Stevens
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA.
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2744
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Kembel SW, Eisen JA, Pollard KS, Green JL. The phylogenetic diversity of metagenomes. PLoS One 2011; 6:e23214. [PMID: 21912589 PMCID: PMC3166145 DOI: 10.1371/journal.pone.0023214] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2011] [Accepted: 07/12/2011] [Indexed: 01/28/2023] Open
Abstract
Phylogenetic diversity—patterns of phylogenetic relatedness among organisms in ecological communities—provides important insights into the mechanisms underlying community assembly. Studies that measure phylogenetic diversity in microbial communities have primarily been limited to a single marker gene approach, using the small subunit of the rRNA gene (SSU-rRNA) to quantify phylogenetic relationships among microbial taxa. In this study, we present an approach for inferring phylogenetic relationships among microorganisms based on the random metagenomic sequencing of DNA fragments. To overcome challenges caused by the fragmentary nature of metagenomic data, we leveraged fully sequenced bacterial genomes as a scaffold to enable inference of phylogenetic relationships among metagenomic sequences from multiple phylogenetic marker gene families. The resulting metagenomic phylogeny can be used to quantify the phylogenetic diversity of microbial communities based on metagenomic data sets. We applied this method to understand patterns of microbial phylogenetic diversity and community assembly along an oceanic depth gradient, and compared our findings to previous studies of this gradient using SSU-rRNA gene and metagenomic analyses. Bacterial phylogenetic diversity was highest at intermediate depths beneath the ocean surface, whereas taxonomic diversity (diversity measured by binning sequences into taxonomically similar groups) showed no relationship with depth. Phylogenetic diversity estimates based on the SSU-rRNA gene and the multi-gene metagenomic phylogeny were broadly concordant, suggesting that our approach will be applicable to other metagenomic data sets for which corresponding SSU-rRNA gene sequences are unavailable. Our approach opens up the possibility of using metagenomic data to study microbial diversity in a phylogenetic context.
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Affiliation(s)
- Steven W Kembel
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America.
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2745
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Vas Z, Lefebvre L, Johnson KP, Reiczigel J, Rózsa L. Clever birds are lousy: co-variation between avian innovation and the taxonomic richness of their amblyceran lice. Int J Parasitol 2011; 41:1295-300. [PMID: 21924269 DOI: 10.1016/j.ijpara.2011.07.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2011] [Revised: 07/21/2011] [Accepted: 07/22/2011] [Indexed: 10/17/2022]
Abstract
Lice (Insecta: Phthiraptera) are ectoparasites that reduce host life expectancy and sexual attractiveness. Their taxonomic richness varies considerably among their hosts. Previous studies have already explored some important factors shaping louse diversity. An unexplored potential correlate of louse taxonomic richness is host behavioural flexibility. In this comparative study, we examine the relationship between louse generic richness, innovative capabilities (as a proxy for behavioural flexibility), and brain size while controlling for host species diversity, phylogeny, body size and research effort. Using data for 108 avian families, we found a highly significant positive relationship between host innovative capabilities and the taxonomic richness of amblyceran lice, but a lack of a similar relationship in ischnoceran lice. Host brain size had only a marginal impact on amblyceran diversity and no correlation with ischnoceran diversity. This suggests that the effect in Amblycera is not mediated by metabolic limitations due to the energetic costs of brain size and maintenance, rather directly caused by the ecological differences between hosts with differing cognitive capabilities. We propose four alternative and mutually non-exclusive hypotheses that may explain this phenomenon.
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Affiliation(s)
- Zoltán Vas
- Szent István University, Faculty of Veterinary Sciences, Department of Biomathematics and Informatics, Budapest H-1078, István u. 2, Hungary.
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2746
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Price TD, Mohan D, Tietze DT, Hooper DM, Orme CDL, Rasmussen PC. Determinants of northerly range limits along the Himalayan bird diversity gradient. Am Nat 2011; 178 Suppl 1:S97-108. [PMID: 21956095 DOI: 10.1086/661926] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The primary explanation for the latitudinal gradient in species diversity must lie in why species fail to expand ranges across different climatic regimes. Theories of species gradients based in niche conservatism assume that whole clades are confined to particular climatic regimes because the traits they share limit adaptation to alternative regimes. We assess these theories in an analysis of the twofold decline in bird species richness along the Himalayas from the southeast to the northwest. The presence of fewer species in the northwest is entirely due to a steep decline in the number of forest species; species occupying more open habitats show a reversed gradient. Forest species numbers are exceptionally high at midelevations (1,000-2,000 m) in the southeast, which experience a warm, wet climate not present in the northwest, and a high proportion of these species fail to expand their range to the northwest. Despite this, many species do have populations or close relatives that straddle different climatic regimes along altitudinal gradients and/or the regional gradient, implying that climate-based niche conservatism per se does not strongly constrain range limits. We argue that climate- and competition-mediated resource distributions are important in setting northerly range limits and show that one measure of forest resources (foliage density) is lower in the northwest.
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Affiliation(s)
- Trevor D Price
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, USA.
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2747
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Martin AR, Thomas SC. A reassessment of carbon content in tropical trees. PLoS One 2011; 6:e23533. [PMID: 21858157 PMCID: PMC3157388 DOI: 10.1371/journal.pone.0023533] [Citation(s) in RCA: 170] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Accepted: 07/19/2011] [Indexed: 11/18/2022] Open
Abstract
Accurate knowledge of carbon (C) content in live wood is essential for quantifying tropical forest C stocks, yet generic assumptions (such as biomass consisting of 50% carbon on a weight/weight basis) remain widely used despite being supported by little chemical analysis. Empirical data from stem cores of 59 Panamanian rainforest tree species demonstrate that wood C content is highly variable among co-occurring species, with an average (47.4±2.51% S.D.) significantly lower than widely assumed values. Prior published values have neglected to account for volatile C content of tropical woods. By comparing freeze- and oven-dried wood samples, we show that volatile C is non-negligible, and excluding the volatile fraction underestimates wood C content by 2.48±1.28% (S.D.) on average. Wood C content varied substantially among species (from 41.9–51.6%), but was neither strongly phylogenetically conserved, nor correlated to ecological (i.e. wood density, maximum tree height) or demographic traits (i.e. relative growth rate, mortality rate). Overall, assuming generic C fractions in tropical wood overestimates forest C stocks by ∼3.3–5.3%, a non-trivial margin of error leading to overestimates of 4.1–6.8 Mg C ha−1 in a 50-ha forest dynamics plot on Barro Colorado Island, Panama. In addition to addressing other sources of error in tropical forest C accounting, such as uncertainties in allometric models and belowground biomass, compilation and use of species-specific C fractions for tropical tree species would substantially improve both local and global estimates of terrestrial C stocks and fluxes.
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Affiliation(s)
- Adam R Martin
- Faculty of Forestry, University of Toronto, Earth Sciences Building, Toronto, Ontario, Canada.
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2748
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Lanfear R, Bromham L. Estimating phylogenies for species assemblages: a complete phylogeny for the past and present native birds of New Zealand. Mol Phylogenet Evol 2011; 61:958-63. [PMID: 21835254 DOI: 10.1016/j.ympev.2011.07.018] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Revised: 07/19/2011] [Accepted: 07/23/2011] [Indexed: 10/17/2022]
Abstract
Phylogenies of species assemblages are vital to many studies of community ecology and macroecology. However, few assemblage phylogenies are currently available, and the approaches that have been used to construct them have had a number of important limitations. Here, we estimate a Bayesian posterior sample of phylogenies for all 275 known extinct and extant native birds of New Zealand. To do this, we use an approach that uses freely-available data and software, can incorporate both extinct and extant taxa, does not rely on having DNA sequence data available for all species in the assemblage, and explicitly accounts for phylogenetic uncertainty. This approach produces a set of phylogenies that describes our knowledge and uncertainty about the relationships among the NZ birds. We also present a python script, GeneFinder, which can be used to efficiently gather publicly available sequence data in order to construct a supermatrix of DNA sequences for constructing assemblage phylogenies. The approach we describe paves the way for estimating assemblage phylogenies for any species assemblage.
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Affiliation(s)
- Robert Lanfear
- Centre for Macroevolution and Macroecology, Evolution Ecology and Genetics, Research School of Biology, The Australian National University, Canberra ACT 0200, Australia.
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2749
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Poulin R, Krasnov BR, Mouillot D. Host specificity in phylogenetic and geographic space. Trends Parasitol 2011; 27:355-61. [PMID: 21680245 DOI: 10.1016/j.pt.2011.05.003] [Citation(s) in RCA: 206] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Revised: 05/11/2011] [Accepted: 05/12/2011] [Indexed: 11/30/2022]
Affiliation(s)
- Robert Poulin
- Department of Zoology, University of Otago, Dunedin, New Zealand.
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2750
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Ives AR, Helmus MR. Generalized linear mixed models for phylogenetic analyses of community structure. ECOL MONOGR 2011. [DOI: 10.1890/10-1264.1] [Citation(s) in RCA: 160] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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