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Bastin S, Reyes-Betancort JA, Siverio de la Rosa F, Percy DM. Origins of the central Macaronesian psyllid lineages (Hemiptera; Psylloidea) with characterization of a new island radiation on endemic Convolvulus floridus (Convolvulaceae) in the Canary Islands. PLoS One 2024; 19:e0297062. [PMID: 38277393 PMCID: PMC10817144 DOI: 10.1371/journal.pone.0297062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 12/27/2023] [Indexed: 01/28/2024] Open
Abstract
A molecular survey of native and adventive psyllids in the central Macaronesian islands provides the first comprehensive phylogenetic assessment of the origins of the psyllid fauna of the Canary and Madeira archipelagos. We employ a maximum likelihood backbone constraint analysis to place the central Macaronesian taxa within the Psylloidea mitogenome phylogeny. The native psyllid fauna in these central Macaronesian islands results from an estimated 26 independent colonization events. Island host plants are predicted by host plants of continental relatives in nearly all cases and six plant genera have been colonized multiple times (Chamaecytisus, Convolvulus, Olea, Pistacia, Rhamnus, and Spartocytisus) from the continent. Post-colonization diversification varies from no further cladogenesis (18 events, represented by a single native taxon) to modest in situ diversification resulting in two to four native taxa and, surprisingly, given the diverse range of islands and habitats, only one substantial species radiation with more than four native species. Specificity to ancestral host plant genera or family is typically maintained during in situ diversification both within and among islands. Characterization of a recently discovered island radiation consisting of four species on Convolvulus floridus in the Canary Islands shows patterns and rates of diversification that reflect island topographic complexity and geological dynamism. Although modest in species diversity, this radiation is atypical in diversification on a single host plant species, but typical in the primary role of allopatry in the diversification process.
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Affiliation(s)
- Saskia Bastin
- Instituto Canario de Investigaciones Agrarias, Unidad de Protección Vegetal, La Laguna, Tenerife, Spain
| | - J. Alfredo Reyes-Betancort
- Instituto Canario de Investigaciones Agrarias, Jardín de Aclimatación de La Oratava, Puerto de la Cruz, Tenerife, Spain
| | - Felipe Siverio de la Rosa
- Instituto Canario de Investigaciones Agrarias, Unidad de Protección Vegetal, La Laguna, Tenerife, Spain
| | - Diana M. Percy
- Botany Department and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
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2
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Chesters D, Ferrari RR, Lin X, Orr MC, Staab M, Zhu CD. Launching insectphylo.org; a new hub facilitating construction and use of synthesis molecular phylogenies of insects. Mol Ecol Resour 2023; 23:1556-1573. [PMID: 37265018 DOI: 10.1111/1755-0998.13817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 05/07/2023] [Accepted: 05/17/2023] [Indexed: 06/03/2023]
Abstract
The Holy Grail of an Insect Tree of Life can only be 'discovered' through extensive collaboration among taxon specialists, phylogeneticists and centralized frameworks such as Open Tree of Life, but insufficient effort from stakeholders has so far hampered this promising approach. The resultant unavailability of synthesis phylogenies is an unfortunate situation given the numerous practical usages of phylogenies in the near term and against the backdrop of the ongoing biodiversity crisis. To resolve this issue, we establish a new online hub that centralizes the collation of relevant phylogenetic data and provides the resultant synthesis molecular phylogenies. This is achieved through key developments in a proposed pipeline for the construction of a species-level insect phylogeny. The functionality of the framework is demonstrated through the construction of a highly supported, species-comprehensive phylogeny of Diptera, built from integrated omics data, COI DNA barcodes, and a compiled database of over 100 standardized, published Diptera phylogenies. Machine-readable forms of the phylogeny (and subsets thereof) are publicly available at insectphylo.org, a new public repository for species-comprehensive phylogenies for biological research.
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Affiliation(s)
- Douglas Chesters
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- International College, University of Chinese Academy of Sciences, Beijing, China
| | - Rafael R Ferrari
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Xiaolong Lin
- Engineering Research Center of Environmental DNA and Ecological Water Health Assessment, Shanghai Ocean University, Shanghai, China
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, China
| | - Michael C Orr
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Entomologie, Staatliches Museum für Naturkunde Stuttgart, Stuttgart, Germany
| | - Michael Staab
- Ecological Networks, Technische Universität Darmstadt, Darmstadt, Germany
| | - Chao-Dong Zhu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- International College, University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Integrated Pest Management, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Biological Sciences, University of Chinese Academy of Sciences, Beijing, China
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3
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Martínez-López V, Ruiz C, Muñoz I, Ornosa C, Higes M, Martín-Hernández R, De la Rúa P. Detection of Microsporidia in Pollinator Communities of a Mediterranean Biodiversity Hotspot for Wild Bees. MICROBIAL ECOLOGY 2022; 84:638-642. [PMID: 34585291 DOI: 10.1007/s00248-021-01854-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 08/30/2021] [Indexed: 06/13/2023]
Abstract
Insect pollination is crucial for the maintenance of natural and managed ecosystems but the functioning of this ecosystem service is threatened by a worldwide decline of pollinators. Key factors in this situation include the spread and interspecific transmission of pathogens worldwide through the movement of managed pollinators. Research on this field has been mainly conducted in some particular species, while studies assessing the interspecific transmission of pathogens at a community level are scarce. However, this information is pivotal to design strategies to protect pollinators. Herein, we analysed the prevalence of two common microsporidia pathogens of managed honey bees (Nosema ceranae and N. apis) in bee communities of semiarid Mediterranean areas from the Southeast of the Iberian Peninsula. Our results confirm the ability of N. ceranae to disperse across wild bee communities in semiarid Mediterranean ecosystems since it was detected in 36 Apoidea species (39% of the sampling; for the first time in nine genera). The prevalence of the pathogen did not show any phylogenetic signal which suggests a superfamily host range of the pathogen or that wild bees may be acting only as vectors of N. ceranae. In addition, N. apis was detected in an Eucera species, which is the second time it has been detected by molecular techniques in a host other than the honey bee. Our study represents the primary assessment of the prevalence of microsporidia at community level in Mediterranean areas and provides outstanding results on the ability of Nosema pathogens to spread across the landscape.
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Affiliation(s)
- Vicente Martínez-López
- Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L69 7ZB, UK.
- Department of Zoology and Physical Anthropology, University of Murcia, Murcia, 30100, Spain.
| | - Carlos Ruiz
- Department of Animal Biology and Edaphology and Geology, University of La Laguna, San Cristobal de la Laguna, 38200, Spain
| | - Irene Muñoz
- Department of Zoology and Physical Anthropology, University of Murcia, Murcia, 30100, Spain
| | - Concepción Ornosa
- Department of Biodiversity, Ecology and Evolution, Complutense University, Madrid, 28040, Spain
| | - Mariano Higes
- Centro de Investigación Apícola y Agroambiental (CIAPA), Honey Bee Pathology Laboratory, Instituto Regional de Investigación y Desarrollo Agroalimentario y Forestal (IRIAF), Marchamalo, 19180, Guadalajara, Spain
| | - Raquel Martín-Hernández
- Centro de Investigación Apícola y Agroambiental (CIAPA), Honey Bee Pathology Laboratory, Instituto Regional de Investigación y Desarrollo Agroalimentario y Forestal (IRIAF), Marchamalo, 19180, Guadalajara, Spain
- Instituto de Recursos Humanos para la Ciencia y la Tecnología (INCRECYT, ESF), Fundación Parque Científico y Tecnológico de Albacete, Albacete, 02006, Spain
| | - Pilar De la Rúa
- Department of Zoology and Physical Anthropology, University of Murcia, Murcia, 30100, Spain
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4
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Majoros SE, Adamowicz SJ. Phylogenetic signal of sub-arctic beetle communities. Ecol Evol 2022; 12:e8520. [PMID: 35222946 PMCID: PMC8848465 DOI: 10.1002/ece3.8520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 11/30/2021] [Accepted: 12/14/2021] [Indexed: 11/07/2022] Open
Abstract
Postglacial dispersal and colonization processes have shaped community patterns in sub-Arctic regions such as Churchill, Manitoba, and Canada. This study investigates evolutionary community structure within the beetle (Coleoptera) families of Churchill and tests whether biological traits have played a role in governing colonization patterns from refugial and southerly geographic regions. This study quantifies sub-Arctic beetle phylogenetic community structure for each family using the net relatedness index (NRI) and nearest taxon index (NTI), calculated using publicly available data from the Barcode of Life Data Systems (BOLD); compares patterns across families with different traits (habitat, diet) using standard statistical analysis (ANOVA) as well as phylogenetic generalized least squares (PGLS) using a family-level beetle phylogeny obtained from the literature; and compares community structure in Churchill with a region in southern Canada (Guelph, Ontario). These analyses were also repeated at a genus level. The dominant pattern detected in our study was that aquatic families were much better represented in Churchill compared to terrestrial families, when compared against richness sampled from across Canada and Alaska. Individually, most families showed significant phylogenetic clustering in Churchill, likely due to the strong environmental filtering present in Arctic environments. There was no significant difference in phylogenetic structure between Churchill and Guelph but with a trend toward stronger clustering in the North. Fungivores were significantly more overdispersed than other feeding modes, predators were significantly more clustered, and aquatic families showed significantly stronger clustering compared to terrestrial. This study contributes to our understanding of the traits and processes structuring insect biodiversity and macroecological trends in the sub-Arctic.
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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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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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7
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Phylogenetic conservatism of fruit development time in Chinese angiosperms and the phylogenetic and climatic correlates. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2021.e01543] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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8
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Affiliation(s)
- Thibaud Decaëns
- CEFE Univ Montpellier, CNRS, EPHE, IRD Univ Paul Valéry Montpellier 3 Montpellier France
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9
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Building a Robust, Densely-Sampled Spider Tree of Life for Ecosystem Research. DIVERSITY 2020. [DOI: 10.3390/d12080288] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Phylogenetic relatedness is a key diversity measure for the analysis and understanding of how species and communities evolve across time and space. Understanding the nonrandom loss of species with respect to phylogeny is also essential for better-informed conservation decisions. However, several factors are known to influence phylogenetic reconstruction and, ultimately, phylogenetic diversity metrics. In this study, we empirically tested how some of these factors (topological constraint, taxon sampling, genetic markers and calibration) affect phylogenetic resolution and uncertainty. We built a densely sampled, species-level phylogenetic tree for spiders, combining Sanger sequencing of species from local communities of two biogeographical regions (Iberian Peninsula and Macaronesia) with a taxon-rich backbone matrix of Genbank sequences and a topological constraint derived from recent phylogenomic studies. The resulting tree constitutes the most complete spider phylogeny to date, both in terms of terminals and background information, and may serve as a standard reference for the analysis of phylogenetic diversity patterns at the community level. We then used this tree to investigate how partial data affect phylogenetic reconstruction, phylogenetic diversity estimates and their rankings, and, ultimately, the ecological processes inferred for each community. We found that the incorporation of a single slowly evolving marker (28S) to the DNA barcode sequences from local communities, had the highest impact on tree topology, closely followed by the use of a backbone matrix. The increase in missing data resulting from combining partial sequences from local communities only had a moderate impact on the resulting trees, similar to the difference observed when using topological constraints. Our study further revealed substantial differences in both the phylogenetic structure and diversity rankings of the analyzed communities estimated from the different phylogenetic treatments, especially when using non-ultrametric trees (phylograms) instead of time-stamped trees (chronograms). Finally, we provide some recommendations on reconstructing phylogenetic trees to infer phylogenetic diversity within ecological studies.
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10
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Xie T, Shen C, Liu C, Fang Y, Guo Y, Lan Q, Wang L, Ge J, Zhou Y, Wen S, Yang Q, Zhu B. Ancestry inference and admixture component estimations of Chinese Kazak group based on 165 AIM-SNPs via NGS platform. J Hum Genet 2020; 65:461-468. [DOI: 10.1038/s10038-020-0725-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 11/04/2019] [Accepted: 11/04/2019] [Indexed: 11/09/2022]
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11
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Worthy SJ, Jiménez Paz RA, Pérez ÁJ, Reynolds A, Cruse-Sanders J, Valencia R, Barone JA, Burgess KS. Distribution and Community Assembly of Trees Along an Andean Elevational Gradient. PLANTS (BASEL, SWITZERLAND) 2019; 8:E326. [PMID: 31491875 PMCID: PMC6783956 DOI: 10.3390/plants8090326] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 08/24/2019] [Accepted: 08/28/2019] [Indexed: 11/18/2022]
Abstract
Highlighting patterns of distribution and assembly of plants involves the use of community phylogenetic analyses and complementary traditional taxonomic metrics. However, these patterns are often unknown or in dispute, particularly along elevational gradients, with studies finding different patterns based on elevation. We investigated how patterns of tree diversity and structure change along an elevation gradient using taxonomic and phylogenetic diversity metrics. We sampled 595 individuals (36 families; 53 genera; 88 species) across 15 plots along an elevational gradient (2440-3330 m) in Ecuador. Seventy species were sequenced for the rbcL and matK gene regions to generate a phylogeny. Species richness, Shannon-Weaver diversity, Simpson's Dominance, Simpson's Evenness, phylogenetic diversity (PD), mean pairwise distance (MPD), and mean nearest taxon distance (MNTD) were evaluated for each plot. Values were correlated with elevation and standardized effect sizes (SES) of MPD and MNTD were generated, including and excluding tree fern species, for comparisons across elevation. Taxonomic and phylogenetic metrics found that species diversity decreases with elevation. We also found that overall the community has a non-random phylogenetic structure, dependent on the presence of tree ferns, with stronger phylogenetic clustering at high elevations. Combined, this evidence supports the ideas that tree ferns have converged with angiosperms to occupy the same habitat and that an increased filtering of clades has led to more closely related angiosperm species at higher elevations.
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Affiliation(s)
- Samantha J Worthy
- Department of Biology, Columbus State University, University System of Georgia, Columbus, GA 31907, USA.
- Department of Biology, University of Maryland, College Park, MD 20742, USA.
| | - Rosa A Jiménez Paz
- Laboratorio de Ecología de Plantas, Escuela de Ciencias Biológicas, Pontificia Universidad Católica del Ecuador, Quito 170143, Ecuador.
| | - Álvaro J Pérez
- Herbario QCA, Escuela de Ciencias Biológicas, Pontificia Universidad Católica del Ecuador, Quito 170143, Ecuador.
| | | | | | - Renato Valencia
- Laboratorio de Ecología de Plantas, Escuela de Ciencias Biológicas, Pontificia Universidad Católica del Ecuador, Quito 170143, Ecuador.
| | - John A Barone
- Department of Biology, Columbus State University, University System of Georgia, Columbus, GA 31907, USA.
| | - Kevin S Burgess
- Department of Biology, Columbus State University, University System of Georgia, Columbus, GA 31907, USA.
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12
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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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13
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Liu J, Liu J, Shan YX, Ge X, Burgess KS. The use of DNA barcodes to estimate phylogenetic diversity in forest communities of southern China. Ecol Evol 2019; 9:5372-5379. [PMID: 31110686 PMCID: PMC6509380 DOI: 10.1002/ece3.5128] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 10/27/2018] [Accepted: 03/13/2019] [Indexed: 12/13/2022] Open
Abstract
To elucidate potential ecological and evolutionary processes associated with the assembly of plant communities, there is now widespread use of estimates of phylogenetic diversity that are based on a variety of DNA barcode regions and phylogenetic construction methods. However, relatively few studies consider how estimates of phylogenetic diversity may be influenced by single DNA barcodes incorporated into a sequence matrix (conservative regions vs. hypervariable regions) and the use of a backbone family-level phylogeny. Here, we use general linear mixed-effects models to examine the influence of different combinations of core DNA barcodes (rbcL, matK, ITS, and ITS2) and phylogeny construction methods on a series of estimates of community phylogenetic diversity for two subtropical forest plots in Guangdong, southern China. We ask: (a) What are the relative influences of single DNA barcodes on estimates phylogenetic diversity metrics? and (b) What is the effect of using a backbone family-level phylogeny to estimate topology-based phylogenetic diversity metrics? The combination of more than one barcode (i.e., rbcL + matK + ITS) and the use of a backbone family-level phylogeny provided the most parsimonious explanation of variation in estimates of phylogenetic diversity. The use of a backbone family-level phylogeny showed a stronger effect on phylogenetic diversity metrics that are based on tree topology compared to those that are based on branch lengths. In addition, the variation in the estimates of phylogenetic diversity that was explained by the top-rank models ranged from 0.1% to 31% and was dependent on the type of phylogenetic community structure metric. Our study underscores the importance of incorporating a multilocus DNA barcode and the use of a backbone family-level phylogeny to infer phylogenetic diversity, where the type of DNA barcode employed and the phylogenetic construction method used can serve as a significant source of variation in estimates of phylogenetic community structure.
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Affiliation(s)
- Jiajia Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical GardenThe Chinese Academy of SciencesGuangzhouChina
| | - Juan Liu
- Collaborative Innovation Center of Jiangxi Typical Trees Cultivation and UtilizationJiangxi Agriculture UniversityNanchangChina
| | - You-Xia Shan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical GardenThe Chinese Academy of SciencesGuangzhouChina
| | - Xue‐Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical GardenThe Chinese Academy of SciencesGuangzhouChina
| | - Kevin S. Burgess
- Department of Biology, College of Letters and SciencesColumbus State University, University System of GeorgiaColumbusGeorgia
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14
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Airborne microbial transport limitation to isolated Antarctic soil habitats. Nat Microbiol 2019; 4:925-932. [DOI: 10.1038/s41564-019-0370-4] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 01/15/2019] [Indexed: 11/08/2022]
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15
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Adeoba M, Tesfamichael SG, Yessoufou K. Preserving the tree of life of the fish family Cyprinidae in Africa in the face of the ongoing extinction crisis. Genome 2019; 62:170-182. [DOI: 10.1139/gen-2018-0023] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Our understanding of how the phylogenetic tree of fishes might be affected by the ongoing extinction risk is poor. This is due to the unavailability of comprehensive DNA data, especially for many African lineages. In addition, the ongoing taxonomic confusion within some lineages, e.g., Cyprinidae, makes it difficult to contribute to the debate on how the fish tree of life might be shaped by extinction. Here, we combine COI sequences and taxonomic information to assemble a fully sampled phylogeny of the African Cyprinidae and investigate whether we might lose more phylogenetic diversity (PD) than expected if currently threatened species go extinct. We found evidence for phylogenetic signal in extinction risk, suggesting that some lineages might be at higher risk than others. Based on simulated extinctions, we found that the loss of all threatened species, which approximates 37% of total PD, would lead to a greater loss of PD than expected, although highly evolutionarily distinct species are not particularly at risk. Pending the reconstruction of an improved multi-gene phylogeny, our results suggest that prioritizing high-EDGE species (evolutionary distinct and globally endangered species) in conservation programmes, particularly in some geographic regions, would contribute significantly to safeguarding the tree of life of the African Cyprinidae.
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Affiliation(s)
- Mariam Adeoba
- Department of Zoology, University of Johannesburg, Kingsway Campus, P.O. Box 524, Auckland Park 2006, South Africa
| | - Solomon G. Tesfamichael
- Department of Geography, Environmental Management and Energy Studies, University of Johannesburg, Kingsway Campus, P.O. Box 524, Auckland Park 2006, South Africa
| | - Kowiyou Yessoufou
- Department of Geography, Environmental Management and Energy Studies, University of Johannesburg, Kingsway Campus, P.O. Box 524, Auckland Park 2006, South Africa
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16
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Tiusanen M, Huotari T, Hebert PDN, Andersson T, Asmus A, Bêty J, Davis E, Gale J, Hardwick B, Hik D, Körner C, Lanctot RB, Loonen MJJE, Partanen R, Reischke K, Saalfeld ST, Senez‐Gagnon F, Smith PA, Šulavík J, Syvänperä I, Urbanowicz C, Williams S, Woodard P, Zaika Y, Roslin T. Flower-visitor communities of an arcto-alpine plant-Global patterns in species richness, phylogenetic diversity and ecological functioning. Mol Ecol 2019; 28:318-335. [PMID: 30418699 PMCID: PMC6378624 DOI: 10.1111/mec.14932] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 10/03/2018] [Accepted: 10/05/2018] [Indexed: 01/13/2023]
Abstract
Pollination is an ecosystem function of global importance. Yet, who visits the flower of specific plants, how the composition of these visitors varies in space and time and how such variation translates into pollination services are hard to establish. The use of DNA barcodes allows us to address ecological patterns involving thousands of taxa that are difficult to identify. To clarify the regional variation in the visitor community of a widespread flower resource, we compared the composition of the arthropod community visiting species in the genus Dryas (mountain avens, family Rosaceae), throughout Arctic and high-alpine areas. At each of 15 sites, we sampled Dryas visitors with 100 sticky flower mimics and identified specimens to Barcode Index Numbers (BINs) using a partial sequence of the mitochondrial COI gene. As a measure of ecosystem functioning, we quantified variation in the seed set of Dryas. To test for an association between phylogenetic and functional diversity, we characterized the structure of local visitor communities with both taxonomic and phylogenetic descriptors. In total, we detected 1,360 different BINs, dominated by Diptera and Hymenoptera. The richness of visitors at each site appeared to be driven by local temperature and precipitation. Phylogeographic structure seemed reflective of geological history and mirrored trans-Arctic patterns detected in plants. Seed set success varied widely among sites, with little variation attributable to pollinator species richness. This pattern suggests idiosyncratic associations, with function dominated by few and potentially different taxa at each site. Taken together, our findings illustrate the role of post-glacial history in the assembly of flower-visitor communities in the Arctic and offer insights for understanding how diversity translates into ecosystem functioning.
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Affiliation(s)
- Mikko Tiusanen
- Department of Agricultural SciencesUniversity of HelsinkiHelsinkiFinland
| | - Tea Huotari
- Department of Agricultural SciencesUniversity of HelsinkiHelsinkiFinland
| | - Paul D. N. Hebert
- Centre for Biodiversity GenomicsBiodiversity Institute of OntarioUniversity of GuelphGuelphOntarioCanada
| | - Tommi Andersson
- Kevo Subarctic Research StationBiodiversity UnitUniversity of TurkuTurkuFinland
| | - Ashley Asmus
- Department of Ecology, Evolution and BehaviorUniversity of MinnesotaMinneapolisMinnesota
- Department of BiologyUniversity of Texas at ArlingtonArlingtonTexas
| | - Joël Bêty
- Département de Biologie and Centre d’études NordiquesUniversité du Québec à RimouskiRimouskiQuebecCanada
| | - Emma Davis
- Department of GeographyUniversity of GuelphGuelphOntarioCanada
| | - Jennifer Gale
- East Bay Southampton Island Shorebird CrewNational Wildlife Research CenterEnvironment CanadaOttawaOntarioCanada
| | - Bess Hardwick
- Department of BiosciencesUniversity of HelsinkiHelsinkiFinland
| | - David Hik
- Department of Biological SciencesSimon Fraser UniversityBurnabyBritish ColumbiaCanada
| | - Christian Körner
- Department of Environmental SciencesInstitute of BotanyUniversity of BaselBaselGermany
| | | | | | - Rauni Partanen
- Kilpisjärvi Biological StationUniversity of HelsinkiKilpisjärviFinland
| | | | | | - Fanny Senez‐Gagnon
- Département des Sciences du Bois et de la ForêtUniversité LavalQuebec CityQuébecCanada
| | - Paul A. Smith
- Wildlife Research Division, Environment and Climate Change CanadaOttawaOntarioCanada
| | - Ján Šulavík
- Department of Environmental SciencesFaculty of Engineering and ScienceWestern Norway University of Applied SciencesSogndalNorway
- Natural History MuseumUniversity of OsloOsloNorway
| | - Ilkka Syvänperä
- Kevo Subarctic Research StationBiodiversity UnitUniversity of TurkuTurkuFinland
| | | | - Sian Williams
- Kluane Lake Research StationYukonSilver City, YukonCanada
| | - Paul Woodard
- Canadian Wildlife Service, Environment and Climate Change Canada/Government of CanadaYellowknifeNorthwest TerritoriesCanada
| | - Yulia Zaika
- Department of GeographyKhibiny Academic Research StationLomonosov Moscow State UniversityMoscowRussia
| | - Tomas Roslin
- Department of Agricultural SciencesUniversity of HelsinkiHelsinkiFinland
- Department of EcologySwedish University of Agricultural SciencesUppsalaSweden
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17
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deWaard JR, Levesque-Beaudin V, deWaard SL, Ivanova NV, McKeown JTA, Miskie R, Naik S, Perez KHJ, Ratnasingham S, Sobel CN, Sones JE, Steinke C, Telfer AC, Young AD, Young MR, Zakharov EV, Hebert PDN. Expedited assessment of terrestrial arthropod diversity by coupling Malaise traps with DNA barcoding 1. Genome 2018; 62:85-95. [PMID: 30257096 DOI: 10.1139/gen-2018-0093] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Monitoring changes in terrestrial arthropod communities over space and time requires a dramatic increase in the speed and accuracy of processing samples that cannot be achieved with morphological approaches. The combination of DNA barcoding and Malaise traps allows expedited, comprehensive inventories of species abundance whose cost will rapidly decline as high-throughput sequencing technologies advance. Aside from detailing protocols from specimen sorting to data release, this paper describes their use in a survey of arthropod diversity in a national park that examined 21 194 specimens representing 2255 species. These protocols can support arthropod monitoring programs at regional, national, and continental scales.
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Affiliation(s)
- Jeremy R deWaard
- a Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Valerie Levesque-Beaudin
- a Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Stephanie L deWaard
- a Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Natalia V Ivanova
- a Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Jaclyn T A McKeown
- a Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Renee Miskie
- a Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Suresh Naik
- a Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Kate H J Perez
- a Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Sujeevan Ratnasingham
- a Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Crystal N Sobel
- a Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Jayme E Sones
- a Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Claudia Steinke
- a Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Angela C Telfer
- a Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Andrew D Young
- a Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada.,b Department of Biology, Carleton University, Ottawa, Ontario, Canada
| | - Monica R Young
- a Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Evgeny V Zakharov
- a Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Paul D N Hebert
- a Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
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18
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Head CEI, Koldewey H, Pavoine S, Pratchett MS, Rogers AD, Taylor ML, Bonsall MB. Trait and phylogenetic diversity provide insights into community assembly of reef-associated shrimps (Palaemonidae) at different spatial scales across the Chagos Archipelago. Ecol Evol 2018; 8:4098-4107. [PMID: 29721283 PMCID: PMC5916300 DOI: 10.1002/ece3.3969] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 01/30/2018] [Accepted: 02/09/2018] [Indexed: 11/17/2022] Open
Abstract
Coral reefs are the most biodiverse marine ecosystem and one of the most threatened by global climate change impacts. The vast majority of diversity on reefs is comprised of small invertebrates that live within the reef structure, termed the cryptofauna. This component of biodiversity is hugely understudied, and many species remain undescribed. This study represents a rare analysis of assembly processes structuring a distinct group of cryptofauna, the Palaemonidae, in the Chagos Archipelago, a reef ecosystem under minimal direct human impacts in the central Indian Ocean. The Palaemonidae are a diverse group of Caridae (infraorder of shrimps) that inhabit many different niches on coral reefs and are of particular interest because of their varied habitat associations. Phylogenetic and trait diversity and phylogenetic signal were used to infer likely drivers of community structure. The mechanisms driving palaemonid community assembly and maintenance in the Chagos Archipelago showed distinct spatial patterns. At local scales, among coral colonies and among reefs fringing individual atolls, significant trait, and phylogenetic clustering patterns suggest environmental filtering may be a dominant ecological process driving Palaemonidae community structure, although local competition through equalizing mechanisms may also play a role in shaping the local community structure. Importantly, we also tested the robustness of phylogenetic diversity to changes in evolutionary information as multi‐gene phylogenies are resource intensive and for large families, such as the Palaemonidae, are often incomplete. These tests demonstrated a very modest impact on phylogenetic community structure, with only one of the four genes (PEPCK gene) in the phylogeny affecting phylogenetic diversity patterns, which provides useful information for future studies on large families with incomplete phylogenies. These findings contribute to our limited knowledge of this component of biodiversity in a marine locality as close to undisturbed by humans as can be found. It also provides a rare evaluation of phylogenetic diversity methods.
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Affiliation(s)
- Catherine E I Head
- Department of Zoology University of Oxford Oxford UK.,Conservation Programmes Zoological Society of London London UK.,Linacre College Oxford UK
| | - Heather Koldewey
- Conservation Programmes Zoological Society of London London UK.,Centre for Ecology & Conservation University of Exeter Cornwall Campus Cornwall UK
| | - Sandrine Pavoine
- Centre d'Ecologie et des Sciences de la Conservation (CESCO UMR7204) Sorbonne Universités, MNHN, CNRS, UPMC, CP51 Paris France
| | - Morgan S Pratchett
- ARC Centre of Excellence for Coral Reef Studies James Cook University Townsville QLD Australia
| | - Alex D Rogers
- Department of Zoology University of Oxford Oxford UK
| | | | - Michael B Bonsall
- Department of Zoology University of Oxford Oxford UK.,St Peter's College Oxford UK
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19
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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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20
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Gibson DJ, Adamowicz SJ, Jacobs SR, Smith MA. Host Specificity in Subarctic Aphids. ENVIRONMENTAL ENTOMOLOGY 2018; 47:77-86. [PMID: 29186477 DOI: 10.1093/ee/nvx176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Plants and herbivorous (or parasitic) insects form the majority of macroscopic life. The specificity of interaction between host plant and parasitic insect depends on the adaptations of both the host and the parasite. Over time, these interactions evolve and change as a result of an 'arms race' between host and parasite, and the resulting species-specific adaptations may be maintained, perpetuating these interactions across speciation events. This can lead to specialisation between species or clades. With speciation and species sorting over time, complex interactions evolve. Here, we elucidate a three-tier method to test these interactions using the aphids (Hemiptera: Aphididae) and plants of Churchill (Manitoba, Canada) as a model system. We analyzed these interactions by testing for three patterns in host specificity: monophagy, phylogenetic clustering, and cophylogeny. We defined monophagy strictly as one species feeding exclusively upon a single host plant species (an association likely driven by arms races in morphology, chemical resistance/tolerance, and visual appearance) and observed this in 7 of 22 aphid species. In all the remaining 'polyphagous' cases, there was a strong trend toward monophagy (80% of individuals were found on a single host plant species). Second, we observed two separate examples of phylogenetic clustering where groups of closely related aphid species fed upon individual plant species. Finally, we found no support for cophylogenetic relationships where both aphids and plants cospeciate to form congruent phylogenetic trees (evidence of coadaptation through an ongoing arms race). One explanation for uncovering species-specific interactions in a recently deglaciated, subarctic locality is that the species involved in the associations moved north together. Testing different levels of specificity in the most predominant species-species interactions on the planet will allow us to elucidate these patterns accurately and gives us insight into where to direct future research.
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Affiliation(s)
- Daniel J Gibson
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
- Churchill Northern Studies Centre, Manitoba, Canada
| | - Sarah J Adamowicz
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
- Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Shoshanah R Jacobs
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - M Alex Smith
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
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21
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Marín MA, Cadavid IC, Valdés L, Álvarez CF, Uribe SI, Vila R, Pyrcz TW. DNA Barcoding of an Assembly of Montane Andean Butterflies (Satyrinae): Geographical Scale and Identification Performance. NEOTROPICAL ENTOMOLOGY 2017; 46:514-523. [PMID: 28116647 DOI: 10.1007/s13744-016-0481-z] [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] [Received: 06/15/2016] [Accepted: 12/28/2016] [Indexed: 06/06/2023]
Abstract
DNA barcoding is a technique used primarily for the documentation and identification of biological diversity based on mitochondrial DNA sequences. Butterflies have received particular attention in DNA barcoding studies, although varied performance may be obtained due to different scales of geographic sampling and speciation processes in various groups. The montane Andean Satyrinae constitutes a challenging study group for taxonomy. The group displays high richness, with more of 550 species, and remarkable morphological similarity among taxa, which renders their identification difficult. In the present study, we evaluated the effectiveness of DNA barcodes in the identification of montane Andean satyrines and the effect of increased geographical scale of sampling on identification performance. Mitochondrial sequences were obtained from 104 specimens of 39 species and 16 genera, collected in a forest remnant in the northwest Andes. DNA barcoding has proved to be a useful tool for the identification of the specimens, with a well-defined gap and producing clusters with unambiguous identifications for all the morphospecies in the study area. The expansion of the geographical scale with published data increased genetic distances within species and reduced those among species, but did not generally reduce the success of specimen identification. Only in Forsterinaria rustica (Butler, 1868), a taxon with high intraspecific variation, the barcode gap was lost and low support for monophyly was obtained. Likewise, expanded sampling resulted in a substantial increase in the intraspecific distance in Morpho sulkowskyi (Kollar, 1850); Panyapedaliodes drymaea (Hewitson, 1858); Lymanopoda obsoleta (Westwood, 1851); and Lymanopoda labda Hewitson, 1861; but for these species, the barcode gap was maintained. These divergent lineages are nonetheless worth a detailed study of external and genitalic morphology variation, as well as ecological features, in order to determine the potential existence of cryptic species. Even including these cases, DNA barcoding performance in specimen identification was 100% successful based on monophyly, an unexpected result in such a taxonomically complicated group.
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Affiliation(s)
- M A Marín
- Depto de Biologia Animal, Instituto de Biologia, Univ Estadual de Campinas - UNICAMP, Rua Monteiro Lobato, 255 - Cidade Universitária Zeferino Vaz - Barão Geraldo, CEP, Campinas, SP, 13083-970, Brazil.
- Univ Nacional de Colombia, Sede Medellín, Grupo de Investigación en Sistemática Molecular, Medellín, Colombia.
| | - I C Cadavid
- Univ Nacional de Colombia, Sede Medellín, Grupo de Investigación en Sistemática Molecular, Medellín, Colombia
| | - L Valdés
- Univ Nacional de Colombia, Sede Medellín, Grupo de Investigación en Sistemática Molecular, Medellín, Colombia
| | - C F Álvarez
- Univ Nacional de Colombia, Sede Medellín, Grupo de Investigación en Sistemática Molecular, Medellín, Colombia
- Corporación Universitaria Lasallista, Antioquia, Colombia
| | - S I Uribe
- Univ Nacional de Colombia, Sede Medellín, Grupo de Investigación en Sistemática Molecular, Medellín, Colombia
| | - R Vila
- Instituto de Biología Evolutiva (CSIC-UPF), Barcelona, Spain
| | - T W Pyrcz
- Zoological Museum, Jagiellonian Univ, Kraków, Poland
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22
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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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