51
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Malaney JL, Cook JA. Using biogeographical history to inform conservation: the case of Preble's meadow jumping mouse. Mol Ecol 2013; 22:6000-17. [DOI: 10.1111/mec.12476] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Revised: 07/05/2013] [Accepted: 07/09/2013] [Indexed: 11/29/2022]
Affiliation(s)
- Jason L. Malaney
- Museum of Southwestern Biology; Department of Biology; University of New Mexico; Albuquerque NM 87131 USA
| | - Joseph A. Cook
- Museum of Southwestern Biology; Department of Biology; University of New Mexico; Albuquerque NM 87131 USA
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52
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Leaché AD, Harris RB, Rannala B, Yang Z. The Influence of Gene Flow on Species Tree Estimation: A Simulation Study. Syst Biol 2013; 63:17-30. [DOI: 10.1093/sysbio/syt049] [Citation(s) in RCA: 249] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Affiliation(s)
- Adam D. Leaché
- Department of Biology and Burke Museum of Natural History and Culture, University of Washington, Seattle, WA 98195 USA
| | - Rebecca B. Harris
- Department of Biology and Burke Museum of Natural History and Culture, University of Washington, Seattle, WA 98195 USA
| | - Bruce Rannala
- Genome Center and Department of Evolution & Ecology, University of California, Davis, CA 95616, USA
- Center for Computational Genomics, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; and
| | - Ziheng Yang
- Center for Computational Genomics, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; and
- Department of Biology, University College London, Gower Street, London WC1E 6BT, UK
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53
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Zhong B, Liu L, Yan Z, Penny D. Origin of land plants using the multispecies coalescent model. TRENDS IN PLANT SCIENCE 2013; 18:492-5. [PMID: 23707196 DOI: 10.1016/j.tplants.2013.04.009] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Revised: 04/18/2013] [Accepted: 04/25/2013] [Indexed: 05/24/2023]
Abstract
The origin of land plants is a fundamental topic in plant evolutionary biology. Despite the crucial importance for knowing the closest lineages of land plants, this question has not been fully answered yet. Using recently available nuclear sequences from streptophyte algae, the multispecies coalescent model produces a congruent phylogeny that is robust to different data sets, in contrast to the conflicting phylogenies produced by the concatenation method. Using phylogenomic data and the coalescent model, in this opinion article we postulate that the Zygnematales are the closest lineages of land plants. We suggest that the coalescent model can accommodate gene tree heterogeneity in deep-level phylogenies and can be potentially used to resolve other deep species phylogenies.
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Affiliation(s)
- Bojian Zhong
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand.
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54
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Species tree reconstruction of a poorly resolved clade of salamanders (Ambystomatidae) using multiple nuclear loci. Mol Phylogenet Evol 2013; 68:671-82. [DOI: 10.1016/j.ympev.2013.04.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Revised: 04/14/2013] [Accepted: 04/16/2013] [Indexed: 11/23/2022]
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55
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DeGiorgio M, Degnan JH. Robustness to divergence time underestimation when inferring species trees from estimated gene trees. Syst Biol 2013; 63:66-82. [PMID: 23988674 DOI: 10.1093/sysbio/syt059] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
To infer species trees from gene trees estimated from phylogenomic data sets, tractable methods are needed that can handle dozens to hundreds of loci. We examine several computationally efficient approaches-MP-EST, STAR, STEAC, STELLS, and STEM-for inferring species trees from gene trees estimated using maximum likelihood (ML) and Bayesian approaches. Among the methods examined, we found that topology-based methods often performed better using ML gene trees and methods employing coalescent times typically performed better using Bayesian gene trees, with MP-EST, STAR, STEAC, and STELLS outperforming STEM under most conditions. We examine why the STEM tree (also called GLASS or Maximum Tree) is less accurate on estimated gene trees by comparing estimated and true coalescence times, performing species tree inference using simulations, and analyzing a great ape data set keeping track of false positive and false negative rates for inferred clades. We find that although true coalescence times are more ancient than speciation times under the multispecies coalescent model, estimated coalescence times are often more recent than speciation times. This underestimation can lead to increased bias and lack of resolution with increased sampling (either alleles or loci) when gene trees are estimated with ML. The problem appears to be less severe using Bayesian gene-tree estimates.
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Affiliation(s)
- Michael DeGiorgio
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA; Department of Biology, Pennsylvania State University, University Park, PA 16802, USA; and Department of Mathematics and Statistics, University of New Mexico, 1 University of New Mexico, Albuquerque, NM 87131, USA
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56
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Hovmöller R, Knowles LL, Kubatko LS. Effects of missing data on species tree estimation under the coalescent. Mol Phylogenet Evol 2013; 69:1057-62. [PMID: 23769751 DOI: 10.1016/j.ympev.2013.06.004] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2013] [Accepted: 06/05/2013] [Indexed: 11/20/2022]
Abstract
With recent advances in genomic sequencing, the importance of taking the effects of the processes that can cause discord between the speciation history and the individual gene histories into account has become evident. For multilocus datasets, it is difficult to achieve complete coverage of all sampled loci across all sample specimens, a problem that also arises when combining incompletely overlapping datasets. Here we examine how missing data affects the accuracy of species tree reconstruction. In our study, 10- and 100-locus sequence datasets were simulated under the coalescent model from shallow and deep speciation histories, and species trees were estimated using the maximum likelihood and Bayesian frameworks (with STEM and (*)BEAST, respectively). The accuracy of the estimated species trees was evaluated using the symmetric difference and the SPR distance. We examine the effects of sampling more than one individual per species, as well as the effects of different patterns of missing data (i.e., different amounts of missing data, which is represented among random taxa as opposed to being concentrated in specific taxa, as is often the case for empirical studies). Our general conclusion is that the species tree estimates are remarkably resilient to the effects of missing data. We find that for datasets with more limited numbers of loci, sampling more than one individual per species has the strongest effect on improving species tree accuracy when there is missing data, especially at higher degrees of missing data. For larger multilocus datasets (e.g., 25-100 loci), the amount of missing data has a negligible effect on species tree reconstruction, even at 50% missing data and a single sampled individual per species.
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Affiliation(s)
- Rasmus Hovmöller
- Department of Statistics, The Ohio State University, 404 Cockins Hall, 1958 Neil Avenue, Columbus, OH 43210, United States
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57
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Corl A, Ellegren H. Sampling strategies for species trees: The effects on phylogenetic inference of the number of genes, number of individuals, and whether loci are mitochondrial, sex-linked, or autosomal. Mol Phylogenet Evol 2013; 67:358-66. [DOI: 10.1016/j.ympev.2013.02.002] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Revised: 01/31/2013] [Accepted: 02/03/2013] [Indexed: 11/16/2022]
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58
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Zapata F. A multilocus phylogenetic analysis of Escallonia (Escalloniaceae): diversification in montane South America. AMERICAN JOURNAL OF BOTANY 2013; 100:526-545. [PMID: 23400495 DOI: 10.3732/ajb.1200297] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
PREMISE OF THE STUDY The mountains of South America are hotspots of plant diversity. How this diversity originated and evolved, and what roles geographic and environmental factors may have played in the diversification of lineages occurring in these regions, is not well understood. Escallonia, a morphologically and ecologically diverse group of shrubs and trees widely distributed in these mountains, provides an ideal opportunity for studying the historical underpinnings that have shaped the extraordinarily distinctive, diverse, and endangered flora of these regions, and for evaluating the role of abiotic factors in the process of lineage divergence. • METHODS I analyzed neutral DNA sequence data from two nuclear loci and one chloroplast locus using maximum parsimony, maximum likelihood, and Bayesian phylogenetic approaches. I used a Bayesian approach to analyze the geographic structure of gene trees, and a phylogenetically controlled decomposition of the variance in bioclimatic variables to analyze the eco-climatic structure of gene trees. • KEY RESULTS I found that Escallonia (1) is monophyletic, (2) has a remarkable level of geographic and climatic phylogenetic structure, (3) likely originated in the tropical Andes, and (4) has a widespread absence of species exclusivity. • CONCLUSIONS Geography played an important role early in the history of Escallonia by separating populations that later diversify likely in isolation. Although geographic isolation was generally accompanied by changes in climate, it is not clear whether environmental gradients along elevation have influenced more recent diversification events or whether species have evolved broader environmental tolerances.
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Affiliation(s)
- Felipe Zapata
- Department of Biology, University of Missouri-St. Louis, One University Blvd., St. Louis, MO 63121, USA.
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59
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Ting N, Sterner KN. Primate molecular phylogenetics in a genomic era. Mol Phylogenet Evol 2013; 66:565-8. [DOI: 10.1016/j.ympev.2012.08.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Revised: 08/12/2012] [Accepted: 08/22/2012] [Indexed: 11/27/2022]
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60
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HOLLEMAN WOUTER, VON DER HEYDEN SOPHIE, ZSILAVECZ GUIDO. Delineating the fishes of the Clinus superciliosus species complex in southern African waters (Blennioidei: Clinidae: Clinini), with the validation of Clinus arborescens Gilchrist & Thompson, 1908 and Clinus ornatus Gilchrist & Thompson, 1908, and with de. Zool J Linn Soc 2012. [DOI: 10.1111/j.1096-3642.2012.00865.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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61
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Rittmeyer EN, Austin CC. The effects of sampling on delimiting species from multi-locus sequence data. Mol Phylogenet Evol 2012; 65:451-63. [DOI: 10.1016/j.ympev.2012.06.031] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Revised: 06/04/2012] [Accepted: 06/30/2012] [Indexed: 11/16/2022]
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62
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Full modeling versus summarizing gene-tree uncertainty: Method choice and species-tree accuracy. Mol Phylogenet Evol 2012; 65:501-9. [DOI: 10.1016/j.ympev.2012.07.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2011] [Revised: 04/06/2012] [Accepted: 07/08/2012] [Indexed: 11/20/2022]
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63
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Lautrédou AC, Hinsinger D, Gallut C, Cheng CH, Berkani M, Ozouf-Costaz C, Cruaud C, Lecointre G, Dettai A. Phylogenetic footprints of an Antarctic radiation: The Trematominae (Notothenioidei, Teleostei). Mol Phylogenet Evol 2012; 65:87-101. [DOI: 10.1016/j.ympev.2012.05.032] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2011] [Revised: 05/11/2012] [Accepted: 05/25/2012] [Indexed: 10/28/2022]
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64
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Coalescent-based species delimitation in an integrative taxonomy. Trends Ecol Evol 2012; 27:480-8. [PMID: 22633974 DOI: 10.1016/j.tree.2012.04.012] [Citation(s) in RCA: 500] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Revised: 04/09/2012] [Accepted: 04/24/2012] [Indexed: 11/21/2022]
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65
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Eight independent nuclear genes support monophyly of the plovers: the role of mutational variance in gene trees. Mol Phylogenet Evol 2012; 65:631-41. [PMID: 22842291 DOI: 10.1016/j.ympev.2012.07.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Revised: 07/18/2012] [Accepted: 07/19/2012] [Indexed: 01/25/2023]
Abstract
Molecular phylogenies of Charadriiformes based on mtDNA genes and one to three nuclear loci do not support the traditional placement of Pluvialis in the plovers (Charadriidae), assigning it instead to oystercatchers, stilts, and avocets (Haematopodidae and Recurvirostridae). To investigate this hypothesis of plover paraphyly, the relationships among Pluvialis and closely related families were revisited by sequencing two individuals of all taxa except Peltohyas for eight independent single copy nuclear protein-coding loci selected for their informativeness at this phylogenetic depth. The species tree estimated jointly with the gene trees in the coalescent programme (*)BEAST strongly supported plover monophyly, as did Bayesian analysis of the concatenated matrix. The data sets that supported plover paraphyly in Baker et al. (2007) and Fain and Houde (2007) reflect two to four independent gene histories, and thus discordance with the plover monophyly species tree might have arisen by chance through stochastic mutational variance. For the plovers we conclude there is no conclusive evidence of coalescent variance from ancient incomplete lineage sorting across the interior branch leading to Pluvialis in the species tree. Rather, earlier studies seem have been misled by faster evolving mtDNA genes with high mutational variance, and a few nuclear genes that had low resolving power at the Pluvialis sister group level. These findings are of general relevance in avian phylogenetics, as they show that careful attention needs to be paid to the number and the phylogenetic informativeness of genes required to obtain accurate estimates of the species tree, especially where there is mutational heterogeneity in gene trees.
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66
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Random roots and lineage sorting. Mol Phylogenet Evol 2012; 64:12-20. [DOI: 10.1016/j.ympev.2012.02.029] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Revised: 02/11/2012] [Accepted: 02/27/2012] [Indexed: 11/16/2022]
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67
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Oatley G, Voelker G, Crowe TM, Bowie RCK. A multi-locus phylogeny reveals a complex pattern of diversification related to climate and habitat heterogeneity in southern African white-eyes. Mol Phylogenet Evol 2012; 64:633-44. [PMID: 22659517 DOI: 10.1016/j.ympev.2012.05.022] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Revised: 05/20/2012] [Accepted: 05/21/2012] [Indexed: 11/17/2022]
Abstract
The recent, rapid radiation of Zosteropidae, coupled with their high levels of colonizing ability and phenotypic diversity, makes species delimitation within this family problematic. Given these problems, challenges to establish the mechanisms driving diversity and speciation within this group have arisen. Four morphologically distinct southern African Zosterops taxa, with a contentious taxonomic past, provide such a challenge. Here, supplemented with morphological and environmental analytical techniques, a combination of mitochondrial and nuclear markers were analyzed using Bayesian and Likelihood methods to determine their speciation patterns and to establish the phylogenetic relationships of these four morphologically diverse southern African Zosterops taxa. Nearly all individuals were phenotypically diagnosable, even those individuals collected in areas of contact between taxa. Localities where two or more taxa co-occur appear to possess intermediate environmental characteristics. Initial Bayesian and Likelihood mitochondrial DNA analyses and Bayesian structure analyses of the combined nuclear markers indicated levels of hybridization in areas of sympatry. A combined mtDNA and nuclear DNA analysis and a species tree analysis (with hybrids excluded) placed Z. pallidus as sister to the other southern African taxa, with Z. senegalensis the putative sister taxon to a clade comprising Z. capensis and Z. virens. The grouping of taxon-specific sampling localities and the apparent intermediate nature of birds from areas of sympatry points toward an influence of habitat type and the associated climatic conditions in driving Zosterops diversification in southern Africa.
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Affiliation(s)
- Graeme Oatley
- Percy FitzPatrick Institute, DST/NRF Centre of Excellence, University of Cape Town, Rondebosch 7701, South Africa.
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68
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Castalanelli MA, Baker AM, Munyard KA, Grimm M, Groth DM. Molecular phylogeny supports the paraphyletic nature of the genus Trogoderma (Coleoptera: Dermestidae) collected in the Australasian ecozone. BULLETIN OF ENTOMOLOGICAL RESEARCH 2012; 102:17-28. [PMID: 21749736 DOI: 10.1017/s0007485311000319] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
To date, a molecular phylogenetic approach has not been used to investigate the evolutionary structure of Trogoderma and closely related genera. Using two mitochondrial genes, Cytochrome Oxidase I and Cytochrome B, and the nuclear gene, 18S, the reported polyphyletic positioning of Trogoderma was examined. Paraphyly in Trogoderma was observed, with one Australian Trogoderma species reconciled as sister to all Dermestidae and the Anthrenocerus genus deeply nested within the Australian Trogoderma clade. In addition, time to most recent common ancestor for a number of Dermestidae was calculated. Based on these estimations, the Dermestidae origin exceeded 175 million years, placing the origins of this family in Pangaea.
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Affiliation(s)
- M A Castalanelli
- Cooperative Research Centre for National Plant Biosecurity, Deakin, ACT, Australia.
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69
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Lanier HC, Knowles LL. Is Recombination a Problem for Species-Tree Analyses? Syst Biol 2012; 61:691-701. [DOI: 10.1093/sysbio/syr128] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Hayley C. Lanier
- Department of Ecology and Evolutionary Biology, Museum of Zoology, University of Michigan, Ann Arbor, MI 48109-1079, USA; E-mail:
| | - L. Lacey Knowles
- Department of Ecology and Evolutionary Biology, Museum of Zoology, University of Michigan, Ann Arbor, MI 48109-1079, USA; E-mail:
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70
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Rintoul TL, Eggertson QA, Lévesque CA. Multigene phylogenetic analyses to delimit new species in fungal plant pathogens. Methods Mol Biol 2012; 835:549-69. [PMID: 22183677 DOI: 10.1007/978-1-61779-501-5_34] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Supporting the identification of unknown strains or specimens by sequencing a genetic marker commonly used for phylogenetics or DNA barcoding is now standard practice for mycologists and plant pathologists. Does one have a new species when a strain differs by a few base pairs when compared to reference sequences from taxonomically well-characterized species that do not differ morphologically from this new strain? If variation at the intra- and interspecific levels for the locus used for identification is already understood for all the closely related species, it is possible to make a reliable prediction of a new species status, but ultimately this question can only be properly addressed by determining the presence or absence of gene flow among a group of strains of the putative new species and strains of previously delimited species. The Phylogenetic Species Concept (PSC) and its assessment using multigene phylogeny and Genealogical Concordance Phylogenetic Species Recognition (GCPSR) are the basis for this chapter. The theoretical framework and a variety of tools to apply these concepts are explained, to assist in the assessment of whether a species is distinct or new when confronted with some sequence divergence from reference data.
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Affiliation(s)
- Tara L Rintoul
- Biodiversity (Mycology), Central Experimental Farm, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
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71
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Melo-Ferreira J, Boursot P, Carneiro M, Esteves PJ, Farelo L, Alves PC. Recurrent Introgression of Mitochondrial DNA Among Hares (Lepus spp.) Revealed by Species-Tree Inference and Coalescent Simulations. Syst Biol 2011; 61:367-81. [DOI: 10.1093/sysbio/syr114] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- J. Melo-Ferreira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485−661 Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, 4099−002 Porto, Portugal
- Université Montpellier 2, CNRS UMR 5554, Institut des Sciences de l'Evolution, 34095 Montpellier cedex 5, France
| | - P. Boursot
- Université Montpellier 2, CNRS UMR 5554, Institut des Sciences de l'Evolution, 34095 Montpellier cedex 5, France
| | - M. Carneiro
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485−661 Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, 4099−002 Porto, Portugal
| | - P. J. Esteves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485−661 Vairão, Portugal
- CITS—Centro de Investigação em Tecnologias da Saúde, IPSN, Gandra, CESPU, Portugal
| | - L. Farelo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485−661 Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, 4099−002 Porto, Portugal
| | - P. C. Alves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485−661 Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, 4099−002 Porto, Portugal
- University of Montana, Wildlife Biology Program, College of Forestry and Conservation, Missoula, MT 59812, USA
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Camargo A, Avila LJ, Morando M, Sites JW. Accuracy and Precision of Species Trees: Effects of Locus, Individual, and Base Pair Sampling on Inference of Species Trees in Lizards of the Liolaemus darwinii Group (Squamata, Liolaemidae). Syst Biol 2011; 61:272-88. [DOI: 10.1093/sysbio/syr105] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Arley Camargo
- Department of Biology and Bean Life Science Museum, Brigham Young University, Provo, UT 84602, USA
| | - Luciano J. Avila
- CONICET-CENPAT, Boulevard Almirante Brown 2825, U9120ACF, Puerto Madryn, Chubut, Argentina
| | - Mariana Morando
- CONICET-CENPAT, Boulevard Almirante Brown 2825, U9120ACF, Puerto Madryn, Chubut, Argentina
| | - Jack W. Sites
- Department of Biology and Bean Life Science Museum, Brigham Young University, Provo, UT 84602, USA
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Distinct origin of the Y and St genome in Elymus species: evidence from the analysis of a large sample of St genome species using two nuclear genes. PLoS One 2011; 6:e26853. [PMID: 22046383 PMCID: PMC3203181 DOI: 10.1371/journal.pone.0026853] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Accepted: 10/05/2011] [Indexed: 12/02/2022] Open
Abstract
Background Previous cytological and single copy nuclear genes data suggested the St and Y genome in the StY-genomic Elymus species originated from different donors: the St from a diploid species in Pseudoroegneria and the Y from an unknown diploid species, which are now extinct or undiscovered. However, ITS data suggested that the Y and St genome shared the same progenitor although rather few St genome species were studied. In a recent analysis of many samples of St genome species Pseudoroegneria spicata (Pursh) À. Löve suggested that one accession of P. spicata species was the most likely donor of the Y genome. The present study tested whether intraspecific variation during sampling could affect the outcome of analyses to determining the origin of Y genome in allotetraploid StY species. We also explored the evolutionary dynamics of these species. Methodology/Principal Findings Two single copy nuclear genes, the second largest subunit of RNA polymerase II (RPB2) and the translation elongation factor G (EF-G) sequences from 58 accessions of Pseudoroegneria and Elymus species, together with those from Hordeum (H), Agropyron (P), Australopyrum (W), Lophopyrum (Ee), Thinopyrum (Ea), Thinopyrum (Eb), and Dasypyrum (V) were analyzed using maximum parsimony, maximum likelihood and Bayesian methods. Sequence comparisons among all these genomes revealed that the St and Y genomes are relatively dissimilar. Extensive sequence variations have been detected not only between the sequences from St and Y genome, but also among the sequences from diploid St genome species. Phylogenetic analyses separated the Y sequences from the St sequences. Conclusions/Significance Our results confirmed that St and Y genome in Elymus species have originated from different donors, and demonstrated that intraspecific variation does not affect the identification of genome origin in polyploids. Moreover, sequence data showed evidence to support the suggestion of the genome convergent evolution in allopolyploid StY genome species.
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74
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Lee JY, Joseph L, Edwards SV. A species tree for the Australo-Papuan Fairy-wrens and allies (Aves: Maluridae). Syst Biol 2011; 61:253-71. [PMID: 21978990 DOI: 10.1093/sysbio/syr101] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We explored the efficacy of species tree methods at the family level in birds, using the Australo-Papuan Fairy-wrens (Passeriformes: Maluridae) as a model system. Fairy-wrens of the genus Malurus are known for high intensities of sexual selection, resulting in some cases in rapid speciation. This history suggests that incomplete lineage sorting (ILS) of neutrally evolving loci could be substantial, a situation that could compromise traditional methods of combining loci in phylogenetic analysis. Using 18 molecular markers (5 anonymous loci, 7 exons, 5 introns, and 1 mitochondrial DNA locus), we show that gene tree monophyly across species could be rejected for 16 of 18 loci, suggesting substantial ILS at the family level in these birds. Using the software Concaterpillar, we also detect three statistically distinct clusters of gene trees among the 18 loci. Despite substantial variation in gene trees, species trees constructed using four different species tree estimation methods (BEST, BUCKy, and STAR) were generally well supported and similar to each other and to the concatenation tree, with a few mild discordances at nodes that could be explained by rapid and recent speciation events. By contrast, minimizing deep coalescences produced a species tree that was topologically more divergent from those of the other methods as measured by multidimensional scaling of trees. Additionally, gene and species trees were topologically more similar in the BEST analysis, presumably because of the species tree prior employed in BEST which appropriately assumes that gene trees are correlated with each other and with the species tree. Among the 18 loci, we also discovered 102 independent indel markers, which also proved phylogenetically informative, primarily among genera, and displayed a ∼4-fold bias towards deletions. As suggested in earlier work, the grasswrens (Amytornis) are sister to the rest of the family and the emu-wrens (Stipiturus) are sister to fairy-wrens (Malurus, Clytomyias). Our study shows that ILS is common at the family level in birds yet, despite this, species tree methods converge on broadly similar results for this family.
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Affiliation(s)
- June Y Lee
- Museum of Comparative Zoology and Department of Organismic & Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
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75
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Abstract
Background Species phylogenies are not estimated directly, but rather through phylogenetic analyses of different gene datasets. However, true gene trees can differ from the true species tree (and hence from one another) due to biological processes such as horizontal gene transfer, incomplete lineage sorting, and gene duplication and loss, so that no single gene tree is a reliable estimate of the species tree. Several methods have been developed to estimate species trees from estimated gene trees, differing according to the specific algorithmic technique used and the biological model used to explain differences between species and gene trees. Relatively little is known about the relative performance of these methods. Results We report on a study evaluating several different methods for estimating species trees from sequence datasets, simulating sequence evolution under a complex model including indels (insertions and deletions), substitutions, and incomplete lineage sorting. The most important finding of our study is that some fast and simple methods are nearly as accurate as the most accurate methods, which employ sophisticated statistical methods and are computationally quite intensive. We also observe that methods that explicitly consider errors in the estimated gene trees produce more accurate trees than methods that assume the estimated gene trees are correct. Conclusions Our study shows that highly accurate estimations of species trees are achievable, even when gene trees differ from each other and from the species tree, and that these estimations can be obtained using fairly simple and computationally tractable methods.
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Affiliation(s)
- Jimmy Yang
- Department of Computer Science, University of Texas at Austin, Austin TX 78712, USA
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76
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Reyda FB, Marques FPL. Diversification and species boundaries of Rhinebothrium (Cestoda; Rhinebothriidea) in South American freshwater stingrays (Batoidea; Potamotrygonidae). PLoS One 2011; 6:e22604. [PMID: 21857936 PMCID: PMC3153936 DOI: 10.1371/journal.pone.0022604] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Accepted: 06/25/2011] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Neotropical freshwater stingrays (Batoidea: Potamotrygonidae) host a diverse parasite fauna, including cestodes. Both cestodes and their stingray hosts are marine-derived, but the taxonomy of this host/parasite system is poorly understood. METHODOLOGY Morphological and molecular (Cytochrome oxidase I) data were used to investigate diversity in freshwater lineages of the cestode genus Rhinebothrium Linton, 1890. Results were based on a phylogenetic hypothesis for 74 COI sequences and morphological analysis of over 400 specimens. Cestodes studied were obtained from 888 individual potamotrygonids, representing 14 recognized and 18 potentially undescribed species from most river systems of South America. RESULTS Morphological species boundaries were based mainly on microthrix characters observed with scanning electron microscopy, and were supported by COI data. Four species were recognized, including two redescribed (Rhinebothrium copianullum and R. paratrygoni), and two newly described (R. brooksi n. sp. and R. fulbrighti n. sp.). Rhinebothrium paranaensis Menoret & Ivanov, 2009 is considered a junior synonym of R. paratrygoni because the morphological features of the two species overlap substantially. The diagnosis of Rhinebothrium Linton, 1890 is emended to accommodate the presence of marginal longitudinal septa observed in R. copianullum and R. brooksi n. sp. Patterns of host specificity and distribution ranged from use of few host species in few river basins, to use of as many as eight host species in multiple river basins. SIGNIFICANCE The level of intra-specific morphological variation observed in features such as total length and number of proglottids is unparalleled among other elasmobranch cestodes. This is attributed to the large representation of host and biogeographical samples. It is unclear whether the intra-specific morphological variation observed is unique to this freshwater system. Nonetheless, caution is urged when using morphological discontinuities to delimit elasmobranch cestode species because the amount of variation encountered is highly dependent on sample size and/or biogeographical representation.
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Affiliation(s)
- Florian B Reyda
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Conneticut, United States of America.
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77
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Estimating phylogenetic relationships despite discordant gene trees across loci: the species tree of a diverse species group of feather mites (Acari: Proctophyllodidae). Parasitology 2011; 138:1750-9. [PMID: 21554840 DOI: 10.1017/s003118201100031x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
With the increased availability of multilocus sequence data, the lack of concordance of gene trees estimated for independent loci has focused attention on both the biological processes producing the discord and the methodologies used to estimate phylogenetic relationships. What has emerged is a suite of new analytical tools for phylogenetic inference--species tree approaches. In contrast to traditional phylogenetic methods that are stymied by the idiosyncrasies of gene trees, approaches for estimating species trees explicitly take into account the cause of discord among loci and, in the process, provides a direct estimate of phylogenetic history (i.e. the history of species divergence, not divergence of specific loci). We illustrate the utility of species tree estimates with an analysis of a diverse group of feather mites, the pinnatus species group (genus Proctophyllodes). Discord among four sequenced nuclear loci is consistent with theoretical expectations, given the short time separating speciation events (as evident by short internodes relative to terminal branch lengths in the trees). Nevertheless, many of the relationships are well resolved in a Bayesian estimate of the species tree; the analysis also highlights ambiguous aspects of the phylogeny that require additional loci. The broad utility of species tree approaches is discussed, and specifically, their application to groups with high speciation rates--a history of diversification with particular prevalence in host/parasite systems where species interactions can drive rapid diversification.
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78
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Phylogenetic relationships in the spoon tarsus subgroup of Hawaiian drosophila: Conflict and concordance between gene trees. Mol Phylogenet Evol 2011; 58:492-501. [DOI: 10.1016/j.ympev.2010.12.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2010] [Revised: 12/24/2010] [Accepted: 12/24/2010] [Indexed: 11/23/2022]
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79
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WELCH ANDREANNAJ, YOSHIDA ALLISONA, FLEISCHER ROBERTC. Mitochondrial and nuclear DNA sequences reveal recent divergence in morphologically indistinguishable petrels. Mol Ecol 2011; 20:1364-77. [DOI: 10.1111/j.1365-294x.2011.05008.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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80
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Flórez-Rodríguez A, Carling MD, Cadena CD. Reconstructing the phylogeny of “Buarremon” brush-finches and near relatives (Aves, Emberizidae) from individual gene trees. Mol Phylogenet Evol 2011; 58:297-303. [DOI: 10.1016/j.ympev.2010.11.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2010] [Revised: 11/02/2010] [Accepted: 11/15/2010] [Indexed: 12/29/2022]
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81
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Than CV, Rosenberg NA. Consistency Properties of Species Tree Inference by Minimizing Deep Coalescences. J Comput Biol 2011; 18:1-15. [PMID: 21210728 DOI: 10.1089/cmb.2010.0102] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Cuong V. Than
- Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan
| | - Noah A. Rosenberg
- Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan
- Department of Human Genetics and the Life Sciences Institute, University of Michigan, Ann Arbor, Michigan
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82
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Leaché AD, Rannala B. The Accuracy of Species Tree Estimation under Simulation: A Comparison of Methods. Syst Biol 2010; 60:126-37. [PMID: 21088009 DOI: 10.1093/sysbio/syq073] [Citation(s) in RCA: 218] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Adam D. Leaché
- Genome Center and Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
| | - Bruce Rannala
- Genome Center and Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
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83
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Hird S, Kubatko L, Carstens B. Rapid and accurate species tree estimation for phylogeographic investigations using replicated subsampling. Mol Phylogenet Evol 2010; 57:888-98. [DOI: 10.1016/j.ympev.2010.08.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2010] [Revised: 08/05/2010] [Accepted: 08/10/2010] [Indexed: 01/24/2023]
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84
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Huang H, He Q, Kubatko LS, Knowles LL. Sources of Error Inherent in Species-Tree Estimation: Impact of Mutational and Coalescent Effects on Accuracy and Implications for Choosing among Different Methods. Syst Biol 2010; 59:573-83. [DOI: 10.1093/sysbio/syq047] [Citation(s) in RCA: 125] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Huateng Huang
- Department of Ecology and Evolutionary Biology, Museum of Zoology, University of Michigan, Ann Arbor, MI 48109-1079, USA
| | - Qixin He
- Department of Ecology and Evolutionary Biology, Museum of Zoology, University of Michigan, Ann Arbor, MI 48109-1079, USA
| | - Laura S. Kubatko
- Department of Statistics
- Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus, OH 43210, USA
| | - L. Lacey Knowles
- Department of Ecology and Evolutionary Biology, Museum of Zoology, University of Michigan, Ann Arbor, MI 48109-1079, USA
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85
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Blair C, Murphy RW. Recent trends in molecular phylogenetic analysis: where to next? J Hered 2010; 102:130-8. [PMID: 20696667 DOI: 10.1093/jhered/esq092] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The acquisition of large multilocus sequence data is providing researchers with an unprecedented amount of information to resolve difficult phylogenetic problems. With these large quantities of data comes the increasing challenge regarding the best methods of analysis. We review the current trends in molecular phylogenetic analysis, focusing specifically on the topics of multiple sequence alignment and methods of tree reconstruction. We suggest that traditional methods are inadequate for these highly heterogeneous data sets and that researchers employ newer more sophisticated search algorithms in their analyses. If we are to best extract the information present in these data sets, a sound understanding of basic phylogenetic principles combined with modern methodological techniques are necessary.
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Affiliation(s)
- Christopher Blair
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada.
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86
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McCormack JE, Heled J, Delaney KS, Peterson AT, Knowles LL. CALIBRATING DIVERGENCE TIMES ON SPECIES TREES VERSUS GENE TREES: IMPLICATIONS FOR SPECIATION HISTORY OF APHELOCOMA JAYS. Evolution 2010; 65:184-202. [DOI: 10.1111/j.1558-5646.2010.01097.x] [Citation(s) in RCA: 210] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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87
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Carstens BC, Dewey TA. Species delimitation using a combined coalescent and information-theoretic approach: an example from North American Myotis bats. Syst Biol 2010; 59:400-14. [PMID: 20547777 PMCID: PMC2885268 DOI: 10.1093/sysbio/syq024] [Citation(s) in RCA: 155] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2009] [Revised: 08/18/2009] [Accepted: 12/11/2009] [Indexed: 11/14/2022] Open
Abstract
Coalescent model-based methods for phylogeny estimation force systematists to confront issues related to the identification of species boundaries. Unlike conventional phylogenetic analysis, where species membership can be assessed qualitatively after the phylogeny is estimated, the phylogenies that are estimated under a coalescent model treat aggregates of individuals as the operational taxonomic units and thus require a priori definition of these sets because the models assume that the alleles in a given lineage are sampled from a single panmictic population. Fortunately, the use of coalescent model-based approaches allows systematists to conduct probabilistic tests of species limits by calculating the probability of competing models of lineage composition. Here, we conduct the first exploration of the issues related to applying such tests to a complex empirical system. Sequence data from multiple loci were used to assess species limits and phylogeny in a clade of North American Myotis bats. After estimating gene trees at each locus, the likelihood of models representing all hierarchical permutations of lineage composition was calculated and Akaike information criterion scores were computed. Metrics borrowed from information theory suggest that there is strong support for several models that include multiple evolutionary lineages within the currently described species Myotis lucifugus and M. evotis. Although these results are preliminary, they illustrate the practical importance of coupled species delimitation and phylogeny estimation.
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Affiliation(s)
- Bryan C Carstens
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70808, USA.
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88
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Abstract
Until recently, it has been common practice for a phylogenetic analysis to use a single gene sequence from a single individual organism as a proxy for an entire species. With technological advances, it is now becoming more common to collect data sets containing multiple gene loci and multiple individuals per species. These data sets often reveal the need to directly model intraspecies polymorphism and incomplete lineage sorting in phylogenetic estimation procedures. For a single species, coalescent theory is widely used in contemporary population genetics to model intraspecific gene trees. Here, we present a Bayesian Markov chain Monte Carlo method for the multispecies coalescent. Our method coestimates multiple gene trees embedded in a shared species tree along with the effective population size of both extant and ancestral species. The inference is made possible by multilocus data from multiple individuals per species. Using a multiindividual data set and a series of simulations of rapid species radiations, we demonstrate the efficacy of our new method. These simulations give some insight into the behavior of the method as a function of sampled individuals, sampled loci, and sequence length. Finally, we compare our new method to both an existing method (BEST 2.2) with similar goals and the supermatrix (concatenation) method. We demonstrate that both BEST and our method have much better estimation accuracy for species tree topology than concatenation, and our method outperforms BEST in divergence time and population size estimation.
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Affiliation(s)
- Joseph Heled
- Department of Computer Science, University of Auckland, New Zealand.
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89
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Knowles LL. Estimating Species Trees: Methods of Phylogenetic Analysis When There Is Incongruence across Genes. Syst Biol 2009; 58:463-7. [DOI: 10.1093/sysbio/syp061] [Citation(s) in RCA: 139] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- L. Lacey Knowles
- Department of Ecology and Evolutionary Biology, Museum of Zoology, University of Michigan, Ann Arbor, MI 48109-1079, USA
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Huang H, Knowles LL. What Is the Danger of the Anomaly Zone for Empirical Phylogenetics? Syst Biol 2009; 58:527-36. [DOI: 10.1093/sysbio/syp047] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Huateng Huang
- Department of Ecology and Evolutionary Biology, Museum of Zoology, University of Michigan, 1109 Geddes Avenue, Ann Arbor, MI 48109-1079, USA; E-mail:
| | - L. Lacey Knowles
- Department of Ecology and Evolutionary Biology, Museum of Zoology, University of Michigan, 1109 Geddes Avenue, Ann Arbor, MI 48109-1079, USA; E-mail:
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