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How to Study Classification. Cladistics 2020. [DOI: 10.1017/9781139047678.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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Classification. Cladistics 2020. [DOI: 10.1017/9781139047678.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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Systematics Association Special Volumes. Cladistics 2020. [DOI: 10.1017/9781139047678.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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Relationship Diagrams. Cladistics 2020. [DOI: 10.1017/9781139047678.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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The Separation of Classification and Phylogenetics. Cladistics 2020. [DOI: 10.1017/9781139047678.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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Beyond Classification. Cladistics 2020. [DOI: 10.1017/9781139047678.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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The Interrelationships of Organisms. Cladistics 2020. [DOI: 10.1017/9781139047678.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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How to Study Classification. Cladistics 2020. [DOI: 10.1017/9781139047678.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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Modern Artificial Methods and Raw Data. Cladistics 2020. [DOI: 10.1017/9781139047678.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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Further Myths and More Misunderstandings. Cladistics 2020. [DOI: 10.1017/9781139047678.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Afterword. Cladistics 2020. [DOI: 10.1017/9781139047678.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Systematics: Exposing Myths. Cladistics 2020. [DOI: 10.1017/9781139047678.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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Essentialism and Typology. Cladistics 2020. [DOI: 10.1017/9781139047678.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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Beyond Classification: How to Study Phylogeny. Cladistics 2020. [DOI: 10.1017/9781139047678.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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How to Study Classification: ‘Total Evidence’ vs. ‘Consensus’, Character Congruence vs. Taxonomic Congruence, Simultaneous Analysis vs. Partitioned Data. Cladistics 2020. [DOI: 10.1017/9781139047678.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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What This Book Is About. Cladistics 2020. [DOI: 10.1017/9781139047678.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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How to Study Classification. Cladistics 2020. [DOI: 10.1017/9781139047678.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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The Cladistic Programme. Cladistics 2020. [DOI: 10.1017/9781139047678.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Index. Cladistics 2020. [DOI: 10.1017/9781139047678.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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Parameters of Classification: Ordo Ab Chao. Cladistics 2020. [DOI: 10.1017/9781139047678.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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Monothetic and Polythetic Taxa. Cladistics 2020. [DOI: 10.1017/9781139047678.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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How to Study Classification: Consensus Techniques and General Classifications. Cladistics 2020. [DOI: 10.1017/9781139047678.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Non-taxa or the Absence of –Phyly: Paraphyly and Aphyly. Cladistics 2020. [DOI: 10.1017/9781139047678.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Introduction: Carving Nature at Its Joints, or Why Birds Are Not Dinosaurs and Men Are Not Apes. Cladistics 2020. [DOI: 10.1017/9781139047678.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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Preface. Cladistics 2020. [DOI: 10.1017/9781139047678.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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Burgess MB, Cushman KR, Doucette ET, Frye CT, Campbell CS. Understanding diploid diversity: A first step in unraveling polyploid, apomictic complexity in Amelanchier. AMERICAN JOURNAL OF BOTANY 2015; 102:2041-2057. [PMID: 26643889 DOI: 10.3732/ajb.1500330] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 10/05/2015] [Indexed: 06/05/2023]
Abstract
PREMISE OF THE STUDY Delimitation of Amelanchier species is difficult because of polyploidy and gametophytic apomixis. A first step in unraveling this species problem is understanding the diversity of the diploids that contributed genomes to polyploid apomicts. This research helps clarify challenging species-delimitation problems attending polyploid, apomictic complexity. METHODS We sampled 431 diploid accessions from 13 species, of which 10 are North American and three are Old World. Quantitative morphological analyses tested the null hypothesis of no discrete groups. Using three to nine diploid accessions per species, we constructed phylogenies with DNA sequences from ETS, ITS, the second intron of LEAFY, and chloroplast regions rpoB-trnC, rpl16, trnD-trnT, and ycf6-psbM. KEY RESULTS Most Amelanchier diploid taxa are morphologically and ecogeographically distinct and genetically exclusive lineages. They rarely hybridize with one another. Nuclear and chloroplast DNA sequences almost completely resolve the Amelanchier phylogeny. The backbone is the mostly western North American clade A, eastern North American clade B, and Old World clade O. DNA sequences and morphology support clades A and O as sister taxa. Despite extensive paralogy, our LEAFY data are phylogenetically informative and identify a clade (T) of three arborescent taxa within clade B. CONCLUSIONS Amelanchier diploids differ strikingly from polyploid apomicts, in that hybridization among them is rare, and they form taxa that would qualify as species by most species concepts. Knowledge of diploid morphology, phylogeny, and ecogeography provides a foundation for understanding the evolutionary history of polyploid apomicts, their patterns of diversification, and their species status.
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Affiliation(s)
- Michael B Burgess
- Department of Biological Sciences, State University of New York Plattsburgh, Plattsburgh, New York 12901, USA
| | - Kevin R Cushman
- School of Biology and Ecology, University of Maine, Orono, Maine 04469, USA
| | - Eric T Doucette
- School of Biology and Ecology, University of Maine, Orono, Maine 04469, USA
| | - Christopher T Frye
- Maryland Department of Natural Resources, Natural Heritage Program, 909 Wye Mills Road, Wye Mills, Maryland 21679, USA
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Starrett J, Hedin M, Ayoub N, Hayashi CY. Hemocyanin gene family evolution in spiders (Araneae), with implications for phylogenetic relationships and divergence times in the infraorder Mygalomorphae. Gene 2013; 524:175-86. [DOI: 10.1016/j.gene.2013.04.037] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Revised: 03/18/2013] [Accepted: 04/15/2013] [Indexed: 10/26/2022]
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Stewart JE, Andrew M, Bao X, Chilvers MI, Carris LM, Peever TL. Development of sequence characterized amplified genomic regions (SCAR) for fungal systematics: proof of principle using Alternaria, Ascochyta and Tilletia. Mycologia 2013; 105:1077-86. [PMID: 23449078 DOI: 10.3852/12-287] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
SCARs were developed by cloning RAPD-PCR amplicons into commercially available vectors, sequencing them and designing specific primers for PCR, direct sequencing and phylogenetic analysis. Eighteen to seventy percent of cloned RAPD-PCR amplicons were phylogenetically informative among closely related small-spored Alternaria spp., Ascochyta spp. and Tilletia spp., taxa that have been resistant to phylogenetic analysis with universally primed, protein-coding sequence data. Selected SCARs were sequenced for larger, population-scale samples of each taxon and demonstrated to be useful for phylogenetic inference. Variation observed in the cloned SCARs generally was higher than variation in nuclear ribosomal internal transcribed spacer (ITS) and several protein-coding sequences commonly used in lower level fungal systematics. Sequence data derived from SCARs will provide sufficient resolution to address lower level phylogenetic hypotheses in Alternaria, Ascochyta, Tilletia and possibly many other fungal groups and organisms.
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Affiliation(s)
- Jane E Stewart
- Department of Plant Pathology, Washington State University, Pullman, WA, USA
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Bacon CD, Baker WJ, Simmons MP. Miocene dispersal drives island radiations in the palm tribe Trachycarpeae (Arecaceae). Syst Biol 2012; 61:426-42. [PMID: 22223444 DOI: 10.1093/sysbio/syr123] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The study of three island groups of the palm tribe Trachycarpeae (Arecaceae/Palmae) permits both the analysis of each independent radiation and comparisons across the tribe to address general processes that drive island diversification. Phylogenetic relationships of Trachycarpeae were inferred from three plastid and three low-copy nuclear genes. The incongruent topological position of Brahea in CISP5 was hypothesized to be caused by a gene duplication event and was addressed using uninode coding. The resulting phylogenetic trees were well-resolved and the genera were all highly supported except for Johannesteijsmannia and Serenoa. Divergence time analysis estimated the stem of the tribe to be approximately 86 Ma and the crown to be 38 Ma, indicating that significant extinction may have occurred along this branch. Historical biogeographic analysis suggested that Trachycarpeae are of southern North American, Central American, or Caribbean origin and supports previous hypotheses of a Laurasian origin. The biogeography and disjunctions within the tribe were interpreted with respect to divergence times, the fossil record, and geological factors such as the formation of the Greater Antilles--Aves Ridge, the Bering and the North Atlantic land bridges, tectonic movement in Southeast Asia, climatic shifts between the Eocene and Pliocene, and volcanism in the Pacific basin. In considering the three major island radiations within Trachycarpeae, Miocene dispersal appears to have been the driving force in allopatric speciation and is highlighted here as an emerging pattern across the tree of life.
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Affiliation(s)
- Christine D Bacon
- Department of Biology, Colorado State University, Fort Collins, CO 80523-1878, USA.
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Abstract
BACKGROUND A phylogenetic tree, showing ancestral relations among organisms, is commonly represented as a rooted tree with sets of bifurcating branches (dichotomies) for simplicity, although polytomies (multifurcating branches) may reflect more accurate evolutionary relationships. To represent the true evolutionary relationships, it is important to systematically identify the polytomies from a bifurcating tree and generate a taxonomy-compatible multifurcating tree. For this purpose we propose a novel approach, "PolyPhy", which would classify a set of bifurcating branches of a phylogenetic tree into a set of branches with dichotomies and polytomies by considering genome distances among genomes and tree topological properties. RESULTS PolyPhy employs a machine learning technique, BLR (Bayesian logistic regression) classifier, to identify possible bifurcating subtrees as polytomies from the trees resulted from ComPhy. Other than considering genome-scale distances between all pairs of species, PolyPhy also takes into account different properties of tree topology between dichotomy and polytomy, such as long-branch retraction and short-branch contraction, and quantifies these properties into comparable rates among different sub-branches. We extract three tree topological features, 'LR' (Leaf rate), 'IntraR' (Intra-subset branch rate) and 'InterR' (Inter-subset branch rate), all of which are calculated from bifurcating tree branch sets for classification. We have achieved F-measure (balanced measure between precision and recall) of 81% with about 0.9 area under the curve (AUC) of ROC. CONCLUSIONS PolyPhy is a fast and robust method to identify polytomies from phylogenetic trees based on genome-wide inference of evolutionary relationships among genomes. The software package and test data can be downloaded from http://digbio.missouri.edu/ComPhy/phyloTreeBiNonBi-1.0.zip.
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Affiliation(s)
- Guan Ning Lin
- Department of Computer Science and C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
- Department of Psychiatry, University of California, San Diego, CA 92093, USA
| | - Chao Zhang
- Department of Computer Science and C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Dong Xu
- Department of Computer Science and C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
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McGowen MR, Clark C, Gatesy J. The vestigial olfactory receptor subgenome of odontocete whales: phylogenetic congruence between gene-tree reconciliation and supermatrix methods. Syst Biol 2010; 57:574-90. [PMID: 18686195 DOI: 10.1080/10635150802304787] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
The macroevolutionary transition of whales (cetaceans) from a terrestrial quadruped to an obligate aquatic form involved major changes in sensory abilities. Compared to terrestrial mammals, the olfactory system of baleen whales is dramatically reduced, and in toothed whales is completely absent. We sampled the olfactory receptor (OR) subgenomes of eight cetacean species from four families. A multigene tree of 115 newly characterized OR sequences from these eight species and published data for Bos taurus revealed a diverse array of class II OR paralogues in Cetacea. Evolution of the OR gene superfamily in toothed whales (Odontoceti) featured a multitude of independent pseudogenization events, supporting anatomical evidence that odontocetes have lost their olfactory sense. We explored the phylogenetic utility of OR pseudogenes in Cetacea, concentrating on delphinids (oceanic dolphins), the product of a rapid evolutionary radiation that has been difficult to resolve in previous studies of mitochondrial DNA sequences. Phylogenetic analyses of OR pseudogenes using both gene-tree reconciliation and supermatrix methods yielded fully resolved, consistently supported relationships among members of four delphinid subfamilies. Alternative minimizations of gene duplications, gene duplications plus gene losses, deep coalescence events, and nucleotide substitutions plus indels returned highly congruent phylogenetic hypotheses. Novel DNA sequence data for six single-copy nuclear loci and three mitochondrial genes (> 5000 aligned nucleotides) provided an independent test of the OR trees. Nucleotide substitutions and indels in OR pseudogenes showed a very low degree of homoplasy in comparison to mitochondrial DNA and, on average, provided more variation than single-copy nuclear DNA. Our results suggest that phylogenetic analysis of the large OR superfamily will be effective for resolving relationships within Cetacea whether supermatrix or gene-tree reconciliation procedures are used.
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Affiliation(s)
- Michael R McGowen
- Department of Biology, University of California, Riverside, California 92521, USA.
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Sanderson MJ, McMahon MM. Inferring angiosperm phylogeny from EST data with widespread gene duplication. BMC Evol Biol 2007; 7 Suppl 1:S3. [PMID: 17288576 PMCID: PMC1796612 DOI: 10.1186/1471-2148-7-s1-s3] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Most studies inferring species phylogenies use sequences from single copy genes or sets of orthologs culled from gene families. For taxa such as plants, with very high levels of gene duplication in their nuclear genomes, this has limited the exploitation of nuclear sequences for phylogenetic studies, such as those available in large EST libraries. One rarely used method of inference, gene tree parsimony, can infer species trees from gene families undergoing duplication and loss, but its performance has not been evaluated at a phylogenomic scale for EST data in plants. RESULTS A gene tree parsimony analysis based on EST data was undertaken for six angiosperm model species and Pinus, an outgroup. Although a large fraction of the tentative consensus sequences obtained from the TIGR database of ESTs was assembled into homologous clusters too small to be phylogenetically informative, some 557 clusters contained promising levels of information. Based on maximum likelihood estimates of the gene trees obtained from these clusters, gene tree parsimony correctly inferred the accepted species tree with strong statistical support. A slight variant of this species tree was obtained when maximum parsimony was used to infer the individual gene trees instead. CONCLUSION Despite the complexity of the EST data and the relatively small fraction eventually used in inferring a species tree, the gene tree parsimony method performed well in the face of very high apparent rates of duplication.
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Affiliation(s)
- Michael J Sanderson
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Michelle M McMahon
- Department of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
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Mort ME, Archibald JK, Randle CP, Levsen ND, O'Leary TR, Topalov K, Wiegand CM, Crawford DJ. Inferring phylogeny at low taxonomic levels: utility of rapidly evolving cpDNA and nuclear ITS loci. AMERICAN JOURNAL OF BOTANY 2007; 94:173-183. [PMID: 21642219 DOI: 10.3732/ajb.94.2.173] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Plant molecular systematic studies of closely related taxa have relied heavily on sequence data from nuclear ITS and cpDNA. Positive attributes of using ITS sequence data include the rapid rate of evolution compared to most plastid loci and availability of universal primers for amplification and sequencing. On the other hand, ITS sequence data may not adequately track organismal phylogeny if concerted evolution and high rDNA array copy number do not permit identification of orthologous copies. Shaw et al. (American Journal of Botany 92: 142-166) recently identified nine plastid regions that appear to provide more potentially informative characters than many other plastid loci. In the present study, sequences of these loci and ITS were obtained for six taxonomic groups in which phylogenetic relationships have been difficult to establish using other data. The relative utility of these regions was compared by assessing the number of parsimony informative characters, character congruence, resolution of inferred trees, clade support, and accuracy. No single locus emerged as the best in all lineages for any of these measures of utility. Results further indicated that in preliminary studies, sampling strategy should include at least four exemplar taxa. The importance of sampling data from independent distributions is also discussed.
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Affiliation(s)
- Mark E Mort
- Department of Ecology and Evolutionary Biology, Natural History Museum, University of Kansas, 1200 Sunnyside Ave., Lawrence, Kansas 66045 USA; and
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Affiliation(s)
- John V Freudenstein
- Department of Evolution, Ecology and Organismal Biology, Ohio State University Herbarium, 1315 Kinnear Road, Columbus, 43212, USA.
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Abstract
Paralogy (common ancestry through gene duplication rather than speciation) is widely recognized as an important problem for molecular systematists. This chapter introduces the concepts of paralogy and orthology and explains why paralogy can complicate both systematic work and other studies of molecular evolution. The definition of paralogy is explicitly phylogenetic, and phylogenetic methods are crucial in elucidating the pattern of paralogy. In particular, knowledge of the species phylogeny is key. I introduce the theory behind methods for detecting paralogy and briefly discuss two particular software implementations of phylogenetic methods to detect paralogy from molecular data. I also introduce a statistical method for detecting paralogy and some future directions for work on paralogy detection.
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Affiliation(s)
- James A Cotton
- Department of Zoology, The Natural History Museum, London SW7 5BD, United Kingdom
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