1
|
Dornburg A, Su Z, Townsend JP. Optimal Rates for Phylogenetic Inference and Experimental Design in the Era of Genome-Scale Data Sets. Syst Biol 2018; 68:145-156. [PMID: 29939341 DOI: 10.1093/sysbio/syy047] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 06/13/2018] [Indexed: 02/02/2023] Open
Abstract
With the rise of genome-scale data sets, there has been a call for increased data scrutiny and careful selection of loci that are appropriate to use in an attempt to resolve a phylogenetic problem. Such loci should maximize phylogenetic information content while minimizing the risk of homoplasy. Theory posits the existence of characters that evolve at an optimum rate, and efforts to determine optimal rates of inference have been a cornerstone of phylogenetic experimental design for over two decades. However, both theoretical and empirical investigations of optimal rates have varied dramatically in their conclusions: spanning no relationship to a tight relationship between the rate of change and phylogenetic utility. Herein, we synthesize these apparently contradictory views, demonstrating both empirical and theoretical conditions under which each is correct. We find that optimal rates of characters-not genes-are generally robust to most experimental design decisions. Moreover, consideration of site rate heterogeneity within a given locus is critical to accurate predictions of utility. Factors such as taxon sampling or the targeted number of characters providing support for a topology are additionally critical to the predictions of phylogenetic utility based on the rate of character change. Further, optimality of rates and predictions of phylogenetic utility are not equivalent, demonstrating the need for further development of comprehensive theory of phylogenetic experimental design. [Divergence time; GC bias; homoplasy; incongruence; information content; internode length; optimal rates; phylogenetic informativeness; phylogenetic theory; phylogenetic utility; phylogenomics; signal and noise; subtending branch length; state space; taxon and character sampling.].
Collapse
Affiliation(s)
- Alex Dornburg
- North Carolina Museum of Natural Sciences, Raleigh, 1671 Goldstar Drive, NC 27601, USA
| | - Zhuo Su
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, 165 Prospect Street, CT 06525, USA
| | - Jeffrey P Townsend
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, 165 Prospect Street, CT 06525, USA
- Department of Biostatistics, Yale University, New Haven, 60 College Street, CT 06510, USA
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, 300 George Street, CT 06511, USA
| |
Collapse
|
2
|
Lewis PO, Chen MH, Kuo L, Lewis LA, Fučíková K, Neupane S, Wang YB, Shi D. Estimating Bayesian Phylogenetic Information Content. Syst Biol 2016; 65:1009-1023. [PMID: 27155008 PMCID: PMC5066063 DOI: 10.1093/sysbio/syw042] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 04/15/2016] [Accepted: 05/01/2016] [Indexed: 11/13/2022] Open
Abstract
Measuring the phylogenetic information content of data has a long history in systematics. Here we explore a Bayesian approach to information content estimation. The entropy of the posterior distribution compared with the entropy of the prior distribution provides a natural way to measure information content. If the data have no information relevant to ranking tree topologies beyond the information supplied by the prior, the posterior and prior will be identical. Information in data discourages consideration of some hypotheses allowed by the prior, resulting in a posterior distribution that is more concentrated (has lower entropy) than the prior. We focus on measuring information about tree topology using marginal posterior distributions of tree topologies. We show that both the accuracy and the computational efficiency of topological information content estimation improve with use of the conditional clade distribution, which also allows topological information content to be partitioned by clade. We explore two important applications of our method: providing a compelling definition of saturation and detecting conflict among data partitions that can negatively affect analyses of concatenated data. [Bayesian; concatenation; conditional clade distribution; entropy; information; phylogenetics; saturation.].
Collapse
Affiliation(s)
- Paul O Lewis
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Road, Unit 3043, Storrs, CT 06269, USA;
| | - Ming-Hui Chen
- Department of Statistics, University of Connecticut, 215 Glenbrook Road, Unit 4120, Storrs, CT 06269, USA
| | - Lynn Kuo
- Department of Statistics, University of Connecticut, 215 Glenbrook Road, Unit 4120, Storrs, CT 06269, USA
| | - Louise A Lewis
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Road, Unit 3043, Storrs, CT 06269, USA
| | - Karolina Fučíková
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Road, Unit 3043, Storrs, CT 06269, USA
| | - Suman Neupane
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Road, Unit 3043, Storrs, CT 06269, USA
| | - Yu-Bo Wang
- Department of Statistics, University of Connecticut, 215 Glenbrook Road, Unit 4120, Storrs, CT 06269, USA
| | - Daoyuan Shi
- Department of Statistics, University of Connecticut, 215 Glenbrook Road, Unit 4120, Storrs, CT 06269, USA
| |
Collapse
|
3
|
Hong WS, Shpak M, Townsend JP. Inferring the Origin of Metastases from Cancer Phylogenies. Cancer Res 2015; 75:4021-5. [PMID: 26260528 PMCID: PMC4833389 DOI: 10.1158/0008-5472.can-15-1889] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 08/04/2015] [Indexed: 01/06/2023]
Abstract
Determining the evolutionary history of metastases is a key problem in cancer biology. Several recent studies have presented inferences regarding the origin of metastases based on phylogenies of cancer lineages. Many of these studies have concluded that the observed monophyly of metastatic subclones favored metastasis-to-metastasis spread ("a metastatic cascade" rather than parallel metastases from the primary tumor). In this article, we argue that identifying a monophyletic clade of metastatic subclones does not provide sufficient evidence to unequivocally establish a history of metastatic cascades. In the absence of a complete phylogeny of the subclones within the primary tumor, a scenario of parallel metastatic events from the primary tumor is an equally plausible interpretation. Future phylogenetic studies on the origin of metastases should obtain a complete phylogeny of subclones within the primary tumor. This complete phylogeny may be obtainable by ultra-deep sequencing and phasing of large sections or by targeted sequencing of many small, spatially heterogeneous sections, followed by phylogenetic reconstruction using well-established molecular evolutionary models. In addition to resolving the evolutionary history of metastases, a complete phylogeny of subclones within the primary tumor facilitates the identification of driver mutations by application of phylogeny-based tests of natural selection.
Collapse
Affiliation(s)
| | - Max Shpak
- NeuroTexas Institute, St. David's Medical Center, Austin, Texas. Center for Systems and Synthetic Biology, University of Texas, Austin, Texas. Fresh Pond Research Institute, Cambridge, Massachusetts.
| | - Jeffrey P Townsend
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut. Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut. Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut
| |
Collapse
|
4
|
Mulder WH, Crawford FW. On the distribution of interspecies correlation for Markov models of character evolution on Yule trees. J Theor Biol 2015; 364:275-83. [PMID: 25240905 PMCID: PMC4256168 DOI: 10.1016/j.jtbi.2014.09.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2014] [Revised: 08/15/2014] [Accepted: 09/09/2014] [Indexed: 10/24/2022]
Abstract
Efforts to reconstruct phylogenetic trees and understand evolutionary processes depend fundamentally on stochastic models of speciation and mutation. The simplest continuous-time model for speciation in phylogenetic trees is the Yule process, in which new species are "born" from existing lineages at a constant rate. Recent work has illuminated some of the structural properties of Yule trees, but it remains mostly unknown how these properties affect sequence and trait patterns observed at the tips of the phylogenetic tree. Understanding the interplay between speciation and mutation under simple models of evolution is essential for deriving valid phylogenetic inference methods and gives insight into the optimal design of phylogenetic studies. In this work, we derive the probability distribution of interspecies covariance under Brownian motion and Ornstein-Uhlenbeck models of phenotypic change on a Yule tree. We compute the probability distribution of the number of mutations shared between two randomly chosen taxa in a Yule tree under discrete Markov mutation models. Our results suggest summary measures of phylogenetic information content, illuminate the correlation between site patterns in sequences or traits of related organisms, and provide heuristics for experimental design and reconstruction of phylogenetic trees.
Collapse
Affiliation(s)
- Willem H Mulder
- Department of Chemistry, The University of the West Indies, Mona Campus, Kingston 7, Jamaica.
| | - Forrest W Crawford
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA.
| |
Collapse
|
5
|
Hilu KW, Black CM, Oza D. Impact of gene molecular evolution on phylogenetic reconstruction: a case study in the rosids (Superorder Rosanae, Angiosperms). PLoS One 2014; 9:e99725. [PMID: 24932884 PMCID: PMC4059714 DOI: 10.1371/journal.pone.0099725] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 05/18/2014] [Indexed: 11/19/2022] Open
Abstract
Rate of substitution of genomic regions is among the most debated intrinsic features that impact phylogenetic informativeness. However, this variable is also coupled with rates of nonsynonymous substitutions that underscore the nature and degree of selection on the selected genes. To empirically address these variables, we constructed four completely overlapping data sets of plastid matK, atpB, rbcL, and mitochondrial matR genes and used the rosid lineage (angiosperms) as a working platform. The genes differ in combinations of overall rates of nucleotide and amino acid substitutions. Tree robustness, homoplasy, accuracy in contrast to a reference tree, and phylogenetic informativeness are evaluated. The rapidly evolving/unconstrained matK faired best, whereas remaining genes varied in degrees of contribution to rosid phylogenetics across the lineage's 108 million years evolutionary history. Phylogenetic accuracy was low with the slowly evolving/unconstrained matR despite least amount of homoplasy. Third codon positions contributed the highest amount of parsimony informative sites, resolution and informativeness, but magnitude varied with gene mode of evolution. These findings are in clear contrast with the views that rapidly evolving regions and the 3rd codon position have inevitable negative impact on phylogenetic reconstruction at deep historic level due to accumulation of multiple hits and subsequent elevation in homoplasy and saturation. Relaxed evolutionary constraint in rapidly evolving genes distributes substitutions across codon positions, an evolutionary mode expected to reduce the frequency of multiple hits. These findings should be tested at deeper evolutionary histories.
Collapse
Affiliation(s)
- Khidir W. Hilu
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Chelsea M. Black
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Dipan Oza
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, United States of America
| |
Collapse
|
6
|
Baeza JA, Fuentes MS. Exploring phylogenetic informativeness and nuclear copies of mitochondrial DNA (numts) in three commonly used mitochondrial genes: mitochondrial phylogeny of peppermint, cleaner, and semi-terrestrial shrimps (Caridea:Lysmata,Exhippolysmata, andMerguia). Zool J Linn Soc 2013. [DOI: 10.1111/zoj.12044] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
|
7
|
Martyn I, Steel M. The impact and interplay of long and short branches on phylogenetic information content. J Theor Biol 2012; 314:157-63. [PMID: 22981922 DOI: 10.1016/j.jtbi.2012.08.040] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Revised: 08/24/2012] [Accepted: 08/27/2012] [Indexed: 10/27/2022]
Abstract
In molecular systematics, evolutionary trees are reconstructed from sequences at the tips under simple models of site substitution. A central question is how much sequence data is required to reconstruct a tree accurately? The answer depends on the lengths of the branches (edges) of the tree, with very short and very long edges requiring long sequences for accurate tree inference, particularly when these branch lengths are arranged in certain ways. For four-taxon trees, the sequence length question has been investigated for the case of a rapid speciation event in the distant past. Here, we generalize results from this earlier study, and show that the same sequence length requirement holds even when the speciation event is recent, provided that at least one of the four taxa is distantly related to the others. However, this equivalence disappears if a molecular clock applies, since the length of the long outgroup edge becomes largely irrelevant in the estimation of the tree topology for a recent divergence. We also discuss briefly some extensions of these results to models in which substitution rates vary across sites and to settings where more than four taxa are involved.
Collapse
Affiliation(s)
- Iain Martyn
- IRMACS and BioSciences, Simon Fraser University, Burnaby, Canada.
| | | |
Collapse
|
8
|
Klopfstein S, Kropf C, Quicke DLJ. An evaluation of phylogenetic informativeness profiles and the molecular phylogeny of diplazontinae (Hymenoptera, Ichneumonidae). Syst Biol 2010; 59:226-41. [PMID: 20525632 DOI: 10.1093/sysbio/syp105] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
How to quantify the phylogenetic information content of a data set is a longstanding question in phylogenetics, influencing both the assessment of data quality in completed studies and the planning of future phylogenetic projects. Recently, a method has been developed that profiles the phylogenetic informativeness (PI) of a data set through time by linking its site-specific rates of change to its power to resolve relationships at different timescales. Here, we evaluate the performance of this method in the case of 2 standard genetic markers for phylogenetic reconstruction, 28S ribosomal RNA and cytochrome oxidase subunit 1 (CO1) mitochondrial DNA, with maximum parsimony, maximum likelihood, and Bayesian analyses of relationships within a group of parasitoid wasps (Hymenoptera: Ichneumonidae, Diplazontinae). Retrieving PI profiles of the 2 genes from our own and from 3 additional data sets, we find that the method repeatedly overestimates the performance of the more quickly evolving CO1 compared with 28S. We explore possible reasons for this bias, including phylogenetic uncertainty, violation of the molecular clock assumption, model misspecification, and nonstationary nucleotide composition. As none of these provides a sufficient explanation of the observed discrepancy, we use simulated data sets, based on an idealized setting, to show that the optimum evolutionary rate decreases with increasing number of taxa. We suggest that this relationship could explain why the formula derived from the 4-taxon case overrates the performance of higher versus lower rates of evolution in our case and that caution should be taken when the method is applied to data sets including more than 4 taxa.
Collapse
Affiliation(s)
- Seraina Klopfstein
- Department of Invertebrates, Natural History Museum, Bernastrasse 15, CH-3005 Bern, Switzerland.
| | | | | |
Collapse
|
9
|
Hoover CA, Slattery M, Targett NM, Marsh AG. Transcriptome and metabolite responses to predation in a South pacific soft coral. THE BIOLOGICAL BULLETIN 2008; 214:319-328. [PMID: 18574108 DOI: 10.2307/25470673] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Sinularia polydactyla, a dioecious, abundant soft coral in the South Pacific, exhibits biochemical phenotypic plasticity in secondary metabolite production in relation to predation intensity. However, it is unclear to what extent changes in secondary metabolites, such as 11beta-acetoxypukalide, may result from specific, induced pathway activities at the level of gene expression. To investigate both chemical changes and differences in mRNA diversity in response to predation stress, artificial predation experiments were conducted in situ on colonies of S. polydactyla. Multivariate statistical analyses of coral biochemical metabolites and our kinetic transcriptome profiling technique indicate that that the induction of 11beta-acetoxypukalide by predation stress likely results from the upregulation of either one dominant transcript or a very small set of transcripts, indicative of a targeted upregulation rather than a generalized, genetic stress response. Overall, this work establishes a routine method for integrating high-throughput transcriptome and metabolome data sets to allow for the identification of metabolites whose intracellular concentrations can be readily linked to gene expression events in response to specific treatments in non-model organisms.
Collapse
Affiliation(s)
- Cindi A Hoover
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, USA.
| | | | | | | |
Collapse
|
10
|
Abstract
The resolution of four controversial topics in phylogenetic experimental design hinges upon the informativeness of characters about the historical relationships among taxa. These controversies regard the power of different classes of phylogenetic character, the relative utility of increased taxonomic versus character sampling, the differentiation between lack of phylogenetic signal and a historical rapid radiation, and the design of taxonomically broad phylogenetic studies optimized by taxonomically sparse genome-scale data. Quantification of the informativeness of characters for resolution of phylogenetic hypotheses during specified historical epochs is key to the resolution of these controversies. Here, such a measure of phylogenetic informativeness is formulated. The optimal rate of evolution of a character to resolve a dated four-taxon polytomy is derived. By scaling the asymptotic informativeness of a character evolving at a nonoptimal rate by the derived asymptotic optimum, and by normalizing so that net phylogenetic informativeness is equivalent for all rates when integrated across all of history, an informativeness profile across history is derived. Calculation of the informativeness per base pair allows estimation of the cost-effectiveness of character sampling. Calculation of the informativeness per million years allows comparison across historical radiations of the utility of a gene for the inference of rapid adaptive radiation. The theory is applied to profile the phylogenetic informativeness of the genes BRCA1, RAG1, GHR, and c-myc from a muroid rodent sequence data set. Bounded integrations of the phylogenetic profile of these genes over four epochs comprising the diversifications of the muroid rodents, the mammals, the lobe-limbed vertebrates, and the early metazoans demonstrate the differential power of these genes to resolve the branching order among ancestral lineages. This measure of phylogenetic informativeness yields a new kind of information for evaluation of phylogenetic experiments. It conveys the utility of the addition of characters a phylogenetic study and it provides a basis for deciding whether appropriate phylogenetic power has been applied to a polytomy that is proposed to be a rapid radiation. Moreover, it provides a quantitative measure of the capacity of a gene to resolve soft polytomies.
Collapse
Affiliation(s)
- Jeffrey P Townsend
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06520, USA.
| |
Collapse
|
11
|
Hoover CA, Slattery M, Marsh AG. A functional approach to transcriptome profiling: linking gene expression patterns to metabolites that matter. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2007; 9:411-9. [PMID: 17473905 DOI: 10.1007/s10126-007-9008-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2007] [Revised: 02/21/2007] [Accepted: 03/08/2007] [Indexed: 05/15/2023]
Abstract
Secondary metabolites or natural products have been isolated from many marine organisms. These metabolites often have important bioactive functions; however, very little information is available regarding the biosynthesis and regulation of many secondary metabolites. At a time when use of marine-derived metabolites is rapidly expanding in industry and pharmacological fields, a better understanding of the genetic mechanisms controlling secondary metabolite production is necessary. We review the recent development of a novel transcriptome profiling methodology that allows for rapid and high-throughput screening of changes in mRNA sequence pools. The application of genomics-based techniques and the integration of both biochemical and molecular data sets in marine organisms complement ongoing drug discovery efforts.
Collapse
Affiliation(s)
- Cindi A Hoover
- Molecular Biology Production Group, Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA.
| | | | | |
Collapse
|
12
|
Hoover CA, Slattery M, Marsh AG. Gene expression profiling of two related soft corals, Sinularia polydactyla and S. maxima, and their putative hybrid at different life-history stages. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2007; 2:135-143. [PMID: 20483287 DOI: 10.1016/j.cbd.2007.01.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2006] [Revised: 01/24/2007] [Accepted: 01/26/2007] [Indexed: 05/29/2023]
Abstract
The soft coral species, Sinularia polydactyla and Sinularia maxima are abundant in shallow coral reef habitats in Guam. Both species are gonochoric and mass spawning events can result in an apparent S. polydactyla-S. maxima hybrid exhibiting morphological characteristics of both parents. These morphological differences prompted our investigation of potential differences in gene expression patterns among these closely related species. In concert with interspecific level differences, intraspecific level differences in transcriptome diversity and complexity were also studied among juvenile, adult male, and adult female S. polydactyla colonies. To uncover these transcriptome-level differences, RNA was extracted from RNAlater(R)-preserved samples and cDNA libraries constructed using a nano-scale synthesis strategy. Changes in transcriptome complexity (mRNA sequence composition) of these libraries were measured using reannealing rate assays that employ an informatics-based analysis of kinetic profiles. This method allows for quick, high-throughput analysis of sequence complexity and has been used to compare transcriptome-level differences in other marine invertebrates. Comparisons of transcriptome data revealed diagnostic differences in the transcriptome pools. Examination of transcriptome changes in closely related species experiencing similar environmental parameters may enable us to understand developmental, morphological, and sex-specific changes in gene expression patterns.
Collapse
Affiliation(s)
- Cindi A Hoover
- College of Marine and Earth Studies, University of Delaware, Lewes, DE 19958 USA
| | | | | |
Collapse
|
13
|
Hoover CA, Slattery M, Marsh AG. Profiling transcriptome complexity and secondary metabolite synthesis in a benthic soft coral, Sinularia polydactyla. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2007; 9:166-78. [PMID: 17186429 DOI: 10.1007/s10126-006-6048-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2006] [Accepted: 09/23/2006] [Indexed: 05/13/2023]
Abstract
Sinularia polydactyla, an abundant Indo-Pacific soft coral species, exhibits biochemical phenotypic plasticity, prompting investigations into differences in mRNA diversity and complexity in response to predation stress. Changes in transcriptome complexity of S. polydactyla cDNA libraries were measured using reannealing rate assays that employ an informatics-based analysis of kinetic profiles. This method allows for quick, high-throughput analysis of sequence complexity and has been used to compare transcriptome-level differences in other marine invertebrates. Here, S. polydactyla colonies were transplanted between two sites exhibiting high and low predation levels. Statistically significant differences between bite scar counts found on different transplant groups suggest site-specific variation in predation. Changes in mRNA pool complexity were quantified to indicate shifts in secondary metabolite concentration between treatment groups. Examining the complexity of the mRNA pool in this soft coral is one of the first steps toward understanding the mechanisms of phenotypic plasticity at a biochemical and molecular level.
Collapse
Affiliation(s)
- Cindi A Hoover
- College of Marine and Earth Studies, University of Delaware, Lewes, Delaware 19958, USA.
| | | | | |
Collapse
|
14
|
LIVEZEY BRADLEYC, ZUSI RICHARDL. Higher-order phylogeny of modern birds (Theropoda, Aves: Neornithes) based on comparative anatomy. II. Analysis and discussion. Zool J Linn Soc 2007; 149:1-95. [PMID: 18784798 PMCID: PMC2517308 DOI: 10.1111/j.1096-3642.2006.00293.x] [Citation(s) in RCA: 281] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
In recent years, avian systematics has been characterized by a diminished reliance on morphological cladistics of modern taxa, intensive palaeornithogical research stimulated by new discoveries and an inundation by analyses based on DNA sequences. Unfortunately, in contrast to significant insights into basal origins, the broad picture of neornithine phylogeny remains largely unresolved. Morphological studies have emphasized characters of use in palaeontological contexts. Molecular studies, following disillusionment with the pioneering, but non-cladistic, work of Sibley and Ahlquist, have differed markedly from each other and from morphological works in both methods and findings. Consequently, at the turn of the millennium, points of robust agreement among schools concerning higher-order neornithine phylogeny have been limited to the two basalmost and several mid-level, primary groups. This paper describes a phylogenetic (cladistic) analysis of 150 taxa of Neornithes, including exemplars from all non-passeriform families, and subordinal representatives of Passeriformes. Thirty-five outgroup taxa encompassing Crocodylia, predominately theropod Dinosauria, and selected Mesozoic birds were used to root the trees. Based on study of specimens and the literature, 2954 morphological characters were defined; these characters have been described in a companion work, approximately one-third of which were multistate (i.e. comprised at least three states), and states within more than one-half of these multistate characters were ordered for analysis. Complete heuristic searches using 10 000 random-addition replicates recovered a total solution set of 97 well-resolved, most-parsimonious trees (MPTs). The set of MPTs was confirmed by an expanded heuristic search based on 10 000 random-addition replicates and a full ratchet-augmented exploration to ascertain global optima. A strict consensus tree of MPTs included only six trichotomies, i.e. nodes differing topologically among MPTs. Bootstrapping (based on 10 000 replicates) percentages and ratchet-minimized support (Bremer) indices indicated most nodes to be robust. Several fossil Neornithes (e.g. Dinornithiformes, Aepyornithiformes) were placed within the ingroup a posteriori either through unconstrained, heursitic searches based on the complete matrix augmented by these taxa separately or using backbone-constraints. Analysis confirmed the topology among outgroup Theropoda and achieved robust resolution at virtually all levels of the Neornithes. Findings included monophyly of the palaeognathous birds, comprising the sister taxa Tinamiformes and ratites, respectively, and the Anseriformes and Galliformes as monophyletic sister-groups, together forming the sister-group to other Neornithes exclusive of the Palaeognathae (Neoaves). Noteworthy inferences include: (i) the sister-group to remaining Neoaves comprises a diversity of marine and wading birds; (ii) Podicipedidae are the sister-group of Gaviidae, and not closely related to the Phoenicopteridae, as recently suggested; (iii) the traditional Pelecaniformes, including the shoebill (Balaeniceps rex) as sister-taxon to other members, are monophyletic; (iv) traditional Ciconiiformes are monophyletic; (v) Strigiformes and Falconiformes are sister-groups; (vi) Cathartidae is the sister-group of the remaining Falconiformes; (vii) Ralliformes (Rallidae and Heliornithidae) are the sister-group to the monophyletic Charadriiformes, with the traditionally composed Gruiformes and Turniciformes (Turnicidae and Mesitornithidae) sequentially paraphyletic to the entire foregoing clade; (viii) Opisthocomus hoazin is the sister-taxon to the Cuculiformes (including the Musophagidae); (ix) traditional Caprimulgiformes are monophyletic and the sister-group of the Apodiformes; (x) Trogoniformes are the sister-group of Coliiformes; (xi) Coraciiformes, Piciformes and Passeriformes are mutually monophyletic and closely related; and (xii) the Galbulae are retained within the Piciformes. Unresolved portions of the Neornithes (nodes having more than one most-parsimonious solution) comprised three parts of the tree: (a) several interfamilial nodes within the Charadriiformes; (b) a trichotomy comprising the (i) Psittaciformes, (ii) Columbiformes and (iii) Trogonomorphae (Trogoniformes, Coliiformes) + Passerimorphae (Coraciiformes, Piciformes, Passeriformes); and (c) a trichotomy comprising the Coraciiformes, Piciformes and Passeriformes. The remaining polytomies were among outgroups, although several of the highest-order nodes were only marginally supported; however, the majority of nodes were resolved and met or surpassed conventional standards of support. Quantitative comparisons with alternative hypotheses, examination of highly supportive and diagnostic characters for higher taxa, correspondences with prior studies, complementarity and philosophical differences with palaeontological phylogenetics, promises and challenges of palaeogeography and calibration of evolutionary rates of birds, and classes of promising evidence and future directions of study are reviewed. Homology, as applied to avian examples of apparent homologues, is considered in terms of recent theory, and a revised annotated classification of higher-order taxa of Neornithes and other closely related Theropoda is proposed. (c) 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149, 1-95.
Collapse
Affiliation(s)
- BRADLEY C LIVEZEY
- Section of Birds, Carnegie Museum of Natural History4400 Forbes Avenue, Pittsburgh, PA 15213-4080, USA
| | - RICHARD L ZUSI
- Division of Birds, National Museum of Natural HistoryWashington, DC 20013-7012, USA
| |
Collapse
|
15
|
Marsh AG, Fielman KT. Transcriptome profiling of individual larvae of two different developmental modes in the poecilogonous polychaete Streblospio benedicti (Spionidae). JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2005; 304:238-49. [PMID: 15834936 DOI: 10.1002/jez.b.21037] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Understanding the range of biochemical and physiological phenotypes in a cohort of embryos or larvae is crucial to understanding the lifespan, dispersal potential, and recruitment success of the early life history stages of a species. In this study, a novel kinetic assay has been employed to profile the transcriptome pool complexity in individual larvae of both planktotrophic and lecithotrophic developmental modes in the poecilogonous polycheate Streblospio benedicti. Using a nano-scale synthesis strategy, the mRNA pool in a single embryo or larva can be amplified into cDNA for quantitative characterization in a high-throughput, kinetic reannealing assay in a 96-well, microtiterplate format. This assay generates transcript-pool complexity estimates at 1 degrees C temperature increments for each sample producing 3,360 quantitative measurements per 96-well plate. Measuring transcriptome complexity on 8 individual planktotrophic and 8 individual lecithotrophic larvae (with 4 duplicate assays for each individual) reveals a more complex gene expression profile in planktotrophic larvae and a lower level of interindividual variation in expression patterns in lecithotrophic larvae. Although differences in these gene expression patterns are more likely due to physiological differences between feeding and non-feeding larval types in these late-stage individuals, this is one of the first assessments of inter-individual variation in gene expression patterns in marine invertebrate larvae and indicates a large potential for developmental variability.
Collapse
Affiliation(s)
- Adam G Marsh
- College of Marine Studies, University of Delaware, Lewes, Delaware 19958, USA.
| | | |
Collapse
|