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Flouri T, Huang J, Jiao X, Kapli P, Rannala B, Yang Z. Bayesian phylogenetic inference using relaxed-clocks and the multispecies coalescent. Mol Biol Evol 2022; 39:6652437. [PMID: 35907248 PMCID: PMC9366188 DOI: 10.1093/molbev/msac161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The multispecies coalescent (MSC) model accommodates both species divergences and within-species coalescent and provides a natural framework for phylogenetic analysis of genomic data when the gene trees vary across the genome. The MSC model implemented in the program bpp assumes a molecular clock and the Jukes–Cantor model, and is suitable for analyzing genomic data from closely related species. Here we extend our implementation to more general substitution models and relaxed clocks to allow the rate to vary among species. The MSC-with-relaxed-clock model allows the estimation of species divergence times and ancestral population sizes using genomic sequences sampled from contemporary species when the strict clock assumption is violated, and provides a simulation framework for evaluating species tree estimation methods. We conducted simulations and analyzed two real datasets to evaluate the utility of the new models. We confirm that the clock-JC model is adequate for inference of shallow trees with closely related species, but it is important to account for clock violation for distant species. Our simulation suggests that there is valuable phylogenetic information in the gene-tree branch lengths even if the molecular clock assumption is seriously violated, and the relaxed-clock models implemented in bpp are able to extract such information. Our Markov chain Monte Carlo algorithms suffer from mixing problems when used for species tree estimation under the relaxed clock and we discuss possible improvements. We conclude that the new models are currently most effective for estimating population parameters such as species divergence times when the species tree is fixed.
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Affiliation(s)
- Tomáš Flouri
- Department of Genetics, Evolution, and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Jun Huang
- Department of Genetics, Evolution, and Environment, University College London, Gower Street, London WC1E 6BT, UK.,School of Biomedical Engineering, Capital Medical University, Beijing, 100069, China
| | - Xiyun Jiao
- Department of Genetics, Evolution, and Environment, University College London, Gower Street, London WC1E 6BT, UK.,Department of Statistics and Data Science, China Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Paschalia Kapli
- Department of Genetics, Evolution, and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Bruce Rannala
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
| | - Ziheng Yang
- Department of Genetics, Evolution, and Environment, University College London, Gower Street, London WC1E 6BT, UK
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2
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Jiao X, Flouri T, Yang Z. Multispecies coalescent and its applications to infer species phylogenies and cross-species gene flow. Natl Sci Rev 2022; 8:nwab127. [PMID: 34987842 PMCID: PMC8692950 DOI: 10.1093/nsr/nwab127] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/10/2021] [Accepted: 07/11/2021] [Indexed: 02/06/2023] Open
Abstract
Multispecies coalescent (MSC) is the extension of the single-population coalescent model to multiple species. It integrates the phylogenetic process of species divergences and the population genetic process of coalescent, and provides a powerful framework for a number of inference problems using genomic sequence data from multiple species, including estimation of species divergence times and population sizes, estimation of species trees accommodating discordant gene trees, inference of cross-species gene flow and species delimitation. In this review, we introduce the major features of the MSC model, discuss full-likelihood and heuristic methods of species tree estimation and summarize recent methodological advances in inference of cross-species gene flow. We discuss the statistical and computational challenges in the field and research directions where breakthroughs may be likely in the next few years.
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Affiliation(s)
- Xiyun Jiao
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Tomáš Flouri
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Ziheng Yang
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
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3
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Hime PM, Lemmon AR, Lemmon ECM, Prendini E, Brown JM, Thomson RC, Kratovil JD, Noonan BP, Pyron RA, Peloso PLV, Kortyna ML, Keogh JS, Donnellan SC, Mueller RL, Raxworthy CJ, Kunte K, Ron SR, Das S, Gaitonde N, Green DM, Labisko J, Che J, Weisrock DW. Phylogenomics Reveals Ancient Gene Tree Discordance in the Amphibian Tree of Life. Syst Biol 2021; 70:49-66. [PMID: 32359157 PMCID: PMC7823230 DOI: 10.1093/sysbio/syaa034] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 04/14/2020] [Accepted: 04/14/2020] [Indexed: 11/30/2022] Open
Abstract
Molecular phylogenies have yielded strong support for many parts of the amphibian Tree of Life, but poor support for the resolution of deeper nodes, including relationships among families and orders. To clarify these relationships, we provide a phylogenomic perspective on amphibian relationships by developing a taxon-specific Anchored Hybrid Enrichment protocol targeting hundreds of conserved exons which are effective across the class. After obtaining data from 220 loci for 286 species (representing 94% of the families and 44% of the genera), we estimate a phylogeny for extant amphibians and identify gene tree-species tree conflict across the deepest branches of the amphibian phylogeny. We perform locus-by-locus genealogical interrogation of alternative topological hypotheses for amphibian monophyly, focusing on interordinal relationships. We find that phylogenetic signal deep in the amphibian phylogeny varies greatly across loci in a manner that is consistent with incomplete lineage sorting in the ancestral lineage of extant amphibians. Our results overwhelmingly support amphibian monophyly and a sister relationship between frogs and salamanders, consistent with the Batrachia hypothesis. Species tree analyses converge on a small set of topological hypotheses for the relationships among extant amphibian families. These results clarify several contentious portions of the amphibian Tree of Life, which in conjunction with a set of vetted fossil calibrations, support a surprisingly younger timescale for crown and ordinal amphibian diversification than previously reported. More broadly, our study provides insight into the sources, magnitudes, and heterogeneity of support across loci in phylogenomic data sets.[AIC; Amphibia; Batrachia; Phylogeny; gene tree-species tree discordance; genomics; information theory.].
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Affiliation(s)
- Paul M Hime
- Biodiversity Institute, University of Kansas, Lawrence, KS 66045, USA
- Department of Biology, University of Kentucky, Lexington, KY 40506, USA
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, FL 32306, USA
| | | | - Elizabeth Prendini
- Division of Vertebrate Zoology: Herpetology, American Museum of Natural History, New York, NY 10024, USA
| | - Jeremy M Brown
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Robert C Thomson
- School of Life Sciences, University of Hawai’i, Honolulu, HI 96822, USA
| | - Justin D Kratovil
- Department of Biology, University of Kentucky, Lexington, KY 40506, USA
- Department of Entomology, University of Kentucky, Lexington, KY 40546, USA
| | - Brice P Noonan
- Department of Biology, University of Mississippi, Oxford, MS 38677, USA
| | - R Alexander Pyron
- Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA
| | - Pedro L V Peloso
- Division of Vertebrate Zoology: Herpetology, American Museum of Natural History, New York, NY 10024, USA
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, 66075-750, Brazil
| | - Michelle L Kortyna
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - J Scott Keogh
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, 2601, Australia
| | - Stephen C Donnellan
- South Australian Museum, North Terrace, Adelaide 5000, Australia
- School of Biological Sciences, University of Adelaide, Adelaide 5005, Australia
| | | | - Christopher J Raxworthy
- Division of Vertebrate Zoology: Herpetology, American Museum of Natural History, New York, NY 10024, USA
| | - Krushnamegh Kunte
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India
| | - Santiago R Ron
- Museo de Zoología, Escuela de Biología, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Sandeep Das
- Forest Ecology and Biodiversity Conservation Division, Kerala Forest Research Institute, Peechi, Kerala 680653, India
| | - Nikhil Gaitonde
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India
| | - David M Green
- Redpath Museum, McGill University, Montreal, Quebec H3A 0C4, Canada
| | - Jim Labisko
- The Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, The University of Kent, Canterbury, Kent, CT2 7NR, UK
- Island Biodiversity and Conservation Centre, University of Seychelles, PO Box 1348, Anse Royale, Mahé, Seychelles
| | - Jing Che
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Kunming 650223, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - David W Weisrock
- Department of Biology, University of Kentucky, Lexington, KY 40506, USA
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Huang J, Flouri T, Yang Z. A Simulation Study to Examine the Information Content in Phylogenomic Data Sets under the Multispecies Coalescent Model. Mol Biol Evol 2020; 37:3211-3224. [DOI: 10.1093/molbev/msaa166] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
AbstractWe use computer simulation to examine the information content in multilocus data sets for inference under the multispecies coalescent model. Inference problems considered include estimation of evolutionary parameters (such as species divergence times, population sizes, and cross-species introgression probabilities), species tree estimation, and species delimitation based on Bayesian comparison of delimitation models. We found that the number of loci is the most influential factor for almost all inference problems examined. Although the number of sequences per species does not appear to be important to species tree estimation, it is very influential to species delimitation. Increasing the number of sites and the per-site mutation rate both increase the mutation rate for the whole locus and these have the same effect on estimation of parameters, but the sequence length has a greater effect than the per-site mutation rate for species tree estimation. We discuss the computational costs when the data size increases and provide guidelines concerning the subsampling of genomic data to enable the application of full-likelihood methods of inference.
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Affiliation(s)
- Jun Huang
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
- Department of Mathematics, Beijing Jiaotong University, Beijing, P.R. China
| | - Tomáš Flouri
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Ziheng Yang
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
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5
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Chow JC, Anderson PE, Shedlock AM. Sea Turtle Population Genomic Discovery: Global and Locus-Specific Signatures of Polymorphism, Selection, and Adaptive Potential. Genome Biol Evol 2020; 11:2797-2806. [PMID: 31504487 PMCID: PMC6786478 DOI: 10.1093/gbe/evz190] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/29/2019] [Indexed: 12/21/2022] Open
Abstract
In the era of genomics, single-nucleotide polymorphisms (SNPs) have become a preferred molecular marker to study signatures of selection and population structure and to enable improved population monitoring and conservation of vulnerable populations. We apply a SNP calling pipeline to assess population differentiation, visualize linkage disequilibrium, and identify loci with sex-specific genotypes of 45 loggerhead sea turtles (Caretta caretta) sampled from the southeastern coast of the United States, including 42 individuals experimentally confirmed for gonadal sex. By performing reference-based SNP calling in independent runs of Stacks, 3,901–6,998 SNPs and up to 30 potentially sex-specific genotypes were identified. Up to 68 pairs of loci were found to be in complete linkage disequilibrium, potentially indicating regions of natural selection and adaptive evolution. This study provides a valuable SNP diagnostic workflow and a large body of new biomarkers for guiding targeted studies of sea turtle genome evolution and for managing legally protected nonmodel iconic species that have high economic and ecological importance but limited genomic resources.
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Affiliation(s)
- Julie C Chow
- Integrative Genetics and Genomics Graduate Group, University of California, Davis
| | - Paul E Anderson
- Department of Computer Science, College of Charleston, Charleston, South Carolina.,Department of Computer Science and Software Engineering, California Polytechnic State University, San Luis Obispo, CA 93407
| | - Andrew M Shedlock
- Department of Biology, College of Charleston, Charleston, South Carolina.,College of Graduate Studies, Medical University of South Carolina.,Marine Genomics Division, Hollings Marine Laboratory, Charleston, South Carolina
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Koparde P, Mehta P, Reddy S, Ramakrishnan U, Mukherjee S, Robin VV. The critically endangered forest owlet Heteroglaux blewitti is nested within the currently recognized Athene clade: A century-old debate addressed. PLoS One 2018; 13:e0192359. [PMID: 29401484 PMCID: PMC5798823 DOI: 10.1371/journal.pone.0192359] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 01/21/2018] [Indexed: 11/23/2022] Open
Abstract
Range-restricted species generally have specific niche requirements and may often have unique evolutionary histories. Unfortunately, many of these species severely lack basic research, resulting in poor conservation strategies. The phylogenetic relationship of the Critically Endangered Forest Owlet Heteroglaux blewitti has been the subject of a century-old debate. The current classifications based on non-phylogenetic comparisons of morphology place the small owls of Asia into three genera, namely, Athene, Glaucidium, and Heteroglaux. Based on morphological and anatomical data, H. blewitti has been alternatively hypothesized to belong within Athene, Glaucidium, or its own monotypic genus Heteroglaux. To test these competing hypotheses, we sequenced six loci (~4300 bp data) and performed phylogenetic analyses of owlets. Mitochondrial and nuclear trees were not congruent in their placement of H. blewitti. However, both mitochondrial and nuclear combined datasets showed strong statistical support with high maximum likelihood bootstrap (>/ = 90) and Bayesian posterior probability values (>/ = 0.98) for H. blewitti being nested in the currently recognized Athene group, but not sister to Indian A. brama. The divergence of H. blewitti from its sister taxa was between 4.3 and 5.7 Ma coinciding with a period of drastic climatic changes in the Indian subcontinent. This study presented the first genetic analysis of H. blewitti, a Critically Endangered species, and addressed the long debate on the relationships of the Athene-Heteroglaux-Glaucidium complex. We recommend further studies with more data and complete taxon sampling to understand the biogeography of Indian Athene species.
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Affiliation(s)
- Pankaj Koparde
- Division of Conservation Biology, Sálim Ali Centre for Ornithology & Natural History, Coimbatore, Tamil Nadu, India
- Manipal Academy of Higher Education, Madhav Nagar, Manipal, Karnataka, India
- Indian Institute of Science Education and Research, Tirupati, Andhra Pradesh, India
- * E-mail:
| | - Prachi Mehta
- Wildlife Research and Conservation Society, Pune, Maharashtra, India
| | - Sushma Reddy
- Loyola University, Chicago, Illinois, United States of America
| | - Uma Ramakrishnan
- National Centre for Biological Science, TIFR, Bangalore, Karnataka, India
| | - Shomita Mukherjee
- Division of Conservation Biology, Sálim Ali Centre for Ornithology & Natural History, Coimbatore, Tamil Nadu, India
| | - V. V. Robin
- Indian Institute of Science Education and Research, Tirupati, Andhra Pradesh, India
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7
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Hasegawa M, Kuroda S. Phylogeny mandalas of birds using the lithographs of John Gould’s folio bird books. Mol Phylogenet Evol 2017; 117:141-149. [DOI: 10.1016/j.ympev.2016.12.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Revised: 10/12/2016] [Accepted: 12/05/2016] [Indexed: 12/19/2022]
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8
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Challenges in Species Tree Estimation Under the Multispecies Coalescent Model. Genetics 2017; 204:1353-1368. [PMID: 27927902 DOI: 10.1534/genetics.116.190173] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 09/25/2016] [Indexed: 11/18/2022] Open
Abstract
The multispecies coalescent (MSC) model has emerged as a powerful framework for inferring species phylogenies while accounting for ancestral polymorphism and gene tree-species tree conflict. A number of methods have been developed in the past few years to estimate the species tree under the MSC. The full likelihood methods (including maximum likelihood and Bayesian inference) average over the unknown gene trees and accommodate their uncertainties properly but involve intensive computation. The approximate or summary coalescent methods are computationally fast and are applicable to genomic datasets with thousands of loci, but do not make an efficient use of information in the multilocus data. Most of them take the two-step approach of reconstructing the gene trees for multiple loci by phylogenetic methods and then treating the estimated gene trees as observed data, without accounting for their uncertainties appropriately. In this article we review the statistical nature of the species tree estimation problem under the MSC, and explore the conceptual issues and challenges of species tree estimation by focusing mainly on simple cases of three or four closely related species. We use mathematical analysis and computer simulation to demonstrate that large differences in statistical performance may exist between the two classes of methods. We illustrate that several counterintuitive behaviors may occur with the summary methods but they are due to inefficient use of information in the data by summary methods and vanish when the data are analyzed using full-likelihood methods. These include (i) unidentifiability of parameters in the model, (ii) inconsistency in the so-called anomaly zone, (iii) singularity on the likelihood surface, and (iv) deterioration of performance upon addition of more data. We discuss the challenges and strategies of species tree inference for distantly related species when the molecular clock is violated, and highlight the need for improving the computational efficiency and model realism of the likelihood methods as well as the statistical efficiency of the summary methods.
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9
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Stöger I, Kocot KM, Poustka AJ, Wilson NG, Ivanov D, Halanych KM, Schrödl M. Monoplacophoran mitochondrial genomes: convergent gene arrangements and little phylogenetic signal. BMC Evol Biol 2016; 16:274. [PMID: 27986078 PMCID: PMC5162086 DOI: 10.1186/s12862-016-0829-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 11/17/2016] [Indexed: 04/07/2023] Open
Abstract
BACKGROUND Although recent studies have greatly advanced understanding of deep molluscan phylogeny, placement of some taxa remains uncertain as different datasets support competing class-relationships. Traditionally, morphologists have placed Monoplacophora, a group of morphologically simple, limpet-like molluscs as sister group to all other conchiferans (shelled molluscs other than Polyplacophora), a grouping that is supported by the latest large-scale phylogenomic study that includes Laevipilina. However, molecular datasets dominated by nuclear ribosomal genes support Monoplacophora + Polyplacophora (Serialia). Here, we evaluate the potential of mitochondrial genome data for resolving placement of Monoplacophora. RESULTS Two complete (Laevipilina antarctica and Vema ewingi) and one partial (Laevipilina hyalina) mitochondrial genomes were sequenced, assembled, and compared. All three genomes show a highly similar architecture including an unusually high number of non-coding regions. Comparison of monoplacophoran gene order shows a gene arrangement pattern not previously reported; there is an inversion of one large gene cluster. Our reanalyses of recently published polyplacophoran mitogenomes show, however, that this feature is also present in some chiton species. Maximum Likelihood and Bayesian Inference analyses of 13 mitochondrial protein-coding genes failed to robustly place Monoplacophora and hypothesis testing could not reject any of the evaluated placements of Monoplacophora. CONCLUSIONS Under both serialian or aculiferan-conchiferan scenarios, the observed gene cluster inversion appears to be a convergent evolution of gene arrangements in molluscs. Our phylogenetic results are inconclusive and sensitive to taxon sampling. Aculifera (Polyplacophora + Aplacophora) and Conchifera were never recovered. However, some analyses recovered Serialia (Monoplacophora + Polyplacophora), Diasoma (Bivalvia + Scaphopoda) or Pleistomollusca (Bivalvia + Gastropoda). Although we could not shed light on deep evolutionary traits of Mollusca we found unique patterns of gene arrangements that are common to monoplacophoran and chitonine polyplacophoran species but not to acanthochitonine Polyplacophora. Complete mitochondrial genome of Laevipilina antarctica.
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Affiliation(s)
- I Stöger
- SNSB-Bavarian State Collection of Zoology, Muenchhausenstrasse 21, 81247, Munich, Germany.
| | - K M Kocot
- Department of Biological Sciences, University of Alabama, Box 870344, Tuscaloosa, AL, 35487, USA
| | - A J Poustka
- Max-Planck Institut fuer Molekulare Genetik, Evolution and Development Group, Ihnestrasse 73, 14195, Berlin, Germany.,Dahlem Center for Genome Research and Medical Systems Biology, Environmental and Phylogenomics Group, Fabeckstraße 60-62, 14195, Berlin, Germany.,Alacris Theranostics GmbH, Fabeckstr. 60-62, 14195, Berlin, Germany
| | - N G Wilson
- Western Australian Museum, Aquatic Zoology/Molecular Systematics Unit, 49 Kew Street, Welshpool, WA, 6106, Australia
| | - D Ivanov
- Zoological Museum, Moscow State University, Bolshaya Nikitskaya Str. 6, 225009, Moscow, Russia
| | - K M Halanych
- Biological Sciences Department, Auburn University, Life Sciences Bld. 101, Auburn, AL, 36849, USA
| | - M Schrödl
- SNSB-Bavarian State Collection of Zoology, Muenchhausenstrasse 21, 81247, Munich, Germany.,Faculty of Biology, Department II, Ludwig-Maximilians-Universitaet Muenchen, Großhaderner Strasse 2-4, 82152, Planegg-Martinsried, Germany.,GeoBio-Center at LMU, Richard-Wagner-Strasse 10, 80333, Munich, Germany
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10
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Irisarri I, Meyer A. The Identification of the Closest Living Relative(s) of Tetrapods: Phylogenomic Lessons for Resolving Short Ancient Internodes. Syst Biol 2016; 65:1057-1075. [PMID: 27425642 DOI: 10.1093/sysbio/syw057] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 06/08/2016] [Indexed: 01/08/2023] Open
Abstract
Identifying the closest living relative(s) of tetrapods is an important, yet still contested question in vertebrate phylogenetics. Three hypotheses are possible and ruling out alternatives has proven difficult even with large molecular data sets due to weak phylogenetic signal coupled nonphylogenetic noise resulting from relatively rapid speciation events that occurred a long time ago ([Formula: see text]400 Ma). Here, we revisit the identity of the closest living relative of land vertebrates from a phylogenomic perspective and include new genomic data for all extant lungfish genera. RNA-seq proves to be a great alternative to genomic sequencing, which currently is technically not feasible in lungfishes due to their huge (50-130 Gb) and repetitive genomes. We examined the most important sources of systematic error, namely long-branch attraction (LBA), compositional heterogeneity and distribution of missing data and applied different correction techniques. A multispecies coalescent approach is used to account for deep coalescence that might come from the short and deep internodes separating early sarcopterygian splits. Concatenation methods favored lungfishes as the closest living relatives of tetrapods with strong statistical support. Amino acid profile mixture models can unambiguously resolve this difficult internode thanks to their ability to avoid systematic error. We assessed the performance of different site-heterogeneous models and data partitioning and compared the ability of different strategies designed to overcome LBA, including taxon manipulation, reduction of among-lineage rate heterogeneity and removal of fast-evolving or compositionally heterogeneous positions. The identification of lungfish as sister group of tetrapods is robust regarding the effects of nonstationary composition and distribution of missing data. The multispecies coalescent method reconstructed strongly supported topologies that were congruent with concatenation, despite pervasive gene tree heterogeneity. We reject alternative topologies for early sarcopterygian relationships by increasing the signal-to-noise ratio in our alignments. The analytical pipeline outlined here combines probabilistic phylogenomic inference with methods for evaluating data quality, model adequacy, and assessing systematic error, and thus is likely to help resolve similarly difficult internodes in the tree of life. [Coalescence; coelacanth; compositional heterogeneity; gene tree; long-branch attraction; lungfish; missing data; model misspecification; phylogenomic; species tree; systematic error.].
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Affiliation(s)
- Iker Irisarri
- Laboratory for Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, 78464 Konstanz, Germany
| | - Axel Meyer
- Laboratory for Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, 78464 Konstanz, Germany
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11
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Verdes A, Cho W, Hossain M, Brennan PLR, Hanley D, Grim T, Hauber ME, Holford M. Nature's Palette: Characterization of Shared Pigments in Colorful Avian and Mollusk Shells. PLoS One 2015; 10:e0143545. [PMID: 26650398 PMCID: PMC4674117 DOI: 10.1371/journal.pone.0143545] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 11/05/2015] [Indexed: 11/21/2022] Open
Abstract
Pigment-based coloration is a common trait found in a variety of organisms across the tree of life. For example, calcareous avian eggs are natural structures that vary greatly in color, yet just a handful of tetrapyrrole pigment compounds are responsible for generating this myriad of colors. To fully understand the diversity and constraints shaping nature's palette, it is imperative to characterize the similarities and differences in the types of compounds involved in color production across diverse lineages. Pigment composition was investigated in eggshells of eleven paleognath bird taxa, covering several extinct and extant lineages, and shells of four extant species of mollusks. Birds and mollusks are two distantly related, calcareous shell-building groups, thus characterization of pigments in their calcareous structures would provide insights to whether similar compounds are found in different phyla (Chordata and Mollusca). An ethylenediaminetetraacetic acid (EDTA) extraction protocol was used to analyze the presence and concentration of biliverdin and protoporphyrin, two known and ubiquitous tetrapyrrole avian eggshell pigments, in all avian and molluscan samples. Biliverdin was solely detected in birds, including the colorful eggshells of four tinamou species. In contrast, protoporphyrin was detected in both the eggshells of several avian species and in the shells of all mollusks. These findings support previous hypotheses about the ubiquitous deposition of tetrapyrroles in the eggshells of various bird lineages and provide evidence for its presence also across distantly related animal taxa.
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Affiliation(s)
- Aida Verdes
- The Graduate Center, City University of New York, New York, New York, United States of America
- Division of Invertebrate Zoology, American Museum of Natural History, New York, New York, United States of America
| | - Wooyoung Cho
- Department of Chemistry, Hunter College Belfer Research Building, City University of New York, New York, New York, United States of America
| | - Marouf Hossain
- Department of Chemistry, Hunter College Belfer Research Building, City University of New York, New York, New York, United States of America
| | - Patricia L. R. Brennan
- Department of Psychology, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - Daniel Hanley
- Department of Zoology and Laboratory of Ornithology, Palacký University, Olomouc, Czech Republic
| | - Tomáš Grim
- Department of Zoology and Laboratory of Ornithology, Palacký University, Olomouc, Czech Republic
| | - Mark E. Hauber
- The Graduate Center, City University of New York, New York, New York, United States of America
- Department of Psychology, Hunter College, City University of New York, New York, New York, United States of America
| | - Mandë Holford
- The Graduate Center, City University of New York, New York, New York, United States of America
- Division of Invertebrate Zoology, American Museum of Natural History, New York, New York, United States of America
- Department of Chemistry, Hunter College Belfer Research Building, City University of New York, New York, New York, United States of America
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A Paleogene origin for crown passerines and the diversification of the Oscines in the New World. Mol Phylogenet Evol 2015; 88:1-15. [PMID: 25837731 DOI: 10.1016/j.ympev.2015.03.018] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Revised: 02/25/2015] [Accepted: 03/18/2015] [Indexed: 11/24/2022]
Abstract
In this study, we present a detailed family-level phylogenetic hypothesis for the largest avian order (Aves: Passeriformes) and an unmatched multi-calibrated, relaxed clock inference for the diversification of crown passerines. Extended taxon sampling allowed the recovery of many challenging clades and elucidated their position in the tree. Acanthisittia appear to have diverged from all other passerines at the early Paleogene, which is considerably later than previously suggested. Thus, Passeriformes may be younger and represent an even more intense adaptive radiation compared to the remaining avian orders. Based on our divergence time estimates, a novel hypothesis for the diversification of modern Suboscines is proposed. According to this hypothesis, the first split between New and Old World lineages would be related to the severing of the Africa-South America biotic connection during the mid-late Eocene, implying an African origin for modern Eurylaimides. The monophyletic status of groups not recovered by any subsequent study since their circumscription, viz. Sylvioidea including Paridae, Remizidae, Hyliotidae, and Stenostiridae; and Muscicapoidea including the waxwing assemblage (Bombycilloidea) were notable topological findings. We also propose possible ecological interactions that may have shaped the distinct Oscine distribution patterns in the New World. The insectivorous endemic Oscines of the Americas, Vireonidae (Corvoidea), Mimidae, and Troglodytidae (Muscicapoidea), probably interfered with autochthonous Suboscines through direct competition. Thus, the Early Miocene arrival of these lineages before any other Oscines may have occupied the few available niches left by Tyrannides, constraining the diversification of insectivorous Oscines that arrived in the Americas later. The predominantly frugivorous-nectarivorous members of Passeroidea, which account for most of the diversity of New World-endemic Oscines, may not have been subjected to competition with Tyrannides. In fact, the vast availability of frugivory niches combined with weak competition with the autochthonous passerine fauna may have been crucial for passeroids to thrive in the New World.
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Baker AJ, Haddrath O, McPherson JD, Cloutier A. Genomic support for a moa-tinamou clade and adaptive morphological convergence in flightless ratites. Mol Biol Evol 2014; 31:1686-96. [PMID: 24825849 DOI: 10.1093/molbev/msu153] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
One of the most startling discoveries in avian molecular phylogenetics is that the volant tinamous are embedded in the flightless ratites, but this topology remains controversial because recent morphological phylogenies place tinamous as the closest relative of a monophyletic ratite clade. Here, we integrate new phylogenomic sequences from 1,448 nuclear DNA loci totaling almost 1 million bp from the extinct little bush moa, Chilean tinamou, and emu with available sequences from ostrich, elegant crested tinamou, four neognaths, and the green anole. Phylogenetic analysis using standard homogeneous models and heterogeneous models robust to common topological artifacts recovered compelling support for ratite paraphyly with the little bush moa closest to tinamous within ratites. Ratite paraphyly was further corroborated by eight independent CR1 retroposon insertions. Analysis of morphological characters reinterpreted on a 27-gene paleognath topology indicates that many characters are convergent in the ratites, probably as the result of adaptation to a cursorial life style.
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Affiliation(s)
- Allan J Baker
- Department of Natural History, Royal Ontario Museum, Toronto, Ontario, CanadaDepartment of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Oliver Haddrath
- Department of Natural History, Royal Ontario Museum, Toronto, Ontario, Canada
| | | | - Alison Cloutier
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
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14
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Nyári ÁS, Joseph L. Comparative phylogeography of Australo-Papuan mangrove-restricted and mangrove-associated avifaunas. Biol J Linn Soc Lond 2013. [DOI: 10.1111/bij.12082] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
| | - Leo Joseph
- Australian National Wildlife Collection; CSIRO Ecosystem Sciences; GPO Box 1700; Canberra; ACT; 2601; Australia
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15
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McCormack JE, Harvey MG, Faircloth BC, Crawford NG, Glenn TC, Brumfield RT. A phylogeny of birds based on over 1,500 loci collected by target enrichment and high-throughput sequencing. PLoS One 2013; 8:e54848. [PMID: 23382987 PMCID: PMC3558522 DOI: 10.1371/journal.pone.0054848] [Citation(s) in RCA: 258] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Accepted: 12/17/2012] [Indexed: 11/18/2022] Open
Abstract
Evolutionary relationships among birds in Neoaves, the clade comprising the vast majority of avian diversity, have vexed systematists due to the ancient, rapid radiation of numerous lineages. We applied a new phylogenomic approach to resolve relationships in Neoaves using target enrichment (sequence capture) and high-throughput sequencing of ultraconserved elements (UCEs) in avian genomes. We collected sequence data from UCE loci for 32 members of Neoaves and one outgroup (chicken) and analyzed data sets that differed in their amount of missing data. An alignment of 1,541 loci that allowed missing data was 87% complete and resulted in a highly resolved phylogeny with broad agreement between the Bayesian and maximum-likelihood (ML) trees. Although results from the 100% complete matrix of 416 UCE loci were similar, the Bayesian and ML trees differed to a greater extent in this analysis, suggesting that increasing from 416 to 1,541 loci led to increased stability and resolution of the tree. Novel results of our study include surprisingly close relationships between phenotypically divergent bird families, such as tropicbirds (Phaethontidae) and the sunbittern (Eurypygidae) as well as between bustards (Otididae) and turacos (Musophagidae). This phylogeny bolsters support for monophyletic waterbird and landbird clades and also strongly supports controversial results from previous studies, including the sister relationship between passerines and parrots and the non-monophyly of raptorial birds in the hawk and falcon families. Although significant challenges remain to fully resolving some of the deep relationships in Neoaves, especially among lineages outside the waterbirds and landbirds, this study suggests that increased data will yield an increasingly resolved avian phylogeny.
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Affiliation(s)
- John E McCormack
- Museum of Natural Science, Louisiana State University, Baton Rouge, Louisiana, USA.
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Kelly LJ, Leitch AR, Clarkson JJ, Knapp S, Chase MW. Reconstructing the complex evolutionary origin of wild allopolyploid tobaccos (Nicotiana section suaveolentes). Evolution 2013; 67:80-94. [PMID: 23289563 DOI: 10.1111/j.1558-5646.2012.01748.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Nicotiana (Solanaceae) provides an ideal system for understanding polyploidization, a pervasive and powerful evolutionary force in plants, as this genus contains several groups of allotetraploids that formed at different times from different diploid progenitors. However, the parental lineages of the largest group of allotetraploids, Nicotiana section Suaveolentes, have been problematic to identify. Using data from four regions of three low-copy nuclear genes, nuclear ribosomal DNA, and regions of the plastid genome, we have reconstructed the evolutionary origin of sect. Suaveolentes and identified the most likely diploid progenitors by using a combination of gene trees and network approaches to uncover the most strongly supported evidence of species relationships. Our analyses best support a scenario where a member of the sect. Sylvestres lineage acted as the paternal progenitor and a member of either sect. Petunioides or sect. Noctiflorae that also contained introgressed DNA from the other, or a hypothetical hybrid species between these two sections, was the maternal progenitor. Nicotiana exemplifies many of the factors that can complicate the reconstruction of polyploid evolutionary history and highlights how reticulate evolution at the diploid level can add even greater complexity to allopolyploid genomes.
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Affiliation(s)
- Laura J Kelly
- School of Biological and Chemical Sciences, Queen Mary University of London, E1 4NS, London, United Kingdom.
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17
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Ng CS, Wu P, Foley J, Foley A, McDonald ML, Juan WT, Huang CJ, Lai YT, Lo WS, Chen CF, Leal SM, Zhang H, Widelitz RB, Patel PI, Li WH, Chuong CM. The chicken frizzle feather is due to an α-keratin (KRT75) mutation that causes a defective rachis. PLoS Genet 2012; 8:e1002748. [PMID: 22829773 PMCID: PMC3400578 DOI: 10.1371/journal.pgen.1002748] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Accepted: 04/19/2012] [Indexed: 12/15/2022] Open
Abstract
Feathers have complex forms and are an excellent model to study the development and evolution of morphologies. Existing chicken feather mutants are especially useful for identifying genetic determinants of feather formation. This study focused on the gene F, underlying the frizzle feather trait that has a characteristic curled feather rachis and barbs in domestic chickens. Our developmental biology studies identified defects in feather medulla formation, and physical studies revealed that the frizzle feather curls in a stepwise manner. The frizzle gene is transmitted in an autosomal incomplete dominant mode. A whole-genome linkage scan of five pedigrees with 2678 SNPs revealed association of the frizzle locus with a keratin gene-enriched region within the linkage group E22C19W28_E50C23. Sequence analyses of the keratin gene cluster identified a 69 bp in-frame deletion in a conserved region of KRT75, an α-keratin gene. Retroviral-mediated expression of the mutated F cDNA in the wild-type rectrix qualitatively changed the bending of the rachis with some features of frizzle feathers including irregular kinks, severe bending near their distal ends, and substantially higher variations among samples in comparison to normal feathers. These results confirmed KRT75 as the F gene. This study demonstrates the potential of our approach for identifying genetic determinants of feather forms. With the availability of a sequenced chicken genome, the reservoir of variant plumage genes found in domestic chickens can provide insight into the molecular mechanisms underlying the diversity of feather forms. In this paper, we identify the molecular basis of the distinctive frizzle (F) feather phenotype that is caused by a single autosomal incomplete dominant gene in which heterozygous individuals show less severe phenotypes than homozygous individuals. Feathers in frizzle chickens curve backward. We used computer-assisted analysis to establish that the rachis of the frizzle feather was irregularly kinked and more severely bent than normal. Moreover, microscopic evaluation of regenerating feathers found reduced proliferating cells that give rise to the frizzle rachis. Analysis of a pedigree of frizzle chickens showed that the phenotype is linked to two single-nucleotide polymorphisms in a cluster of keratin genes within the linkage group E22C19W28_E50C23. Sequencing of the gene cluster identified a 69-base pair in-frame deletion of the protein coding sequence of the α-keratin-75 gene. Forced expression of the mutated gene in normal chickens produced a twisted rachis. Although chicken feathers are primarily composed of beta-keratins, our findings indicate that alpha-keratins have an important role in establishing the structure of feathers.
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Affiliation(s)
- Chen Siang Ng
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Ping Wu
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - John Foley
- Department of Anatomy and Cell Biology, Indiana University School of Medicine, Bloomington, Indiana, United States of America
- Department of Dermatology, Indiana University School of Medicine, Bloomington, Indiana, United States of America
| | - Anne Foley
- Department of Anatomy and Cell Biology, Indiana University School of Medicine, Bloomington, Indiana, United States of America
- Department of Dermatology, Indiana University School of Medicine, Bloomington, Indiana, United States of America
| | - Merry-Lynn McDonald
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Wen-Tau Juan
- Institute of Physics, Academia Sinica, Taipei, Taiwan
| | - Chih-Jen Huang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Yu-Ting Lai
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Wen-Sui Lo
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Chih-Feng Chen
- Department of Animal Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Suzanne M. Leal
- Department of Dermatology, Indiana University School of Medicine, Bloomington, Indiana, United States of America
| | - Huanmin Zhang
- Avian Disease and Oncology Laboratory, Agriculture Research Service, United States Department of Agriculture, East Lansing, Michigan, United States of America
| | - Randall B. Widelitz
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Pragna I. Patel
- Institute for Genetic Medicine and Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, California, United States of America
| | - Wen-Hsiung Li
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States of America
- * E-mail: (W-HL); (C-MC)
| | - Cheng-Ming Chuong
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
- Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan
- * E-mail: (W-HL); (C-MC)
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CR1 retroposons provide a new insight into the phylogeny of Phasianidae species (Aves: Galliformes). Gene 2012; 502:125-32. [PMID: 22565186 DOI: 10.1016/j.gene.2012.04.068] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2011] [Revised: 04/20/2012] [Accepted: 04/22/2012] [Indexed: 01/21/2023]
Abstract
Chicken repeat 1 (CR1) elements, a class of retroposons belonging to non-long-terminal repeats, have been recognized as powerful tools for phylogenetic studies. Here we examine the phylogenetic relationships of 11 Phasianidae species based on CR1 retroposons. Together with 19 loci reported previously, a total of 99 CR1 loci were identified from chicken genome and turkey BAC clone sequences. 75 insertion events were used to address the branching order of 11 species in Phasianidae. The topology of our tree suggests that: 1) Gallus gallus possessed a basal phylogenetic position within Phasianidae and was related to Bambusicola thoracica (BSP=100%); 2) After the split of G. gallus and B. thoracica, Arborophila rufipectus diverged from Phasianidae (BSP=100%). Nine unambiguous insertion events supported a phylogenetic position of A. rufipectus different to previous mitochondrial data suggesting a hybrid origin or an ancient introgression of A. rufipectus; and 3) 22 CR1 insertion events strongly supported the eight phasianids under investigation sharing a common ancestor. Our study has revisited the phylogenetic position of G. gallus and A. rufipectus and provided a new insight into the phylogeny of Phasianidae birds. It showed that a CR1-based methodology has a great potential to be informative within Phasianidae in resolving relationships of closely related species whose radiation and speciation have occurred very recently.
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19
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Gibson R, Baker A. Multiple gene sequences resolve phylogenetic relationships in the shorebird suborder Scolopaci (Aves: Charadriiformes). Mol Phylogenet Evol 2012; 64:66-72. [PMID: 22491071 DOI: 10.1016/j.ympev.2012.03.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2011] [Revised: 03/09/2012] [Accepted: 03/09/2012] [Indexed: 11/19/2022]
Abstract
Shorebirds (Charadriiformes) are a diverse assemblage of species renowned for their variation in behavior, morphology, and life-history traits, but comparative studies of trait variation remain limited by the lack of a well-supported phylogeny based on DNA sequences. In this study we build upon previous shorebird phylogenies to construct the first sequence-based species-level phylogeny for the Scolopaci, one of three shorebird suborders. We sampled 84 species in the Scolopaci, and collected data for five genes (one nuclear and four mitochondrial) via PCR and sequencing or from GenBank. The phylogeny was estimated using Bayesian inference on a partitioned dataset of 6365 aligned base pairs, and was well-supported except for the radiations within Tringa and Calidris. The shanks and phalaropes are sister to the snipes, woodcocks and dowitchers, which in turn are sister to the sandpipers. The godwits and curlews are successive sister-groups to these clades, and the morphologically disparate taxa (jacanas, painted snipes, seedsnipes, and the Plains-wanderer) are the basal sister-group in the Scolopaci. We show that Tringa, Gallinago, and Calidris are paraphyletic assemblages, and thus are in need of taxonomic revision. The clade of Calidridine sandpipers has very short internal branches indicative of a relatively recent rapid radiation, and will require a gene tree/species tree approach to resolve relationships among species.
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Affiliation(s)
- Rosemary Gibson
- Royal Ontario Museum, 100 Queen’s Park, Toronto, Ontario, Canada.
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20
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Nyári ÁS, Joseph L. Evolution in Australasian mangrove forests: multilocus phylogenetic analysis of the Gerygone warblers (Aves: Acanthizidae). PLoS One 2012; 7:e31840. [PMID: 22363748 PMCID: PMC3280719 DOI: 10.1371/journal.pone.0031840] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Accepted: 01/12/2012] [Indexed: 11/18/2022] Open
Abstract
The mangrove forests of Australasia have many endemic bird species but their evolution and radiation in those habitats has been little studied. One genus with several mangrove specialist species is Gerygone (Passeriformes: Acanthizidae). The phylogeny of the Acanthizidae is reasonably well understood but limited taxon sampling for Gerygone has constrained understanding of its evolution and historical biogeography in mangroves. Here we report on a phylogenetic analysis of Gerygone based on comprehensive taxon sampling and a multilocus dataset of thirteen loci spread across the avian genome (eleven nuclear and two mitochondrial loci). Since Gerygone includes three species restricted to Australia's coastal mangrove forests, we particularly sought to understand the biogeography of their evolution in that ecosystem. Analyses of individual loci, as well as of a concatenated dataset drawn from previous molecular studies indicates that the genus as currently defined is not monophyletic, and that the Grey Gerygone (G. cinerea) from New Guinea should be transferred to the genus Acanthiza. The multilocus approach has permitted the nuanced view of the group's evolution into mangrove ecosystems having occurred on multiple occasions, in three non-overlapping time frames, most likely first by the G. magnirostris lineage, and subsequently followed by those of G. tenebrosa and G. levigaster.
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Affiliation(s)
- Árpád S Nyári
- Department of Ecology and Evolutionary Biology, Biodiversity Institute, The University of Kansas, Lawrence, Kansas, United States of America.
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21
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Weisrock DW, Smith SD, Chan LM, Biebouw K, Kappeler PM, Yoder AD. Concatenation and concordance in the reconstruction of mouse lemur phylogeny: an empirical demonstration of the effect of allele sampling in phylogenetics. Mol Biol Evol 2012; 29:1615-30. [PMID: 22319174 DOI: 10.1093/molbev/mss008] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The systematics and speciation literature is rich with discussion relating to the potential for gene tree/species tree discordance. Numerous mechanisms have been proposed to generate discordance, including differential selection, long-branch attraction, gene duplication, genetic introgression, and/or incomplete lineage sorting. For speciose clades in which divergence has occurred recently and rapidly, recovering the true species tree can be particularly problematic due to incomplete lineage sorting. Unfortunately, the availability of multilocus or "phylogenomic" data sets does not simply solve the problem, particularly when the data are analyzed with standard concatenation techniques. In our study, we conduct a phylogenetic study for a nearly complete species sample of the dwarf and mouse lemur clade, Cheirogaleidae. Mouse lemurs (genus, Microcebus) have been intensively studied over the past decade for reasons relating to their high level of cryptic species diversity, and although there has been emerging consensus regarding the evolutionary diversity contained within the genus, there is no agreement as to the inter-specific relationships within the group. We attempt to resolve cheirogaleid phylogeny, focusing especially on the mouse lemurs, by employing a large multilocus data set. We compare the results of Bayesian concordance methods with those of standard gene concatenation, finding that though concatenation yields the strongest results as measured by statistical support, these results are found to be highly misleading. By employing an approach where individual alleles are treated as operational taxonomic units, we show that phylogenetic results are substantially influenced by the selection of alleles in the concatenation process.
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22
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Trautwein MD, Wiegmann BM, Beutel R, Kjer KM, Yeates DK. Advances in insect phylogeny at the dawn of the postgenomic era. ANNUAL REVIEW OF ENTOMOLOGY 2012; 57:449-468. [PMID: 22149269 DOI: 10.1146/annurev-ento-120710-100538] [Citation(s) in RCA: 142] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Most species on Earth are insects and thus, understanding their evolutionary relationships is key to understanding the evolution of life. Insect relationships are increasingly well supported, due largely to technological advances in molecular sequencing and phylogenetic computational analysis. In this postgenomic era, insect systematics will be furthered best by integrative methods aimed at hypothesis corroboration from molecular, morphological, and paleontological evidence. This review of the current consensus of insect relationships provides a foundation for comparative study and offers a framework to evaluate incoming genomic evidence. Notable recent phylogenetic successes include the resolution of Holometabola, including the identification of the enigmatic Strepsiptera as a beetle relative and the early divergence of Hymenoptera; the recognition of hexapods as a crustacean lineage within Pancrustacea; and the elucidation of Dictyoptera orders, with termites placed as social cockroaches. Regions of the tree that require further investigation include the earliest winged insects (Palaeoptera) and Polyneoptera (orthopteroid lineages).
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Affiliation(s)
- Michelle D Trautwein
- Department of Entomology, North Carolina State University, Raleigh, North Carolina 27695, USA.
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23
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Jacobsen F, Omland KE. Species tree inference in a recent radiation of orioles (Genus Icterus): Multiple markers and methods reveal cytonuclear discordance in the northern oriole group. Mol Phylogenet Evol 2011; 61:460-9. [DOI: 10.1016/j.ympev.2011.06.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2011] [Revised: 06/13/2011] [Accepted: 06/20/2011] [Indexed: 10/18/2022]
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24
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Paśko Ł, Ericson PGP, Elzanowski A. Phylogenetic utility and evolution of indels: a study in neognathous birds. Mol Phylogenet Evol 2011; 61:760-71. [PMID: 21843647 DOI: 10.1016/j.ympev.2011.07.021] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2011] [Revised: 07/28/2011] [Accepted: 07/30/2011] [Indexed: 11/25/2022]
Abstract
Indels are increasingly used in phylogenetics and play a major role in genome size evolution, and yet both the phylogenetic information content of indels and their evolutionary significance remain to be better assessed. Using three presumably independently evolving nuclear gene fragments (28S rDNA, β-fibrinogen, ornithine decarboxylase) from 29 families of neognathous birds, we have obtained a topology that is in general agreement with the current molecular consensus tree, supports the monophyly of Metaves, and provides evidence for the unresolved relationships within the Charadriiformes. Based on the retrieved topology, we assess the relative impact of indels and nucleotide substitutions and demonstrate that the superposition of the two kinds of data yields a topology that could not be obtained from either data set alone. Although only two out of three gene fragments reveal the deletion bias, the combined nucleotide insertion-to-deletion ratio is 0.22, indicating a rapid decrease of intron length. The average indel fixation rate in the neognaths is 2.5 times faster than that in therian (placental) mammals of similar geologic age. As in mammals, there is a considerable variation of indel fixation rate that is 1.5 times higher in Galloanseres compared to Neoaves, and 2.4 times higher in the Rallidae compared to the average for Neoaves (8.2 times higher compared to the related Gruidae). Our results add to the evidence that indel fixation rates correlate with lineage-specific evolutionary rates.
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Affiliation(s)
- Łukasz Paśko
- Institute of Zoology, University of Wrocław, 21 Sienkiewicz Street, PL-50-335 Wrocław, Poland
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25
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Campagna L, Geale K, Handford P, Lijtmaer DA, Tubaro PL, Lougheed SC. A molecular phylogeny of the Sierra-Finches (Phrygilus, Passeriformes): extreme polyphyly in a group of Andean specialists. Mol Phylogenet Evol 2011; 61:521-33. [PMID: 21807104 DOI: 10.1016/j.ympev.2011.07.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2011] [Revised: 07/11/2011] [Accepted: 07/12/2011] [Indexed: 11/29/2022]
Abstract
The unparalleled avian diversity of the Neotropics has long been argued to be in large part the evolutionary consequence of the incredible habitat diversity and rugged topography of the Andes mountains. Various scenarios have been proposed to explain how the Andean context could have generated lineage diversification (e.g. vicariant speciation or parapatric speciation across vertical ecological gradients), yet further study on Andean taxa is needed to reveal the relative importance of the different processes. Here we use mitochondrial and nuclear DNA sequences to derive the first phylogenetic hypothesis for Phrygilus (Sierra-Finches), one of the most species-rich genera of mainly Andean passerines. We find strong evidence that the genus is polyphyletic, comprising four distantly related clades with at least nine other genera interspersed between them (Acanthidops, Catamenia, Diglossa, Haplospiza, Idiopsar, Melanodera, Rowettia, Sicalis and Xenodacnis). These four Phrygilus clades coincide with groups previously established mainly on the basis of plumage characters, suggesting single evolutionary origins for each of these. We consider the history of diversification of each clade, analyzing the timing of splitting events, ancestral reconstruction of altitudinal ranges and current geographical distributions. Phrygilus species origins date mainly to the Pleistocene, with representatives diversifying within, out of, and into the Andes. Finally, we explored whether Phrygilus species, especially those with broad altitudinal and latitudinal Andean distributions, showed phylogeographic structure. Our best-sampled taxon (Phrygilus fruticeti) exhibited no clear pattern; however, we found deep genetic splits within other surveyed species, with Phrygilus unicolor being the most extreme case and deserving of further research.
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Affiliation(s)
- Leonardo Campagna
- División de Ornitología, Museo Argentino de Ciencias Naturales Bernardino Rivadavia, Av. Ángel Gallardo 470, Ciudad de Buenos Aires, C1405DJR Buenos Aires, Argentina
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26
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Janes DE, Organ CL, Fujita MK, Shedlock AM, Edwards SV. Genome evolution in Reptilia, the sister group of mammals. Annu Rev Genomics Hum Genet 2010; 11:239-64. [PMID: 20590429 DOI: 10.1146/annurev-genom-082509-141646] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The genomes of birds and nonavian reptiles (Reptilia) are critical for understanding genome evolution in mammals and amniotes generally. Despite decades of study at the chromosomal and single-gene levels, and the evidence for great diversity in genome size, karyotype, and sex chromosome diversity, reptile genomes are virtually unknown in the comparative genomics era. The recent sequencing of the chicken and zebra finch genomes, in conjunction with genome scans and the online publication of the Anolis lizard genome, has begun to clarify the events leading from an ancestral amniote genome--predicted to be large and to possess a diverse repeat landscape on par with mammals and a birdlike sex chromosome system--to the small and highly streamlined genomes of birds. Reptilia exhibit a wide range of evolutionary rates of different subgenomes and, from isochores to mitochondrial DNA, provide a critical contrast to the genomic paradigms established in mammals.
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Affiliation(s)
- Daniel E Janes
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
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Bryson RW, de Oca ANM, Jaeger JR, Riddle BR. Elucidation of cryptic diversity in a widespread nearctic treefrog reveals episodes of mitochondrial gene capture as frogs diversified across a dynamic landscape. Evolution 2010; 64:2315-30. [PMID: 20394664 DOI: 10.1111/j.1558-5646.2010.01014.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
We investigate the evolutionary history of the wide-ranging Nearctic treefrog Hyla arenicolor through the integration of extensive range-wide sampling, phylogenetic analyses of multilocus genetic data, and divergence dating. Previous phylogeographic studies of this frog documented a potential signature of introgressive hybridization from an ecologically and morphologically divergent sister species. Based on our Bayesian phylogenetic analyses of mitochondrial DNA, we inferred strong phylogeographic structure in H. arenicolor as indicated by seven well-supported clades, five of which correspond to well-defined biogeographic regions. Clades from the Balsas Basin and southwestern Central Mexican Plateau in Mexico, and the Grand Canyon of Arizona, group with the morphologically, behaviorally, and ecologically divergent mountain treefrogs in the H. eximia group, rendering H. arenicolor as paraphyletic. The phylogenetic position of at least two of these three H. arenicolor clades within the H. eximia group, however, is most likely the result of several episodes of introgressive hybridization and subsequent mitochondrial gene capture separated in time and space, as supported by evidence from the nuclear genes. Hyla arenicolor from the Balsas Basin appear to be deeply divergent from other H. arenicolor and represent a distinctly different species. Results suggests that introgressive hybridization events, both ancient and contemporary, coupled with late Neogene vicariance and Pleistocene climate-driven range shifts, have all played a role in the historical diversification of H. arenicolor.
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Affiliation(s)
- Robert W Bryson
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada 89154, USA.
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Steiger SS, Kuryshev VY, Stensmyr MC, Kempenaers B, Mueller JC. A comparison of reptilian and avian olfactory receptor gene repertoires: species-specific expansion of group gamma genes in birds. BMC Genomics 2009; 10:446. [PMID: 19772566 PMCID: PMC2758906 DOI: 10.1186/1471-2164-10-446] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2009] [Accepted: 09/21/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The detection of odorants is mediated by olfactory receptors (ORs). ORs are G-protein coupled receptors that form a remarkably large protein superfamily in vertebrate genomes. We used data that became available through recent sequencing efforts of reptilian and avian genomes to identify the complete OR gene repertoires in a lizard, the green anole (Anolis carolinensis), and in two birds, the chicken (Gallus gallus) and the zebra finch (Taeniopygia guttata). RESULTS We identified 156 green anole OR genes, including 42 pseudogenes. The OR gene repertoire of the two bird species was substantially larger with 479 and 553 OR gene homologs in the chicken and zebra finch, respectively (including 111 and 221 pseudogenes, respectively). We show that the green anole has a higher fraction of intact OR genes (approximately 72%) compared with the chicken (approximately 66%) and the zebra finch (approximately 38%). We identified a larger number and a substantially higher proportion of intact OR gene homologs in the chicken genome than previously reported (214 versus 82 genes and 66% versus 15%, respectively). Phylogenetic analysis showed that lizard and bird OR gene repertoires consist of group alpha, theta and gamma genes. Interestingly, the vast majority of the avian OR genes are confined to a large expansion of a single branch (the so called gamma-c clade). An analysis of the selective pressure on the paralogous genes of each gamma-c clade revealed that they have been subjected to adaptive evolution. This expansion appears to be bird-specific and not sauropsid-specific, as it is lacking from the lizard genome. The gamma-c expansions of the two birds do not intermix, i.e., they are lineage-specific. Almost all (group gamma-c) OR genes mapped to the unknown chromosome. The remaining OR genes mapped to six homologous chromosomes plus three to four additional chromosomes in the zebra finch and chicken. CONCLUSION We identified a surprisingly large number of potentially functional avian OR genes. Our data supports recent evidence that avian olfactory ability may be better developed than previously thought. We hypothesize that the radiation of the group gamma-c OR genes in each bird lineage parallels the evolution of specific olfactory sensory functions.
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Affiliation(s)
- Silke S Steiger
- Department of Behavioural Ecology & Evolutionary Genetics, Max-Planck Institute for Ornithology, Eberhard-Gwinner-Strasse, 82319 Seewiesen, Germany.
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Chapus C, Edwards SV. Genome evolution in Reptilia: in silico chicken mapping of 12,000 BAC-end sequences from two reptiles and a basal bird. BMC Genomics 2009; 10 Suppl 2:S8. [PMID: 19607659 PMCID: PMC2966332 DOI: 10.1186/1471-2164-10-s2-s8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND With the publication of the draft chicken genome and the recent production of several BAC clone libraries from non-avian reptiles and birds, it is now possible to undertake more detailed comparative genomic studies in Reptilia. Of interest in particular are the genomic events that transformed the large, repeat-rich genomes of mammals and non-avian reptiles into the minimalist chicken genome. We have used paired BAC end sequences (BESs) from the American alligator (Alligator mississippiensis), painted turtle (Chrysemys picta) and emu (Dromaius novaehollandiae) to investigate patterns of sequence divergence, gene and retroelement content, and microsynteny between these species and chicken. RESULTS From a total of 11,967 curated BESs, we successfully mapped 725, 773 and 2597 sequences in alligator, turtle, and emu, respectively, to sites in the draft chicken genome using a stringent BLAST protocol. Most commonly, sequences mapped to a single site in the chicken genome. Of 1675, 1828 and 2936 paired BESs obtained for alligator, turtle, and emu, respectively, a total of 34 (alligator, 2%), 24 (turtle, 1.3%) and 479 (emu, 16.3%) pairs were found to map with high confidence and in the correct orientation and with BAC-sized intermarker distances to single chicken chromosomes, including 25 such paired hits in emu mapping to the chicken Z chromosome. By determining the insert sizes of a subset of BAC clones from these three species, we also found a significant correlation between the intermarker distance in alligator and turtle and in chicken, with slopes as expected on the basis of the ratio of the genome sizes. CONCLUSION Our results suggest that a large number of small-scale chromosomal rearrangements and deletions in the lineage leading to chicken have drastically reduced the number of detected syntenies observed between the chicken and alligator, turtle, and emu genomes and imply that small deletions occurring widely throughout the genomes of reptilian and avian ancestors led to the ~50% reduction in genome size observed in birds compared to reptiles. We have also mapped and identified likely gene regions in hundreds of new BAC clones from these species.
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Affiliation(s)
- Charles Chapus
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
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Degnan JH, Rosenberg NA. Gene tree discordance, phylogenetic inference and the multispecies coalescent. Trends Ecol Evol 2009; 24:332-40. [PMID: 19307040 DOI: 10.1016/j.tree.2009.01.009] [Citation(s) in RCA: 1087] [Impact Index Per Article: 72.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2008] [Revised: 12/17/2008] [Accepted: 01/05/2009] [Indexed: 01/29/2023]
Affiliation(s)
- James H Degnan
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA.
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Nie W, O'Brien PCM, Ng BL, Fu B, Volobouev V, Carter NP, Ferguson-Smith MA, Yang F. Avian comparative genomics: reciprocal chromosome painting between domestic chicken (Gallus gallus) and the stone curlew (Burhinus oedicnemus, Charadriiformes)--an atypical species with low diploid number. Chromosome Res 2009; 17:99-113. [PMID: 19172404 PMCID: PMC2697597 DOI: 10.1007/s10577-009-9021-6] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2008] [Revised: 11/27/2008] [Accepted: 11/27/2008] [Indexed: 11/30/2022]
Abstract
The chicken is the most extensively studied species in birds and thus constitutes an ideal reference for comparative genomics in birds. Comparative cytogenetic studies indicate that the chicken has retained many chromosome characters of the ancestral avian karyotype. The homology between chicken macrochromosomes (1-9 and Z) and their counterparts in more than 40 avian species of 10 different orders has been established by chromosome painting. However, the avian homologues of chicken microchromosomes remain to be defined. Moreover, no reciprocal chromosome painting in birds has been performed due to the lack of chromosome-specific probes from other avian species. Here we have generated a set of chromosome-specific paints using flow cytometry that cover the whole genome of the stone curlew (Burhinus oedicnemus, Charadriiformes), a species with one of the lowest diploid number so far reported in birds, as well as paints from more microchromosomes of the chicken. A genome-wide comparative map between the chicken and the stone curlew has been constructed for the first time based on reciprocal chromosome painting. The results indicate that extensive chromosome fusions underlie the sharp decrease in the diploid number in the stone curlew. To a lesser extent, chromosome fissions and inversions occurred also during the evolution of the stone curlew. It is anticipated that this complete set of chromosome painting probes from the first Neoaves species will become an invaluable tool for avian comparative cytogenetics.
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Affiliation(s)
- Wenhui Nie
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, PRC
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Amniote phylogenomics: testing evolutionary hypotheses with BAC library scanning and targeted clone analysis of large-scale DNA sequences from reptiles. Methods Mol Biol 2008; 422:91-117. [PMID: 18629663 DOI: 10.1007/978-1-59745-581-7_7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Phylogenomics research integrating established principles of systematic biology and taking advantage of the wealth of DNA sequences being generated by genome science holds promise for answering long-standing evolutionary questions with orders of magnitude more primary data than in the past. Although it is unrealistic to expect whole-genome initiatives to proceed rapidly for commercially unimportant species such as reptiles, practical approaches utilizing genomic libraries of large-insert clones pave the way for a phylogenomics of species that are nevertheless essential for testing evolutionary hypotheses within a phylogenetic framework. This chapter reviews the case for adopting genome-enabled approaches to evolutionary studies and outlines a program for using bacterial artificial chromosome (BAC) libraries or plasmid libraries as a basis for completing "genome scans" of reptiles. We have used BACs to close a critical gap in the genome database for Reptilia, the sister group of mammals, and present the methodological approaches taken to achieve this as a guideline for designing similar comparative studies. In addition, we provide a detailed step-by-step protocol for BAC-library screening and shotgun sequencing of specific clones containing target genes of evolutionary interest. Taken together, the genome scanning and shotgun sequencing techniques offer complementary diagnostic potential and can substantially increase the scale and power of analyses aimed at testing evolutionary hypotheses for nonmodel species.
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Multilocus phylogeography and phylogenetics using sequence-based markers. Genetica 2008; 135:439-55. [DOI: 10.1007/s10709-008-9293-3] [Citation(s) in RCA: 218] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2008] [Accepted: 06/28/2008] [Indexed: 10/21/2022]
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Wiens JJ, Kuczynski CA, Smith SA, Mulcahy DG, Sites JW, Townsend TM, Reeder TW. Branch Lengths, Support, and Congruence: Testing the Phylogenomic Approach with 20 Nuclear Loci in Snakes. Syst Biol 2008; 57:420-31. [DOI: 10.1080/10635150802166053] [Citation(s) in RCA: 121] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Affiliation(s)
- John J. Wiens
- Department of Ecology and Evolution, Stony Brook University Stony Brook, NY 11794-5245, USA; E-mail: (J.J.W.)
| | - Caitlin A. Kuczynski
- Department of Ecology and Evolution, Stony Brook University Stony Brook, NY 11794-5245, USA; E-mail: (J.J.W.)
| | - Sarah A. Smith
- Department of Ecology and Evolution, Stony Brook University Stony Brook, NY 11794-5245, USA; E-mail: (J.J.W.)
| | - Daniel G. Mulcahy
- Department of Integrative Biology, Brigham Young University Provo, UT 84602, USA
| | - Jack W. Sites
- Department of Integrative Biology, Brigham Young University Provo, UT 84602, USA
| | - Ted M. Townsend
- Department of Biology, San Diego State University San Diego, CA 92182-4614, USA
| | - Tod W. Reeder
- Department of Biology, San Diego State University San Diego, CA 92182-4614, USA
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36
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Treplin S, Siegert R, Bleidorn C, Thompson HS, Fotso R, Tiedemann R. Molecular phylogeny of songbirds (Aves: Passeriformes) and the relative utility of common nuclear marker loci. Cladistics 2008. [DOI: 10.1111/j.1096-0031.2007.00178.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Abstract
The polymerase chain reaction has been a boon to the study of molecular ecology and population genetics of birds. But the nagging truth is that for many bird species, the number of polymerase chain reaction (PCR) primer pairs that one can pick off the shelf and expect to amplify their target loci with ease is frustratingly small. Now, studying DNA sequence variation in natural populations of birds just got a whole lot easier. This issue of Molecular Ecology reports a large-scale bioinformatics search for exonic sequences conserved between the chicken and zebra finch genomes and flanking polymorphic introns that has generated a staggering 242 PCR primer pairs that readily amplify their single-copy target loci in five avian species spanning approximately 100 million years of avian evolution (Backström et al. 2008). As proof of principle, these primers have also been used to survey the genomic landscape in over 110 kb of intronic sequence in the collared flycatcher, a model species in ecology and evolution. These resources pave the way for easy multilocus study of evolving populations and lineages of birds, and bring the goal of quickly turning nonmodel species in to ecological genomic models tantalizingly close.
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Kriegs JO, Matzke A, Churakov G, Kuritzin A, Mayr G, Brosius J, Schmitz J. Waves of genomic hitchhikers shed light on the evolution of gamebirds (Aves: Galliformes). BMC Evol Biol 2007; 7:190. [PMID: 17925025 PMCID: PMC2169234 DOI: 10.1186/1471-2148-7-190] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2007] [Accepted: 10/09/2007] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND The phylogenetic tree of Galliformes (gamebirds, including megapodes, currassows, guinea fowl, New and Old World quails, chicken, pheasants, grouse, and turkeys) has been considerably remodeled over the last decades as new data and analytical methods became available. Analyzing presence/absence patterns of retroposed elements avoids the problems of homoplastic characters inherent in other methodologies. In gamebirds, chicken repeats 1 (CR1) are the most prevalent retroposed elements, but little is known about the activity of their various subtypes over time. Ascertaining the fixation patterns of CR1 elements would help unravel the phylogeny of gamebirds and other poorly resolved avian clades. RESULTS We analyzed 1,978 nested CR1 elements and developed a multidimensional approach taking advantage of their transposition in transposition character (TinT) to characterize the fixation patterns of all 22 known chicken CR1 subtypes. The presence/absence patterns of those elements that were active at different periods of gamebird evolution provided evidence for a clade (Cracidae + (Numididae + (Odontophoridae + Phasianidae))) not including Megapodiidae; and for Rollulus as the sister taxon of the other analyzed Phasianidae. Genomic trace sequences of the turkey genome further demonstrated that the endangered African Congo Peafowl (Afropavo congensis) is the sister taxon of the Asian Peafowl (Pavo), rejecting other predominantly morphology-based groupings, and that phasianids are monophyletic, including the sister taxa Tetraoninae and Meleagridinae. CONCLUSION The TinT information concerning relative fixation times of CR1 subtypes enabled us to efficiently investigate gamebird phylogeny and to reconstruct an unambiguous tree topology. This method should provide a useful tool for investigations in other taxonomic groups as well.
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Affiliation(s)
- Jan Ole Kriegs
- Institute of Experimental Pathology (ZMBE) University of Münster, Von-Esmarch-Str. 56, D-48149 Münster, Germany
| | - Andreas Matzke
- Institute of Experimental Pathology (ZMBE) University of Münster, Von-Esmarch-Str. 56, D-48149 Münster, Germany
| | - Gennady Churakov
- Institute of Experimental Pathology (ZMBE) University of Münster, Von-Esmarch-Str. 56, D-48149 Münster, Germany
| | - Andrej Kuritzin
- Department of Physics and Mathematics, Saint Petersburg State Institute of Technology, 26 Moskovsky av., St.-Petersburg 198013, Russia
| | - Gerald Mayr
- Forschungsinstitut Senckenberg, Division of Ornithology, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
| | - Jürgen Brosius
- Institute of Experimental Pathology (ZMBE) University of Münster, Von-Esmarch-Str. 56, D-48149 Münster, Germany
| | - Jürgen Schmitz
- Institute of Experimental Pathology (ZMBE) University of Münster, Von-Esmarch-Str. 56, D-48149 Münster, Germany
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Backström N, Fagerberg S, Ellegren H. Genomics of natural bird populations: a gene-based set of reference markers evenly spread across the avian genome. Mol Ecol 2007; 17:964-80. [PMID: 17927703 DOI: 10.1111/j.1365-294x.2007.03551.x] [Citation(s) in RCA: 133] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Although there is growing interest to take genomics into the complex realms of natural populations, there is a general shortage of genomic resources and tools available for wild species. This applies not at least to birds, for which genomic approaches should be helpful to questions such as adaptation, speciation and population genetics. In this study, we describe a genome-wide reference set of conserved avian gene markers, broadly applicable across birds. By aligning protein-coding sequences from the recently assembled chicken genome with orthologous sequences in zebra finch, we identified particularly conserved exonic regions flanking introns of suitable size for subsequent amplification and sequencing. Primers were designed for 242 gene markers evenly distributed across the chicken genome, with a mean inter-marker interval of 4.2 Mb. Between 78% and 93% of the markers amplified a specific product in five species tested (chicken, peregrine falcon, collared flycatcher, great reed warbler and blue tit). Two hundred markers were sequenced in collared flycatcher, yielding a total of 122.41 kb of genomic DNA sequence (12096 bp coding sequence and 110 314 bp noncoding). Intron size of collared flycatcher and chicken was highly correlated, as was GC content. A polymorphism screening using these markers in a panel of 10 unrelated collared flycatchers identified 871 single nucleotide polymorphisms (pi = 0.0029) and 33 indels (mainly very short). Avian genome characteristics such as uniform genome size and low rate of syntenic rearrangements suggest that this marker set will find broad utility as a genome-wide reference resource for molecular ecological and population genomic analysis of birds. We envision that it will be particularly useful for obtaining large-scale orthologous targets in different species--important in, for instance, phylogenetics--and for large-scale identification of evenly distributed single nucleotide polymorphisms needed in linkage mapping or in studies of gene flow and hybridization.
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Affiliation(s)
- Niclas Backström
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
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40
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Burt DW. Emergence of the chicken as a model organism: implications for agriculture and biology. Poult Sci 2007; 86:1460-71. [PMID: 17575197 DOI: 10.1093/ps/86.7.1460] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Many of the features of the chicken make it an ideal model organism for phylogenetics and embryology, along with applications in agriculture and medicine. The availability of new tools such as whole genome gene expression arrays and single nucleotide polymorphism panels, coupled with the genome sequence, will enhance this position. These advances are reviewed and their implications are discussed.
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Affiliation(s)
- D W Burt
- Roslin Institute, Edinburgh, Midlothian EH25 9PS, United Kingdom.
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Griffin DK, Robertson LBW, Tempest HG, Skinner BM. The evolution of the avian genome as revealed by comparative molecular cytogenetics. Cytogenet Genome Res 2007; 117:64-77. [PMID: 17675846 DOI: 10.1159/000103166] [Citation(s) in RCA: 157] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2006] [Accepted: 09/04/2006] [Indexed: 12/15/2022] Open
Abstract
Birds are characterised by feathers, flight, a small genome and a very distinctive karyotype. Despite the large numbers of chromosomes, the diploid count of 2n approximately 80 has remained remarkably constant with 63% of birds where 2n = 74-86, 24% with 2n = 66-74 and extremes of 2n = 40 and 2n = 142. Of these, the most studied is the chicken (2n = 78), and molecular cytogenetic probes generated from this species have been used to further understand the evolution of the avian genome. The ancestral karyotype is, it appears, very similar to that of the chicken, with chicken chromosomes 1, 2, 3, 4q, 5, 6, 7, 8, 9, 4p and Z representing the ancestral avian chromosomes 1-10 + Z; chromosome 4 being the most ancient. Avian evolution occurred primarily in three stages: the divergence of the group represented by extant ratites (emu, ostrich etc.) from the rest; divergence of the Galloanserae (chicken, turkey, duck, goose etc.)--the most studied group; and divergence of the 'land' and 'water' higher birds. Other than sex chromosome differentiation in the first divergence there are no specific changes associated with any of these evolutionary milestones although certain families and orders have undergone multiple fusions (and some fissions), which has reduced their chromosome number; the Falconiformes are the best described. Most changes, overall, seem to involve chromosomes 1, 2, 4, 10 and Z where the Z changes are intrachromosomal; there are also some recurring (convergent) events. Of these, the most puzzling involves chromosomes 4 and 10, which appear to have undergone multiple fissions and/or fusions throughout evolution - three possible hypotheses are presented to explain the findings. We conclude by speculating as to the reasons for the strange behaviour of these chromosomes as well as the role of telomeres and nuclear organisation in avian evolution.
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Affiliation(s)
- D K Griffin
- University of Kent, Department of Biosciences, Canterbury, UK.
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42
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Burt DW, White SJ. Avian genomics in the 21st century. Cytogenet Genome Res 2007; 117:6-13. [PMID: 17675839 DOI: 10.1159/000103159] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2007] [Accepted: 02/01/2007] [Indexed: 11/19/2022] Open
Abstract
The chicken has long been an important model organism for developmental biology, as well as a major source of protein with billions of birds used in meat and egg production each year. Chicken genomics has been transformed in recent years, with the characterisation of large EST collections and most recently with the assembly of the chicken genome sequence. As the first livestock genome to be fully sequenced it leads the way for others to follow--with zebra finch later this year. The genome sequence and the availability of three million genetic polymorphisms are expected to aid the identification of genes that control traits of importance in poultry. As the first bird genome to be sequenced it is a model for the remaining 9,600 species thought to exist today. Many of the features of avian biology and organisation of the chicken genome make it an ideal model organism for phylogenetics and embryology, along with applications in agriculture and medicine. The availability of new tools such as whole-genome gene expression arrays and SNP panels, coupled with information resources on the genes and proteins are likely to enhance this position.
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Affiliation(s)
- D W Burt
- Department of Genomics and Genetics, Roslin Institute (Edinburgh), Roslin, Midlothian, UK.
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Kubatko LS, Degnan JH. Inconsistency of phylogenetic estimates from concatenated data under coalescence. Syst Biol 2007; 56:17-24. [PMID: 17366134 DOI: 10.1080/10635150601146041] [Citation(s) in RCA: 671] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Although multiple gene sequences are becoming increasingly available for molecular phylogenetic inference, the analysis of such data has largely relied on inference methods designed for single genes. One of the common approaches to analyzing data from multiple genes is concatenation of the individual gene data to form a single supergene to which traditional phylogenetic inference procedures - e.g., maximum parsimony (MP) or maximum likelihood (ML) - are applied. Recent empirical studies have demonstrated that concatenation of sequences from multiple genes prior to phylogenetic analysis often results in inference of a single, well-supported phylogeny. Theoretical work, however, has shown that the coalescent can produce substantial variation in single-gene histories. Using simulation, we combine these ideas to examine the performance of the concatenation approach under conditions in which the coalescent produces a high level of discord among individual gene trees and show that it leads to statistically inconsistent estimation in this setting. Furthermore, use of the bootstrap to measure support for the inferred phylogeny can result in moderate to strong support for an incorrect tree under these conditions. These results highlight the importance of incorporating variation in gene histories into multilocus phylogenetics.
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Affiliation(s)
- Laura Salter Kubatko
- Department of Statistics and Evolution, The Ohio State University, Columbus, Ohio 43210, USA.
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Brumfield RT, Edwards SV. EVOLUTION INTO AND OUT OF THE ANDES: A BAYESIAN ANALYSIS OF HISTORICAL DIVERSIFICATION INTHAMNOPHILUSANTSHRIKES. Evolution 2007; 61:346-67. [PMID: 17348945 DOI: 10.1111/j.1558-5646.2007.00039.x] [Citation(s) in RCA: 107] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Andean uplift played important roles in the historical diversification of Neotropical organisms, both by producing new high-elevation habitats that could be colonized and by isolating organisms on either side of the mountains. Here, we present a molecular phylogeny of Thamnophlius antshrikes, a clade of 30 species whose collective distribution spans nearly the entirety of lowland habitats in tropical South America, the eastern slope foothills of the Andes, and the tepuis of northern South America. Our goal was to examine the role of the Andes in the diversification of lowland and foothill species. Using parsimony and Bayesian ancestral state reconstructions of a three-state distribution character (lowland-restricted, lowland-to-highland, highland-restricted), we found that the Andes were colonized twice independently and the tepuis once from lowland-restricted ancestors. Over the entire evolutionary history of Thamnophilus, the highest transition rates were between highland-restricted and lowland-to-highland distributions, with extremely low rates into and out of lowland-restricted distributions. This pattern suggests lowland-restricted distributions are limited not by physiological constraints, but by other forces, such as competition. These results highlight the need for additional comparative studies in elucidating processes associated with the colonization of high-elevation habitats and the differentiation of populations within them.
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Affiliation(s)
- Robb T Brumfield
- Museum of Natural Science, 119 Foster Hall, Louisiana State University, Baton Rouge, Louisiana 70803, USA.
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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.
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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
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Shafer ABA, Stewart DT. Phylogenetic relationships among Nearctic shrews of the genus Sorex (Insectivora, Soricidae) inferred from combined cytochrome b and inter-SINE fingerprint data using Bayesian analysis. Mol Phylogenet Evol 2006; 44:192-203. [PMID: 17275347 DOI: 10.1016/j.ympev.2006.12.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2006] [Revised: 11/22/2006] [Accepted: 12/07/2006] [Indexed: 11/27/2022]
Abstract
The field of molecular systematics has relied heavily on mitochondrial DNA (mtDNA) analysis since its inception. Despite the obvious utility of mtDNA, such data inevitably only presents a limited (i.e., single genome) perspective on species evolution. A combination of mitochondrial and nuclear markers is essential for reconstructing more robust phylogenetic trees. To evaluate the utility of one category of nuclear marker (short interspersed elements or SINEs) for resolving phylogenetic relationships, we constructed an inter-SINE fingerprint for nine putative species of the genus Sorex. In addition, we analyzed 1011 nucleotides of the cytochrome b gene. Traditional neighbor-joining and maximum parsimony analyses were applied to the individual cytochrome b and inter-SINE fingerprint data sets, along with Bayesian analysis to the combined data sets. We found inter-SINE fingerprinting to be an effective species level marker; however, we were unable to reconstruct deeper branching patterns within the Sorex genus using these data. The combined data analyzed under a Bayesian analysis showed higher levels of structuring within the Otisorex subgenus, most notably recognizing a monophyletic group consisting of sister-taxa S. palustris and S. monticolus, S. cinereus and S. haydeni, and S. hoyi. An additional noteworthy result was the detection of an historic mitochondrial introgression event between S. monticolus and S. palustris. When combining disparate data sets, we emphasize researcher diligence as certain types of data and processes may overly influence the analysis. However, there is considerable phylogenetic potential stemming from inter-SINE fingerprinting.
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Affiliation(s)
- Aaron B A Shafer
- Department of Biology, Acadia University, Wolfville, Nova Scotia, Canada.
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Abstract
It is unlikely that taxonomically diverse phylogenetic studies will be completed rapidly in the near future for nonmodel organisms on a whole-genome basis. However, one approach to advancing the field of "phylogenomics" is to estimate the structure of poorly known genomes by mining libraries of clones from suites of taxa, rather than from single species. The present analysis adopts this approach by taking advantage of megabase-scale end-sequence scanning of reptilian genomic clones to characterize diversity of CR1-like LINEs, the dominant family of transposable elements (TEs) in the sister group of mammals. As such, it helps close an important gap in the literature on the molecular systematics and evolution of retroelements in nonavian reptiles. Results from aligning more than 14 Mb of sequence from the American alligator (Alligator mississippiensis), painted turtle (Chrysemys picta), Bahamian green anole (Anolis smaragdinus), Tuatara (Sphenodon punctatus), Emu (Dromaius novaehollandiae), and Zebra Finch (Taeniopygia guttata) against a comprehensive library approximately 3000 TE-encoding peptides reflect an increasing abundance of LINE and non-long-terminal-repeat (non-LTR) retrotransposon repeat types with the age of common ancestry among exemplar reptilian clades. The hypothesis that repeat diversity is correlated with basal metabolic rate was tested using comparative methods and a significant nonlinear relationship was indicated. This analysis suggests that the age of divergence between an exemplary clade and its sister group as well as metabolic correlates should be considered in addition to genome size in explaining patterns of retroelement diversity. The first phylogenetic analysis of the largely unexplored chicken repeat 1 (CR1) 3' reverse transcriptase (RT) conserved domains 8 and 9 in nonavian reptiles reveals a pattern of multiple lineages with variable branch lengths, suggesting presence of both old and young elements and the existence of several distinct well-supported clades not apparent from previous characterization of CR1 subfamily structure in birds and the turtle. This mode of CR1 evolution contrasts with historical patterns of LINE 1 diversification in mammals and hints toward the existence of a rich but still largely unexplored diversity of nonavian retroelements of importance to advancing both comparative vertebrate genomics and amniote systematics.
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Affiliation(s)
- Andrew M Shedlock
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, Massachusetts 02138, USA.
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Shedlock AM. Exploring Frontiers in the DNA Landscape: An Introduction to the Symposium “Genome Analysis and the Molecular Systematics of Retroelements”. Syst Biol 2006; 55:871-4. [PMID: 17345669 DOI: 10.1080/10635150601077634] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The emerging field of phylogenomics is influencing both the amount and type of characters being brought to bear on long-standing problems in systematic biology. Moreover, the proliferation of sequence information from genome projects in concert with the development of new informatics tools is widening access to comparative data on retroelements to a broad cross section of investigators. Motivated by this, the Society of Systematic Biologists sponsored a symposium entitled "Genome Analysis and the Molecular Systematics of Retroelements," and the resulting papers illustrate this theme of new discoveries and cover three basic areas of research: (i) the taxonomic distribution and phylogenetic structure of families of retroelements; (II) the use of SINE and LINE insertions for phylogenetic inference; and (III) the informatics and classification of repetitive elements. Contributions of each article are briefly discussed in this context and particularly fruitful directions for future research illuminated by results of this symposium are reviewed.
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Affiliation(s)
- Andrew M Shedlock
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, Massachusetts 02138, USA.
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Matocq MD, Shurtliff QR, Feldman CR. Phylogenetics of the woodrat genus Neotoma (Rodentia: Muridae): implications for the evolution of phenotypic variation in male external genitalia. Mol Phylogenet Evol 2006; 42:637-52. [PMID: 17208019 DOI: 10.1016/j.ympev.2006.08.011] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2005] [Accepted: 08/15/2006] [Indexed: 11/26/2022]
Abstract
Interspecific morphological variation in animal genitalia has long attracted the attention of evolutionary biologists because of the role genital form may play in the generation and/or maintenance of species boundaries. Here we examine the origin and evolution of genital variation in rodents of the muroid genus Neotoma. We test the hypothesis that a relatively rare genital form has evolved only once in Neotoma. We use four mitochondrial and four nuclear markers to evaluate this hypothesis by establishing a phylogenetic framework in which to examine genital evolution. We find intron seven of the beta-fibrinogen gene to be a highly informative nuclear marker for the levels of differentiation that characterize Neotoma with this locus evolving at a rate slower than cytochrome b but faster than 12S. We estimate phylogenetic relationships within Neotoma using both maximum parsimony and maximum likelihood-based Bayesian methods. Our Bayesian and parsimony reconstructions differ in significant ways, but we show that our parsimony analysis may be influenced by long-branch attraction. Furthermore, our estimate of Neotoma phylogeny remains consistent across various data partitioning strategies in the Bayesian analyses. Using ancestral state reconstruction, we find support for the monophyly of taxa that possess the relatively rare genital form. However, we also find support for the independent evolution of the common genital form and discuss possible underlying developmental shifts that may have contributed to our observed patterns of morphological evolution.
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Affiliation(s)
- Marjorie D Matocq
- Department of Biological Sciences, Idaho State University, Campus Box 8007, Pocatello, ID 83209, USA.
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Short-wavelength sensitive opsin (SWS1) as a new marker for vertebrate phylogenetics. BMC Evol Biol 2006; 6:97. [PMID: 17107620 PMCID: PMC1664589 DOI: 10.1186/1471-2148-6-97] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2006] [Accepted: 11/15/2006] [Indexed: 11/23/2022] Open
Abstract
Background Vertebrate SWS1 visual pigments mediate visual transduction in response to light at short wavelengths. Due to their importance in vision, SWS1 genes have been isolated from a surprisingly wide range of vertebrates, including lampreys, teleosts, amphibians, reptiles, birds, and mammals. The SWS1 genes exhibit many of the characteristics of genes typically targeted for phylogenetic analyses. This study investigates both the utility of SWS1 as a marker for inferring vertebrate phylogenetic relationships, and the characteristics of the gene that contribute to its phylogenetic utility. Results Phylogenetic analyses of vertebrate SWS1 genes produced topologies that were remarkably congruent with generally accepted hypotheses of vertebrate evolution at both higher and lower taxonomic levels. The few exceptions were generally associated with areas of poor taxonomic sampling, or relationships that have been difficult to resolve using other molecular markers. The SWS1 data set was characterized by a substantial amount of among-site rate variation, and a relatively unskewed substitution rate matrix, even when the data were partitioned into different codon sites and individual taxonomic groups. Although there were nucleotide biases in some groups at third positions, these biases were not convergent across different taxonomic groups. Conclusion Our results suggest that SWS1 may be a good marker for vertebrate phylogenetics due to the variable yet consistent patterns of sequence evolution exhibited across fairly wide taxonomic groups. This may result from constraints imposed by the functional role of SWS1 pigments in visual transduction.
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