1
|
Stains M, Harshman J, Barker MK, Chasteen SV, Cole R, DeChenne-Peters SE, Eagan MK, Esson JM, Knight JK, Laski FA, Levis-Fitzgerald M, Lee CJ, Lo SM, McDonnell LM, McKay TA, Michelotti N, Musgrove A, Palmer MS, Plank KM, Rodela TM, Sanders ER, Schimpf NG, Schulte PM, Smith MK, Stetzer M, Van Valkenburgh B, Vinson E, Weir LK, Wendel PJ, Wheeler LB, Young AM. Anatomy of STEM teaching in North American universities. Science 2018; 359:1468-1470. [PMID: 29599232 PMCID: PMC6310123 DOI: 10.1126/science.aap8892] [Citation(s) in RCA: 120] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
National and local initiatives focused on the transformation of STEM teaching in higher education have multiplied over the last decade. These initiatives often focus on measuring change in instructional practices, but it is difficult to monitor such change without a national picture of STEM educational practices, especially as characterized by common observational instruments. We characterized a snapshot of this landscape by conducting the first large scale observation-based study. We found that lecturing was prominent throughout the undergraduate STEM curriculum, even in classrooms with infrastructure designed to support active learning, indicating that further work is required to reform STEM education. Additionally, we established that STEM faculty’s instructional practices can vary substantially within a course, invalidating the commonly-used teaching evaluations based on a one-time observation. Although lecture is prominent throughout the undergraduate STEM curriculum, STEM faculty employ varied teaching practices within the same course.
Collapse
Affiliation(s)
- M Stains
- The list of author affiliations is provided in the supplementary materials.
| | - J Harshman
- The list of author affiliations is provided in the supplementary materials
| | - M K Barker
- The list of author affiliations is provided in the supplementary materials
| | - S V Chasteen
- The list of author affiliations is provided in the supplementary materials
| | - R Cole
- The list of author affiliations is provided in the supplementary materials
| | | | - M K Eagan
- The list of author affiliations is provided in the supplementary materials
| | - J M Esson
- The list of author affiliations is provided in the supplementary materials
| | - J K Knight
- The list of author affiliations is provided in the supplementary materials
| | - F A Laski
- The list of author affiliations is provided in the supplementary materials
| | - M Levis-Fitzgerald
- The list of author affiliations is provided in the supplementary materials
| | - C J Lee
- The list of author affiliations is provided in the supplementary materials
| | - S M Lo
- The list of author affiliations is provided in the supplementary materials
| | - L M McDonnell
- The list of author affiliations is provided in the supplementary materials
| | - T A McKay
- The list of author affiliations is provided in the supplementary materials
| | - N Michelotti
- The list of author affiliations is provided in the supplementary materials
| | - A Musgrove
- The list of author affiliations is provided in the supplementary materials
| | - M S Palmer
- The list of author affiliations is provided in the supplementary materials
| | - K M Plank
- The list of author affiliations is provided in the supplementary materials
| | - T M Rodela
- The list of author affiliations is provided in the supplementary materials
| | - E R Sanders
- The list of author affiliations is provided in the supplementary materials
| | - N G Schimpf
- The list of author affiliations is provided in the supplementary materials
| | - P M Schulte
- The list of author affiliations is provided in the supplementary materials
| | - M K Smith
- The list of author affiliations is provided in the supplementary materials
| | - M Stetzer
- The list of author affiliations is provided in the supplementary materials
| | - B Van Valkenburgh
- The list of author affiliations is provided in the supplementary materials
| | - E Vinson
- The list of author affiliations is provided in the supplementary materials
| | - L K Weir
- The list of author affiliations is provided in the supplementary materials
| | - P J Wendel
- The list of author affiliations is provided in the supplementary materials
| | - L B Wheeler
- The list of author affiliations is provided in the supplementary materials
| | - A M Young
- The list of author affiliations is provided in the supplementary materials
| |
Collapse
|
2
|
Reddy S, Kimball RT, Pandey A, Hosner PA, Braun MJ, Hackett SJ, Han KL, Harshman J, Huddleston CJ, Kingston S, Marks BD, Miglia KJ, Moore WS, Sheldon FH, Witt CC, Yuri T, Braun EL. Why Do Phylogenomic Data Sets Yield Conflicting Trees? Data Type Influences the Avian Tree of Life more than Taxon Sampling. Syst Biol 2018; 66:857-879. [PMID: 28369655 DOI: 10.1093/sysbio/syx041] [Citation(s) in RCA: 171] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Accepted: 03/22/2017] [Indexed: 01/27/2023] Open
Abstract
Phylogenomics, the use of large-scale data matrices in phylogenetic analyses, has been viewed as the ultimate solution to the problem of resolving difficult nodes in the tree of life. However, it has become clear that analyses of these large genomic data sets can also result in conflicting estimates of phylogeny. Here, we use the early divergences in Neoaves, the largest clade of extant birds, as a "model system" to understand the basis for incongruence among phylogenomic trees. We were motivated by the observation that trees from two recent avian phylogenomic studies exhibit conflicts. Those studies used different strategies: 1) collecting many characters [$\sim$ 42 mega base pairs (Mbp) of sequence data] from 48 birds, sometimes including only one taxon for each major clade; and 2) collecting fewer characters ($\sim$ 0.4 Mbp) from 198 birds, selected to subdivide long branches. However, the studies also used different data types: the taxon-poor data matrix comprised 68% non-coding sequences whereas coding exons dominated the taxon-rich data matrix. This difference raises the question of whether the primary reason for incongruence is the number of sites, the number of taxa, or the data type. To test among these alternative hypotheses we assembled a novel, large-scale data matrix comprising 90% non-coding sequences from 235 bird species. Although increased taxon sampling appeared to have a positive impact on phylogenetic analyses the most important variable was data type. Indeed, by analyzing different subsets of the taxa in our data matrix we found that increased taxon sampling actually resulted in increased congruence with the tree from the previous taxon-poor study (which had a majority of non-coding data) instead of the taxon-rich study (which largely used coding data). We suggest that the observed differences in the estimates of topology for these studies reflect data-type effects due to violations of the models used in phylogenetic analyses, some of which may be difficult to detect. If incongruence among trees estimated using phylogenomic methods largely reflects problems with model fit developing more "biologically-realistic" models is likely to be critical for efforts to reconstruct the tree of life. [Birds; coding exons; GTR model; model fit; Neoaves; non-coding DNA; phylogenomics; taxon sampling.].
Collapse
Affiliation(s)
- Sushma Reddy
- Biology Department, Loyola University Chicago, 1032 West Sheridan Road, Chicago, IL 60660, USA
| | - Rebecca T Kimball
- Department of Biology, University of Florida, Gainesville, FL 32607, USA
| | - Akanksha Pandey
- Department of Biology, University of Florida, Gainesville, FL 32607, USA
| | - Peter A Hosner
- Department of Biology, University of Florida, Gainesville, FL 32607, USA.,Florida Museum of Natural History, University of Florida, Gainesville, FL 32607, USA
| | - Michael J Braun
- Behavior, Ecology, Evolution, and Systematics Program, University of Maryland, College Park, MD 20742, USA.,Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution-MRC 163, PO Box 37012, Washington, DC 20013-7012, USA
| | - Shannon J Hackett
- Zoology Department, Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL 60605, USA
| | - Kin-Lan Han
- Department of Biology, University of Florida, Gainesville, FL 32607, USA
| | | | - Christopher J Huddleston
- Collections Program, National Museum of Natural History, Smithsonian Institution, 4210 Silver Hill Road, Suitland, MD 20746, USA
| | - Sarah Kingston
- Behavior, Ecology, Evolution, and Systematics Program, University of Maryland, College Park, MD 20742, USA.,Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution-MRC 163, PO Box 37012, Washington, DC 20013-7012, USA.,Bowdoin College, Department of Biology and Coastal Studies Center, 6500 College Station, Brunwick, ME 04011, USA
| | - Ben D Marks
- Zoology Department, Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL 60605, USA
| | - Kathleen J Miglia
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI 48202, USA
| | - William S Moore
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI 48202, USA
| | - Frederick H Sheldon
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, 119 Foster Hall, Baton Rouge, LA 70803, USA
| | - Christopher C Witt
- Department of Biology and Museum of Southwestern Biology, University 15 of New Mexico, Albuquerque, New Mexico 87131, USA
| | - Tamaki Yuri
- Department of Biology, University of Florida, Gainesville, FL 32607, USA.,Sam Noble Museum, University of Oklahoma, 2401 Chautauqua Avenue, Norman, OK 73072, USA
| | - Edward L Braun
- Department of Biology, University of Florida, Gainesville, FL 32607, USA.,Genetics Institute, University of Florida, Gainesville, FL 32607, USA
| |
Collapse
|
3
|
Yuri T, Kimball RT, Harshman J, Bowie RCK, Braun MJ, Chojnowski JL, Han KL, Hackett SJ, Huddleston CJ, Moore WS, Reddy S, Sheldon FH, Steadman DW, Witt CC, Braun EL. Parsimony and model-based analyses of indels in avian nuclear genes reveal congruent and incongruent phylogenetic signals. Biology (Basel) 2013; 2:419-44. [PMID: 24832669 PMCID: PMC4009869 DOI: 10.3390/biology2010419] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Revised: 02/21/2013] [Accepted: 02/22/2013] [Indexed: 11/19/2022]
Abstract
Insertion/deletion (indel) mutations, which are represented by gaps in multiple sequence alignments, have been used to examine phylogenetic hypotheses for some time. However, most analyses combine gap data with the nucleotide sequences in which they are embedded, probably because most phylogenetic datasets include few gap characters. Here, we report analyses of 12,030 gap characters from an alignment of avian nuclear genes using maximum parsimony (MP) and a simple maximum likelihood (ML) framework. Both trees were similar, and they exhibited almost all of the strongly supported relationships in the nucleotide tree, although neither gap tree supported many relationships that have proven difficult to recover in previous studies. Moreover, independent lines of evidence typically corroborated the nucleotide topology instead of the gap topology when they disagreed, although the number of conflicting nodes with high bootstrap support was limited. Filtering to remove short indels did not substantially reduce homoplasy or reduce conflict. Combined analyses of nucleotides and gaps resulted in the nucleotide topology, but with increased support, suggesting that gap data may prove most useful when analyzed in combination with nucleotide substitutions.
Collapse
Affiliation(s)
- Tamaki Yuri
- Department of Biology, University of Florida, Gainesville, FL 32611, USA; E-Mails: (T.Y.); (R.T.K.); (J.L.C.); (K.-L.H.)
- Sam Noble Oklahoma Museum of Natural History, University of Oklahoma, Norman, OK 73072, USA
| | - Rebecca T. Kimball
- Department of Biology, University of Florida, Gainesville, FL 32611, USA; E-Mails: (T.Y.); (R.T.K.); (J.L.C.); (K.-L.H.)
| | - John Harshman
- 4869 Pepperwood Way, San Jose, CA 95124, USA; E-Mail:
| | - Rauri C. K. Bowie
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720, USA; E-Mail:
| | - Michael J. Braun
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 4210 Silver Hill Road, Suitland, MD 20746, USA; E-Mails: (M.J.B.); (C.J.H.)
- Behavior, Ecology, Evolution and Systematics Program, University of Maryland, College Park, MD 20742, USA
| | - Jena L. Chojnowski
- Department of Biology, University of Florida, Gainesville, FL 32611, USA; E-Mails: (T.Y.); (R.T.K.); (J.L.C.); (K.-L.H.)
| | - Kin-Lan Han
- Department of Biology, University of Florida, Gainesville, FL 32611, USA; E-Mails: (T.Y.); (R.T.K.); (J.L.C.); (K.-L.H.)
| | - Shannon J. Hackett
- Zoology Department, Field Museum of Natural History, 1400 South Lakeshore Drive, Chicago, IL 60605, USA; E-Mail:
| | - Christopher J. Huddleston
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 4210 Silver Hill Road, Suitland, MD 20746, USA; E-Mails: (M.J.B.); (C.J.H.)
| | - William S. Moore
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI 48202, USA; E-Mail:
| | - Sushma Reddy
- Biology Department, Loyola University Chicago, Chicago, IL 60660, USA; E-Mail:
| | - Frederick H. Sheldon
- Museum of Natural Science, 119 Foster Hall, Louisiana State University, Baton Rouge, LA 70803, USA; E-Mail:
| | - David W. Steadman
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA; E-Mail:
| | - Christopher C. Witt
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA; E-Mail:
| | - Edward L. Braun
- Department of Biology, University of Florida, Gainesville, FL 32611, USA; E-Mails: (T.Y.); (R.T.K.); (J.L.C.); (K.-L.H.)
| |
Collapse
|
4
|
Braun EL, Kimball RT, Han KL, Iuhasz-Velez NR, Bonilla AJ, Chojnowski JL, Smith JV, Bowie RCK, Braun MJ, Hackett SJ, Harshman J, Huddleston CJ, Marks BD, Miglia KJ, Moore WS, Reddy S, Sheldon FH, Witt CC, Yuri T. Homoplastic microinversions and the avian tree of life. BMC Evol Biol 2011; 11:141. [PMID: 21612607 PMCID: PMC3123225 DOI: 10.1186/1471-2148-11-141] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2010] [Accepted: 05/25/2011] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Microinversions are cytologically undetectable inversions of DNA sequences that accumulate slowly in genomes. Like many other rare genomic changes (RGCs), microinversions are thought to be virtually homoplasy-free evolutionary characters, suggesting that they may be very useful for difficult phylogenetic problems such as the avian tree of life. However, few detailed surveys of these genomic rearrangements have been conducted, making it difficult to assess this hypothesis or understand the impact of microinversions upon genome evolution. RESULTS We surveyed non-coding sequence data from a recent avian phylogenetic study and found substantially more microinversions than expected based upon prior information about vertebrate inversion rates, although this is likely due to underestimation of these rates in previous studies. Most microinversions were lineage-specific or united well-accepted groups. However, some homoplastic microinversions were evident among the informative characters. Hemiplasy, which reflects differences between gene trees and the species tree, did not explain the observed homoplasy. Two specific loci were microinversion hotspots, with high numbers of inversions that included both the homoplastic as well as some overlapping microinversions. Neither stem-loop structures nor detectable sequence motifs were associated with microinversions in the hotspots. CONCLUSIONS Microinversions can provide valuable phylogenetic information, although power analysis indicates that large amounts of sequence data will be necessary to identify enough inversions (and similar RGCs) to resolve short branches in the tree of life. Moreover, microinversions are not perfect characters and should be interpreted with caution, just as with any other character type. Independent of their use for phylogenetic analyses, microinversions are important because they have the potential to complicate alignment of non-coding sequences. Despite their low rate of accumulation, they have clearly contributed to genome evolution, suggesting that active identification of microinversions will prove useful in future phylogenomic studies.
Collapse
Affiliation(s)
- Edward L Braun
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Rebecca T Kimball
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Kin-Lan Han
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | | | - Amber J Bonilla
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Jena L Chojnowski
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Jordan V Smith
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Rauri CK Bowie
- Zoology Department, Field Museum of Natural History, 1400 S. Lakeshore Drive, Chicago, IL 60605, USA
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Michael J Braun
- Department of Vertebrate Zoology, Smithsonian Institution, 4210 Silver Hill Road, Suitland, MD 20746, USA
- Behavior, Ecology, Evolution, and Systematics Program, University of Maryland, College Park, MD 20742, USA
| | - Shannon J Hackett
- Zoology Department, Field Museum of Natural History, 1400 S. Lakeshore Drive, Chicago, IL 60605, USA
| | - John Harshman
- Zoology Department, Field Museum of Natural History, 1400 S. Lakeshore Drive, Chicago, IL 60605, USA
- 4869 Pepperwood Way, San Jose, CA 95124, USA
| | - Christopher J Huddleston
- Department of Vertebrate Zoology, Smithsonian Institution, 4210 Silver Hill Road, Suitland, MD 20746, USA
| | - Ben D Marks
- Museum of Natural Science and Department of Biological Sciences, 119 Foster Hall, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Kathleen J Miglia
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI 48202, USA
| | - William S Moore
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI 48202, USA
| | - Sushma Reddy
- Zoology Department, Field Museum of Natural History, 1400 S. Lakeshore Drive, Chicago, IL 60605, USA
- Biology Department, Loyola University Chicago, Chicago, IL 60626, USA
| | - Frederick H Sheldon
- Museum of Natural Science and Department of Biological Sciences, 119 Foster Hall, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Christopher C Witt
- Museum of Natural Science and Department of Biological Sciences, 119 Foster Hall, Louisiana State University, Baton Rouge, LA 70803, USA
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA
| | - Tamaki Yuri
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
- Department of Vertebrate Zoology, Smithsonian Institution, 4210 Silver Hill Road, Suitland, MD 20746, USA
- Sam Noble Oklahoma Museum of Natural History, University of Oklahoma, Norman, OK 73072, USA
| |
Collapse
|
5
|
Han KL, Braun EL, Kimball RT, Reddy S, Bowie RCK, Braun MJ, Chojnowski JL, Hackett SJ, Harshman J, Huddleston CJ, Marks BD, Miglia KJ, Moore WS, Sheldon FH, Steadman DW, Witt CC, Yuri T. Are transposable element insertions homoplasy free?: an examination using the avian tree of life. Syst Biol 2011; 60:375-86. [PMID: 21303823 DOI: 10.1093/sysbio/syq100] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Kin-Lan Han
- Department of Biology, University of Florida, Gainesville, FL 32611, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
6
|
Hennig L, Olsen C, Felderman K, Ulbright J, Rees S, Harshman J, Silvers WM. Oxygen Consumption With Various Modes Of Video Game Interaction. Med Sci Sports Exerc 2009. [DOI: 10.1249/01.mss.0000356229.90186.08] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
7
|
Kimball RT, Braun EL, Barker FK, Bowie RCK, Braun MJ, Chojnowski JL, Hackett SJ, Han KL, Harshman J, Heimer-Torres V, Holznagel W, Huddleston CJ, Marks BD, Miglia KJ, Moore WS, Reddy S, Sheldon FH, Smith JV, Witt CC, Yuri T. A well-tested set of primers to amplify regions spread across the avian genome. Mol Phylogenet Evol 2008; 50:654-60. [PMID: 19084073 DOI: 10.1016/j.ympev.2008.11.018] [Citation(s) in RCA: 154] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2008] [Revised: 11/16/2008] [Accepted: 11/18/2008] [Indexed: 11/16/2022]
Affiliation(s)
- Rebecca T Kimball
- Department of Zoology, University of Florida, P.O. Box 118525, Gainesville, FL 32611, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
8
|
Harshman J, Braun EL, Braun MJ, Huddleston CJ, Bowie RCK, Chojnowski JL, Hackett SJ, Han KL, Kimball RT, Marks BD, Miglia KJ, Moore WS, Reddy S, Sheldon FH, Steadman DW, Steppan SJ, Witt CC, Yuri T. Phylogenomic evidence for multiple losses of flight in ratite birds. Proc Natl Acad Sci U S A 2008; 105:13462-7. [PMID: 18765814 PMCID: PMC2533212 DOI: 10.1073/pnas.0803242105] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2008] [Indexed: 11/18/2022] Open
Abstract
Ratites (ostriches, emus, rheas, cassowaries, and kiwis) are large, flightless birds that have long fascinated biologists. Their current distribution on isolated southern land masses is believed to reflect the breakup of the paleocontinent of Gondwana. The prevailing view is that ratites are monophyletic, with the flighted tinamous as their sister group, suggesting a single loss of flight in the common ancestry of ratites. However, phylogenetic analyses of 20 unlinked nuclear genes reveal a genome-wide signal that unequivocally places tinamous within ratites, making ratites polyphyletic and suggesting multiple losses of flight. Phenomena that can mislead phylogenetic analyses, including long branch attraction, base compositional bias, discordance between gene trees and species trees, and sequence alignment errors, have been eliminated as explanations for this result. The most plausible hypothesis requires at least three losses of flight and explains the many morphological and behavioral similarities among ratites by parallel or convergent evolution. Finally, this phylogeny demands fundamental reconsideration of proposals that relate ratite evolution to continental drift.
Collapse
Affiliation(s)
- John Harshman
- Zoology Department, Field Museum of Natural History, 1400 South Lakeshore Drive, Chicago, IL 60605
- 4869 Pepperwood Way, San Jose, CA 95124
| | - Edward L. Braun
- Department of Zoology, University of Florida, Gainesville, FL 32611
| | - Michael J. Braun
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 4210 Silver Hill Road, Suitland, MD 20746
- Behavior, Ecology, Evolution, and Systematics Program, University of Maryland, College Park, MD 20742
| | - Christopher J. Huddleston
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 4210 Silver Hill Road, Suitland, MD 20746
| | - Rauri C. K. Bowie
- Zoology Department, Field Museum of Natural History, 1400 South Lakeshore Drive, Chicago, IL 60605
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720
- Department of Science and Technology/National Resource Foundation Centre of Excellence at the Percy FitzPatrick Institute, Department of Botany and Zoology, Stellenbosch University, Matieland 7602, South Africa
| | | | - Shannon J. Hackett
- Zoology Department, Field Museum of Natural History, 1400 South Lakeshore Drive, Chicago, IL 60605
| | - Kin-Lan Han
- Department of Zoology, University of Florida, Gainesville, FL 32611
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 4210 Silver Hill Road, Suitland, MD 20746
- Behavior, Ecology, Evolution, and Systematics Program, University of Maryland, College Park, MD 20742
| | | | - Ben D. Marks
- Museum of Natural Science, 119 Foster Hall, Louisiana State University, Baton Rouge, LA 70803
| | - Kathleen J. Miglia
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI 48202
| | - William S. Moore
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI 48202
| | - Sushma Reddy
- Zoology Department, Field Museum of Natural History, 1400 South Lakeshore Drive, Chicago, IL 60605
| | - Frederick H. Sheldon
- Museum of Natural Science, 119 Foster Hall, Louisiana State University, Baton Rouge, LA 70803
| | - David W. Steadman
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611
| | - Scott J. Steppan
- Department of Biological Science, Florida State University, Tallahassee, FL 32306; and
| | - Christopher C. Witt
- Museum of Natural Science, 119 Foster Hall, Louisiana State University, Baton Rouge, LA 70803
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131
| | - Tamaki Yuri
- Department of Zoology, University of Florida, Gainesville, FL 32611
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 4210 Silver Hill Road, Suitland, MD 20746
| |
Collapse
|
9
|
Hackett SJ, Kimball RT, Reddy S, Bowie RCK, Braun EL, Braun MJ, Chojnowski JL, Cox WA, Han KL, Harshman J, Huddleston CJ, Marks BD, Miglia KJ, Moore WS, Sheldon FH, Steadman DW, Witt CC, Yuri T. A Phylogenomic Study of Birds Reveals Their Evolutionary History. Science 2008; 320:1763-8. [DOI: 10.1126/science.1157704] [Citation(s) in RCA: 1489] [Impact Index Per Article: 93.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
|
10
|
Leebens-Mack J, Vision T, Brenner E, Bowers JE, Cannon S, Clement MJ, Cunningham CW, dePamphilis C, deSalle R, Doyle JJ, Eisen JA, Gu X, Harshman J, Jansen RK, Kellogg EA, Koonin EV, Mishler BD, Philippe H, Pires JC, Qiu YL, Rhee SY, Sjölander K, Soltis DE, Soltis PS, Stevenson DW, Wall K, Warnow T, Zmasek C. Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA). OMICS 2006; 10:231-7. [PMID: 16901231 PMCID: PMC3167193 DOI: 10.1089/omi.2006.10.231] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
In the eight years since phylogenomics was introduced as the intersection of genomics and phylogenetics, the field has provided fundamental insights into gene function, genome history and organismal relationships. The utility of phylogenomics is growing with the increase in the number and diversity of taxa for which whole genome and large transcriptome sequence sets are being generated. We assert that the synergy between genomic and phylogenetic perspectives in comparative biology would be enhanced by the development and refinement of minimal reporting standards for phylogenetic analyses. Encouraged by the development of the Minimum Information About a Microarray Experiment (MIAME) standard, we propose a similar roadmap for the development of a Minimal Information About a Phylogenetic Analysis (MIAPA) standard. Key in the successful development and implementation of such a standard will be broad participation by developers of phylogenetic analysis software, phylogenetic database developers, practitioners of phylogenomics, and journal editors.
Collapse
Affiliation(s)
- Jim Leebens-Mack
- Department of Biology, Institute of Molecular Evolutionary Genetics, and Huck Institutes of Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
11
|
Abstract
The phylogeny of Crocodylia offers an unusual twist on the usual molecules versus morphology story. The true gharial (Gavialis gangeticus) and the false gharial (Tomistoma schlegelii), as their common names imply, have appeared in all cladistic morphological analyses as distantly related species, convergent upon a similar morphology. In contrast, all previous molecular studies have shown them to be sister taxa. We present the first phylogenetic study of Crocodylia using a nuclear gene. We cloned and sequenced the c-myc proto-oncogene from Alligator mississippiensis to facilitate primer design and then sequenced an 1,100-base pair fragment that includes both coding and noncoding regions and informative indels for one species in each extant crocodylian genus and six avian outgroups. Phylogenetic analyses using parsimony, maximum likelihood, and Bayesian inference all strongly agreed on the same tree, which is identical to the tree found in previous molecular analyses: Gavialis and Tomistoma are sister taxa and together are the sister group of Crocodylidae. Kishino-Hasegawa tests rejected the morphological tree in favor of the molecular tree. We excluded long-branch attraction and variation in base composition among taxa as explanations for this topology. To explore the causes of discrepancy between molecular and morphological estimates of crocodylian phylogeny, we examined puzzling features of the morphological data using a priori partitions of the data based on anatomical regions and investigated the effects of different coding schemes for two obvious morphological similarities of the two gharials.
Collapse
Affiliation(s)
- John Harshman
- Department of Systematic Biology, National Museum of Natural History, Smithsonian Institution, Suitland, Maryland 20746, USA.
| | | | | | | | | |
Collapse
|
12
|
Affiliation(s)
- J Harshman
- National Museum of Natural History, Laboratory of Molecular Systematics, 4210 Silver Hill Rd., Suitland, MD 20746, USA.
| |
Collapse
|
13
|
McCracken KG, Harshman J, McClellan DA, Afton AD. Data set incongruence and correlated character evolution: an example of functional convergence in the hind-limbs of stifftail diving ducks. Syst Biol 1999; 48:683-714. [PMID: 12066296 DOI: 10.1080/106351599259979] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
Abstract
The unwitting inclusion of convergent characters in phylogenetic estimates poses a serious problem for efforts to recover phylogeny. Convergence is not inscrutable, however, particularly when one group of characters tracks phylogeny and another set tracks adaptive history. In such cases, convergent characters may be correlated with one or a few functional anatomical units and readily identifiable by using comparative methods. Stifftail ducks (Oxyurinae) offer one such opportunity to study correlated character evolution and function in the context of phylogenetic reconstruction. Morphological analyses place stifftail ducks as part of a large clade of diving ducks that includes the sea ducks (Mergini), Hymenolaimus, Merganetta, and Tachyeres, and possibly the pochards (Aythyini). Molecular analyses, on the other hand, place stifftails far from other diving ducks and suggest, moreover, that stifftails are polyphyletic. Mitochondrial cytochrome b gene sequences of eight stifftail species traditionally supposed to form a clade were compared with each other and with sequences from 50 other anseriform and galliform species. Stifftail ducks are not the sister group of sea ducks but lie outside the typical ducks (Anatinae). Of the four traditional stifftail genera, monophyly of Oxyura and its sister group relationship with Nomonyx are strongly supported. Heteronetta probably is the sister group of that clade, but support is weak. Biziura is not a true stifftail. Within Oxyura, Old World species (O. australis, O. leucocephala, O. maccoa) appear to form a clade, with New World species (O. jamaicensis, O. vittata) branching basally. Incongruence between molecules and morphology is interpreted to be the result of adaptive specialization and functional convergence in the hind limbs of Biziura and true stifftails. When morphological characters are divided into classes, only hind-limb characters are significantly in conflict with the molecular tree. Likewise, null models of synonymous and nonsynonymous substitution based on patterns of codon-degeneracy and chemical dissimilarity indicate that the nucleotide and amino acid changes postulated by the molecular tree are more plausible than those postulated by the morphological tree. These findings teach general lessons about the utility of highly adaptive characters (in particular those related to foraging ecology) and underscore the problems that convergence can pose for attempts to recover phylogeny. They also demonstrate how the concept of natural data partitions and simple models of evolution (e.g., parsimony, likelihood, neutrality) can be used to test the accuracy of independent phylogenetic estimates and provide arguments in favor of one tree topology over another.
Collapse
Affiliation(s)
- K G McCracken
- School of Forestry, Wildlife, and Fisheries, Louisiana State University, Baton Rouge, Louisiana 70803, USA.
| | | | | | | |
Collapse
|
14
|
|
15
|
Harshman J. The Effect of Irrelevant Characters on Bootstrap Values. Syst Biol 1994. [DOI: 10.2307/2413676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
|