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Hoekzema H, Baskir E, Kozlowski C, Elden M, Powell DM. Breeding season behaviors of captive tawny frogmouth (Podargus strigoides) pairs. Zoo Biol 2023; 42:616-624. [PMID: 37092593 DOI: 10.1002/zoo.21769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 01/16/2023] [Accepted: 03/30/2023] [Indexed: 04/25/2023]
Abstract
While courtship and breeding in birds is a topic of much study, behaviors of nocturnal species are difficult to observe. This study provides an ethogram and comparative analysis of relevant breeding and nonbreeding behaviors of three captive tawny frogmouth (Podargus strigoides) pairs at the Saint Louis Zoo. Infrared cameras were used to record nighttime activity, and 30 h of footage per pair were analyzed. Notable behaviors included a significant increase in nest-building activity in a pair 9-13 days before egg-laying, and a difference in the use of copulation signals between the two breeding females, with one accepting copulation attempts more readily than the other. Bill gaping behavior was determined to not be directly related to courtship. These results provide a preliminary description of tawny frogmouth behaviors during the breeding season and provide a basis on which further studies of both captive and wild tawny frogmouths can build.
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Affiliation(s)
- Han Hoekzema
- Department of Zoology (OEP Biology Program), University of Bonn, Bonn, Germany
| | - Eli Baskir
- Department of Reproductive and Behavioral Sciences, Saint Louis Zoo, St. Louis, Missouri, USA
| | - Corinne Kozlowski
- Department of Reproductive and Behavioral Sciences, Saint Louis Zoo, St. Louis, Missouri, USA
| | - Marija Elden
- Bird House, Saint Louis Zoo, St. Louis, Missouri, USA
| | - David M Powell
- Department of Reproductive and Behavioral Sciences, Saint Louis Zoo, St. Louis, Missouri, USA
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Skeels A, Boschman LM, McFadden IR, Joyce EM, Hagen O, Jiménez Robles O, Bach W, Boussange V, Keggin T, Jetz W, Pellissier L. Paleoenvironments shaped the exchange of terrestrial vertebrates across Wallace's Line. Science 2023; 381:86-92. [PMID: 37410831 DOI: 10.1126/science.adf7122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 06/01/2023] [Indexed: 07/08/2023]
Abstract
Faunal turnover in Indo-Australia across Wallace's Line is one of the most recognizable patterns in biogeography and has catalyzed debate about the role of evolutionary and geoclimatic history in biotic interchanges. Here, analysis of more than 20,000 vertebrate species with a model of geoclimate and biological diversification shows that broad precipitation tolerance and dispersal ability were key for exchange across the deep-time precipitation gradient spanning the region. Sundanian (Southeast Asian) lineages evolved in a climate similar to the humid "stepping stones" of Wallacea, facilitating colonization of the Sahulian (Australian) continental shelf. By contrast, Sahulian lineages predominantly evolved in drier conditions, hampering establishment in Sunda and shaping faunal distinctiveness. We demonstrate how the history of adaptation to past environmental conditions shapes asymmetrical colonization and global biogeographic structure.
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Affiliation(s)
- A Skeels
- Department of Environmental Systems Science, Ecosystems and Landscape Evolution, Institute of Terrestrial Ecosystems, ETH Zurich, 8092 Zurich, Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, 8903 Birmensdorf, Switzerland
- Research School of Biology, Australian National University, Canberra 0200, Australia
| | - L M Boschman
- Department of Earth Sciences, Utrecht University, 3584 CB Utrecht, Netherlands
| | - I R McFadden
- Department of Environmental Systems Science, Ecosystems and Landscape Evolution, Institute of Terrestrial Ecosystems, ETH Zurich, 8092 Zurich, Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, 8903 Birmensdorf, Switzerland
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090 GE Amsterdam, Netherlands
| | - E M Joyce
- Systematics, Biodiversity and Evolution of Plants, Ludwig Maximilian University of Munich, 80331 Munich, Germany
| | - O Hagen
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
| | - O Jiménez Robles
- Research School of Biology, Australian National University, Canberra 0200, Australia
- Institute of Biology, École Normale Supérieure, 75005 Paris, France
| | - W Bach
- Department of Environmental Systems Science, Ecosystems and Landscape Evolution, Institute of Terrestrial Ecosystems, ETH Zurich, 8092 Zurich, Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, 8903 Birmensdorf, Switzerland
| | - V Boussange
- Department of Environmental Systems Science, Ecosystems and Landscape Evolution, Institute of Terrestrial Ecosystems, ETH Zurich, 8092 Zurich, Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, 8903 Birmensdorf, Switzerland
| | - T Keggin
- Department of Environmental Systems Science, Ecosystems and Landscape Evolution, Institute of Terrestrial Ecosystems, ETH Zurich, 8092 Zurich, Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, 8903 Birmensdorf, Switzerland
| | - W Jetz
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
- Center for Biodiversity and Global Change, Yale University, New Haven, CT 06520, USA
| | - L Pellissier
- Department of Environmental Systems Science, Ecosystems and Landscape Evolution, Institute of Terrestrial Ecosystems, ETH Zurich, 8092 Zurich, Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, 8903 Birmensdorf, Switzerland
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3
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OUP accepted manuscript. Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Xu N, Ding J, Que Z, Xu W, Ye W, Liu H. The mitochondrial genome and phylogenetic characteristics of the Thick-billed Green-Pigeon, Treron curvirostra: the first sequence for the genus. Zookeys 2021; 1041:167-182. [PMID: 34149293 PMCID: PMC8190031 DOI: 10.3897/zookeys.1041.60150] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 02/17/2021] [Indexed: 11/12/2022] Open
Abstract
Members of the genus Treron (Columbidae) are widely distributed in southern Asia and the Indo-Malayan Region but their relationships are poorly understood. Better knowledge of the systematic status of this genus may help studies of historical biogeography and taxonomy. The complete mitochondrial genome of T.curvirostra was characterized, a first for the genus. It is 17,414 base pairs in length, containing two rRNAs, 22 tRNAs, 13 protein coding genes (PCGs), and one D-loop with a primary structure that is similar to that found in most members of Columbidae. Most PCGs start with the common ATG codon but are terminated by different codons. The highest value of the Ka/Ks ratio within 13 PCGs was found in ATP8 with 0.1937, suggesting that PCGs of the mitochondrial genome tend to be conservative in Columbidae. Moreover, the phylogenetic relationships within Columbidae, which was based on sequences of 13 PCGs, showed that (T.curvirostra + Hemiphaganovaeseelandiae) were clustered in one clade, suggesting a potentially close relationship between Treron and Hemiphaga. However, the monophyly of the subfamilies of Columbidae recognized by the Interagency Taxonomic Information System could not be corroborated. Hence, the position of the genus Treron in the classification of Columbidae may have to be revised.
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Affiliation(s)
- Nan Xu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China Nanjing Forestry University Nanjing China
| | - Jiayu Ding
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China Nanjing Forestry University Nanjing China
| | - Ziting Que
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China Nanjing Forestry University Nanjing China
| | - Wei Xu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China Nanjing Forestry University Nanjing China
| | - Wentao Ye
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China Nanjing Forestry University Nanjing China
| | - Hongyi Liu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China Nanjing Forestry University Nanjing China
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White ND, Braun MJ. Extracting phylogenetic signal from phylogenomic data: Higher-level relationships of the nightbirds (Strisores). Mol Phylogenet Evol 2019; 141:106611. [DOI: 10.1016/j.ympev.2019.106611] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 09/04/2019] [Accepted: 09/06/2019] [Indexed: 12/22/2022]
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Total-Evidence Framework Reveals Complex Morphological Evolution in Nightbirds (Strisores). DIVERSITY-BASEL 2019. [DOI: 10.3390/d11090143] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Strisores is a clade of neoavian birds that include diurnal aerial specialists such as swifts and hummingbirds, as well as several predominantly nocturnal lineages such as nightjars and potoos. Despite the use of genome-scale molecular datasets, the phylogenetic interrelationships among major strisorean groups remain controversial. Given the availability of next-generation sequence data for Strisores and the clade’s rich fossil record, we reassessed the phylogeny of Strisores by incorporating a large-scale sequence dataset with anatomical data from living and fossil strisoreans within a Bayesian total-evidence framework. Combined analyses of molecular and morphological data resulted in a phylogenetic topology for Strisores that is congruent with the findings of two recent molecular phylogenomic studies, supporting nightjars (Caprimulgidae) as the extant sister group of the remainder of Strisores. This total-evidence framework allowed us to identify morphological synapomorphies for strisorean clades previously recovered using molecular-only datasets. However, a combined analysis of molecular and morphological data highlighted strong signal conflict between sequence and anatomical data in Strisores. Furthermore, simultaneous analysis of molecular and morphological data recovered differing placements for some fossil taxa compared with analyses of morphological data under a molecular scaffold, highlighting the importance of analytical decisions when conducting morphological phylogenetic analyses of taxa with molecular phylogenetic data. We suggest that multiple strisorean lineages have experienced convergent evolution across the skeleton, obfuscating the phylogenetic position of certain fossils, and that many distinctive specializations of strisorean subclades were acquired early in their evolutionary history. Despite this apparent complexity in the evolutionary history of Strisores, our results provide fossil support for aerial foraging as the ancestral ecological strategy of Strisores, as implied by recent phylogenetic topologies derived from molecular data.
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Mays SE, Newberry GN, Riley L, Britten HB, Swanson DL. Common Nighthawks (Chordeiles Minor) in Agricultural Landscapes: Genetic Structure of Populations Restricted to Urban Rooftop Nesting. AMERICAN MIDLAND NATURALIST 2019. [DOI: 10.1674/0003-0031-181.1.29] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Sarah E. Mays
- Department of Biology, University of South Dakota, Vermillion 57069
| | | | - Lynn Riley
- Department of Biology, University of South Dakota, Vermillion 57069
| | - Hugh B. Britten
- Department of Biology, University of South Dakota, Vermillion 57069
| | - David L. Swanson
- Department of Biology, University of South Dakota, Vermillion 57069
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Kumar A, Natarajan C, Moriyama H, Witt CC, Weber RE, Fago A, Storz JF. Stability-Mediated Epistasis Restricts Accessible Mutational Pathways in the Functional Evolution of Avian Hemoglobin. Mol Biol Evol 2017; 34:1240-1251. [PMID: 28201714 PMCID: PMC5400398 DOI: 10.1093/molbev/msx085] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
If the fitness effects of amino acid mutations are conditional on genetic background, then mutations can have different effects depending on the sequential order in which they occur during evolutionary transitions in protein function. A key question concerns the fraction of possible mutational pathways connecting alternative functional states that involve transient reductions in fitness. Here we examine the functional effects of multiple amino acid substitutions that contributed to an evolutionary transition in the oxygenation properties of avian hemoglobin (Hb). The set of causative changes included mutations at intradimer interfaces of the Hb tetramer. Replacements at such sites may be especially likely to have epistatic effects on Hb function since residues at intersubunit interfaces are enmeshed in networks of salt bridges and hydrogen bonds between like and unlike subunits; mutational reconfigurations of these atomic contacts can affect allosteric transitions in quaternary structure and the propensity for tetramer-dimer dissociation. We used ancestral protein resurrection in conjunction with a combinatorial protein engineering approach to synthesize genotypes representing the complete set of mutational intermediates in all possible forward pathways that connect functionally distinct ancestral and descendent genotypes. The experiments revealed that 1/2 of all possible forward pathways included mutational intermediates with aberrant functional properties because particular combinations of mutations promoted tetramer-dimer dissociation. The subset of mutational pathways with unstable intermediates may be selectively inaccessible, representing evolutionary roads not taken. The experimental results also demonstrate how epistasis for particular functional properties of proteins may be mediated indirectly by mutational effects on quaternary structural stability.
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Affiliation(s)
- Amit Kumar
- School of Biological Sciences, University of Nebraska, Lincoln, NE
| | | | - Hideaki Moriyama
- School of Biological Sciences, University of Nebraska, Lincoln, NE
| | - Christopher C. Witt
- Department of Biology, University of New Mexico, Albuquerque, NM
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM
| | - Roy E. Weber
- Zoophysiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Angela Fago
- Zoophysiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Jay F. Storz
- School of Biological Sciences, University of Nebraska, Lincoln, NE
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Claramunt S. Phylogenetic relationships among Synallaxini spinetails (Aves: Furnariidae) reveal a new biogeographic pattern across the Amazon and Paraná river basins. Mol Phylogenet Evol 2014; 78:223-31. [PMID: 24867462 DOI: 10.1016/j.ympev.2014.05.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Revised: 05/05/2014] [Accepted: 05/06/2014] [Indexed: 10/25/2022]
Abstract
Relationships among genera in the tribe Synallaxini have proved difficult to resolve. In this study, I investigate relationships among Synallaxis, Certhiaxis and Schoeniophylax using DNA sequences from the mitochondrion and three nuclear regions. I implemented novel primers and protocols for amplifying and sequencing autosomal and sex-linked introns in Furnariidae that resolved basal relationships in the Synallaxini with strong support. Synallaxis propinqua is sister to Schoeniophylax phryganophilus, and together they form a clade with Certhiaxis. The results are robust to analytical approaches when all genomic regions are analyzed jointly (parsimony, maximum likelihood, and species-tree analysis) and the same basal relationships are recovered by most genomic regions when analyzed separately. A sister relationship between S. propinqua, an Amazonian river island specialist, and S. phryganophilus, from the Paraná River basin region, reveals a new biogeographic pattern shared by at least other four pairs of taxa with similar distributions and ecologies. Estimates of divergence times for these five pairs span from the late Miocene to the Pleistocene. Identification of the historical events that produced this pattern is difficult and further advances will require additional studies of the taxa involved and a better understanding of the recent environmental history of South America. A new classification is proposed for the Synallaxini, including the description of a new genus for S. propinqua.
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Affiliation(s)
- Santiago Claramunt
- Department of Ornithology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA.
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Sigurðsson S, Cracraft J. Deciphering the diversity and history of New World nightjars (Aves: Caprimulgidae) using molecular phylogenetics. Zool J Linn Soc 2014. [DOI: 10.1111/zoj.12109] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Snorri Sigurðsson
- Department of Ornithology; American Museum of Natural History; Central Park West at 79th Street New York NY 10024 USA
- The Graduate Center; City University of New York; 365 Fifth Avenue New York NY 10016 USA
| | - Joel Cracraft
- Department of Ornithology; American Museum of Natural History; Central Park West at 79th Street New York NY 10024 USA
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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 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] [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.
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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.)
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Fisher-Reid MC, Wiens JJ. What are the consequences of combining nuclear and mitochondrial data for phylogenetic analysis? Lessons from Plethodon salamanders and 13 other vertebrate clades. BMC Evol Biol 2011; 11:300. [PMID: 21995558 PMCID: PMC3203092 DOI: 10.1186/1471-2148-11-300] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2011] [Accepted: 10/13/2011] [Indexed: 11/15/2022] Open
Abstract
Background The use of mitochondrial DNA data in phylogenetics is controversial, yet studies that combine mitochondrial and nuclear DNA data (mtDNA and nucDNA) to estimate phylogeny are common, especially in vertebrates. Surprisingly, the consequences of combining these data types are largely unexplored, and many fundamental questions remain unaddressed in the literature. For example, how much do trees from mtDNA and nucDNA differ? How are topological conflicts between these data types typically resolved in the combined-data tree? What determines whether a node will be resolved in favor of mtDNA or nucDNA, and are there any generalities that can be made regarding resolution of mtDNA-nucDNA conflicts in combined-data trees? Here, we address these and related questions using new and published nucDNA and mtDNA data for Plethodon salamanders and published data from 13 other vertebrate clades (including fish, frogs, lizards, birds, turtles, and mammals). Results We find widespread discordance between trees from mtDNA and nucDNA (30-70% of nodes disagree per clade), but this discordance is typically not strongly supported. Despite often having larger numbers of variable characters, mtDNA data do not typically dominate combined-data analyses, and combined-data trees often share more nodes with trees from nucDNA alone. There is no relationship between the proportion of nodes shared between combined-data and mtDNA trees and relative numbers of variable characters or levels of homoplasy in the mtDNA and nucDNA data sets. Congruence between trees from mtDNA and nucDNA is higher on branches that are longer and deeper in the combined-data tree, but whether a conflicting node will be resolved in favor mtDNA or nucDNA is unrelated to branch length. Conflicts that are resolved in favor of nucDNA tend to occur at deeper nodes in the combined-data tree. In contrast to these overall trends, we find that Plethodon have an unusually large number of strongly supported conflicts between data types, which are generally resolved in favor of mtDNA in the combined-data tree (despite the large number of nuclear loci sampled). Conclusions Overall, our results from 14 vertebrate clades show that combined-data analyses are not necessarily dominated by the more variable mtDNA data sets. However, given cases like Plethodon, there is also the need for routine checking of incongruence between mtDNA and nucDNA data and its impacts on combined-data analyses.
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Affiliation(s)
- M Caitlin Fisher-Reid
- Department of Ecology and Evolution, Stony Brook University, Stony Brook NY, 11794-5245, USA.
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