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Abstract
Cytochrome oxidase subunit I (COI) gene has been recognized as an authentic tool for species identification. Besides its potential barcoding capacity, COI sequences have also been used for inferring the phylogeny. Phylogenetic relationships among genera of Columbidae (pigeons and doves family) have not been fully resolved because of scarce sampling of taxa and limited availability of sequence data. In this study, we have evaluated the efficiency of COI barcodes for species identification and phylogenetic analysis of various doves. We sequenced the 693 bp region of COI gene of three species of doves including Oena capensis, Streptopelia decaocto, and Streptopelia senegalensis. After retrieving the relevant sequences from the GenBank, the entire data-set of 85 sequences represented 25 dove species from 11 different genera of the family Columbidae. The COI sequences of four species including Chalcophaps indica (two specimens), Columbina inca (five specimens), Geopelia striata (three specimens), and Macropygia phasianella (three specimens) were identical. The mean intraspecific base differences ranged from 0 to 37 while the P-distances ranged between 0 and 0.058. For most of the species, the P-distances were ≤ 0.008. Phylogenetic analysis differentiated the taxa into three major clusters. One of the clusters grouped five genera including Claravis, Columbina, Gallicolumba, Geopelia, and Geotrygon. The remaining two clusters grouped three genera each including Chalcophaps, Oena, and Turtur in one cluster and Macropygia, Streptopelia, and Zenaida in another cluster. Further sub-clustering clearly separated all the genera into individual clusters except two discrepancies for the genera Streptopelia and Turtur. Species-level cladistics clearly separated all the species into distinctive clades. In conclusion, COI barcoding is a powerful tool for species identification with added information on phylogenetic inference. The finding of this study will help to understand the complex phylogeny of the family Columbidae.
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Affiliation(s)
- Haseeb Ahmad Khan
- Prince Sultan Research Chair for Environment and Wildlife, Department of Botany and Microbiology, College of Science, King Saud University, Riyadh , Saudi Arabia
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52
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Affiliation(s)
- Hans Ellegren
- Department of Evolutionary Biology, Evolutionary Biology Center, Uppsala University, SE-752 36 Uppsala, Sweden;
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Romiguier J, Ranwez V, Delsuc F, Galtier N, Douzery EJP. Less is more in mammalian phylogenomics: AT-rich genes minimize tree conflicts and unravel the root of placental mammals. Mol Biol Evol 2013; 30:2134-44. [PMID: 23813978 DOI: 10.1093/molbev/mst116] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Despite the rapid increase of size in phylogenomic data sets, a number of important nodes on animal phylogeny are still unresolved. Among these, the rooting of the placental mammal tree is still a controversial issue. One difficulty lies in the pervasive phylogenetic conflicts among genes, with each one telling its own story, which may be reliable or not. Here, we identified a simple criterion, that is, the GC content, which substantially helps in determining which gene trees best reflect the species tree. We assessed the ability of 13,111 coding sequence alignments to correctly reconstruct the placental phylogeny. We found that GC-rich genes induced a higher amount of conflict among gene trees and performed worse than AT-rich genes in retrieving well-supported, consensual nodes on the placental tree. We interpret this GC effect mainly as a consequence of genome-wide variations in recombination rate. Indeed, recombination is known to drive GC-content evolution through GC-biased gene conversion and might be problematic for phylogenetic reconstruction, for instance, in an incomplete lineage sorting context. When we focused on the AT-richest fraction of the data set, the resolution level of the placental phylogeny was greatly increased, and a strong support was obtained in favor of an Afrotheria rooting, that is, Afrotheria as the sister group of all other placentals. We show that in mammals most conflicts among gene trees, which have so far hampered the resolution of the placental tree, are concentrated in the GC-rich regions of the genome. We argue that the GC content-because it is a reliable indicator of the long-term recombination rate-is an informative criterion that could help in identifying the most reliable molecular markers for species tree inference.
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Affiliation(s)
- Jonathan Romiguier
- CNRS, Université Montpellier, Institut des Sciences de l'Evolution, Montpellier, France.
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54
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Alcaide M, Liu M, Edwards SV. Major histocompatibility complex class I evolution in songbirds: universal primers, rapid evolution and base compositional shifts in exon 3. PeerJ 2013; 1:e86. [PMID: 23781408 PMCID: PMC3685324 DOI: 10.7717/peerj.86] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Accepted: 05/23/2013] [Indexed: 01/04/2023] Open
Abstract
Genes of the Major Histocompatibility Complex (MHC) have become an important marker for the investigation of adaptive genetic variation in vertebrates because of their critical role in pathogen resistance. However, despite significant advances in the last few years the characterization of MHC variation in non-model species still remains a challenging task due to the redundancy and high variation of this gene complex. Here we report the utility of a single pair of primers for the cross-amplification of the third exon of MHC class I genes, which encodes the more polymorphic half of the peptide-binding region (PBR), in oscine passerines (songbirds; Aves: Passeriformes), a group especially challenging for MHC characterization due to the presence of large and complex MHC multigene families. In our survey, although the primers failed to amplify exon 3 from two suboscine passerine birds, they amplified exon 3 of multiple MHC class I genes in all 16 species of oscine songbirds tested, yielding a total of 120 sequences. The 16 songbird species belong to 14 different families, primarily within the Passerida, but also in the Corvida. Using a conservative approach based on the analysis of cloned amplicons (n = 16) from each species, we found between 3 and 10 MHC sequences per individual. Each allele repertoire was highly divergent, with the overall number of polymorphic sites per species ranging from 33 to 108 (out of 264 sites) and the average number of nucleotide differences between alleles ranging from 14.67 to 43.67. Our survey in songbirds allowed us to compare macroevolutionary dynamics of exon 3 between songbirds and non-passerine birds. We found compelling evidence of positive selection acting specifically upon peptide-binding codons across birds, and we estimate the strength of diversifying selection in songbirds to be about twice that in non-passerines. Analysis using comparative methods suggest weaker evidence for a higher GC content in the 3rd codon position of exon 3 in non-passerine birds, a pattern that contrasts with among-clade GC patterns found in other avian studies and may suggests different mutational mechanisms. Our primers represent a useful tool for the characterization of functional and evolutionarily relevant MHC variation across the hyperdiverse songbirds.
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Affiliation(s)
- Miguel Alcaide
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Mark Liu
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Scott V. Edwards
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
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55
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Betancur-R. R, Li C, Munroe TA, Ballesteros JA, Ortí G. Addressing Gene Tree Discordance and Non-Stationarity to Resolve a Multi-Locus Phylogeny of the Flatfishes (Teleostei: Pleuronectiformes). Syst Biol 2013; 62:763-85. [DOI: 10.1093/sysbio/syt039] [Citation(s) in RCA: 104] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Ricardo Betancur-R.
- Department of Biological Sciences, The George Washington University, 2023 G St. NW, Washington, D.C. 20052, USA; 2College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China; and 3National Systematics Laboratory NMFS/NOAA, Post Office Box 37012, Smithsonian Institution NHB, WC 60, MRC-153, Washington, D.C. 20013-7012, USA
| | - Chenhong Li
- Department of Biological Sciences, The George Washington University, 2023 G St. NW, Washington, D.C. 20052, USA; 2College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China; and 3National Systematics Laboratory NMFS/NOAA, Post Office Box 37012, Smithsonian Institution NHB, WC 60, MRC-153, Washington, D.C. 20013-7012, USA
| | - Thomas A. Munroe
- Department of Biological Sciences, The George Washington University, 2023 G St. NW, Washington, D.C. 20052, USA; 2College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China; and 3National Systematics Laboratory NMFS/NOAA, Post Office Box 37012, Smithsonian Institution NHB, WC 60, MRC-153, Washington, D.C. 20013-7012, USA
| | - Jesus A. Ballesteros
- Department of Biological Sciences, The George Washington University, 2023 G St. NW, Washington, D.C. 20052, USA; 2College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China; and 3National Systematics Laboratory NMFS/NOAA, Post Office Box 37012, Smithsonian Institution NHB, WC 60, MRC-153, Washington, D.C. 20013-7012, USA
| | - Guillermo Ortí
- Department of Biological Sciences, The George Washington University, 2023 G St. NW, Washington, D.C. 20052, USA; 2College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China; and 3National Systematics Laboratory NMFS/NOAA, Post Office Box 37012, Smithsonian Institution NHB, WC 60, MRC-153, Washington, D.C. 20013-7012, USA
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56
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Cui R, Schumer M, Kruesi K, Walter R, Andolfatto P, Rosenthal GG. Phylogenomics reveals extensive reticulate evolution in Xiphophorus fishes. Evolution 2013; 67:2166-79. [PMID: 23888843 DOI: 10.1111/evo.12099] [Citation(s) in RCA: 124] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Accepted: 02/26/2013] [Indexed: 01/25/2023]
Abstract
Hybridization is increasingly being recognized as a widespread process, even between ecologically and behaviorally divergent animal species. Determining phylogenetic relationships in the presence of hybridization remains a major challenge for evolutionary biologists, but advances in sequencing technology and phylogenetic techniques are beginning to address these challenges. Here we reconstruct evolutionary relationships among swordtails and platyfishes (Xiphophorus: Poeciliidae), a group of species characterized by remarkable morphological diversity and behavioral barriers to interspecific mating. Past attempts to reconstruct phylogenetic relationships within Xiphophorus have produced conflicting results. Because many of the 26 species in the genus are interfertile, these conflicts are likely due to hybridization. Using genomic data, we resolve a high-confidence species tree of Xiphophorus that accounts for both incomplete lineage sorting and hybridization. Our results allow us to reexamine a long-standing controversy about the evolution of the sexually selected sword in Xiphophorus, and demonstrate that hybridization has been strikingly widespread in the evolutionary history of this genus.
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Affiliation(s)
- Rongfeng Cui
- Department of Biology, Texas A&M University, TAMU, College Station, Texas, 77843, USA.
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57
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Hughes GM, Gang L, Murphy WJ, Higgins DG, Teeling EC. Using Illumina next generation sequencing technologies to sequence multigene families in de novo species. Mol Ecol Resour 2013; 13:510-21. [PMID: 23480365 DOI: 10.1111/1755-0998.12087] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Revised: 01/27/2013] [Accepted: 01/29/2013] [Indexed: 11/27/2022]
Abstract
The advent of Next Generation Sequencing Technology (NGST) has revolutionized molecular biology research, allowing for rapid gene/genome sequencing from a multitude of diverse species. As high throughput sequencing becomes more accessible, more efficient workflows must be developed to deal with the amounts of data produced and better assemble the genomes of de novo lineages. We combine traditional laboratory methods with Illumina NGST to amplify and sequence the largest mammalian multigene family, the Olfactory Receptor gene family, for species with and without a reference genome. We develop novel assembly methods to annotate and filter these data, which can be utilized for any gene family or any species. We find no significant difference between the ratio of genes within their respective gene families of our data compared with available genomic data. Using simulated data we explore the limitations of short-read sequence data and our assembly in recovering this gene family. We highlight the benefits and shortcomings of these methods. Compared with data generated from traditional polymerase chain reaction, cloning and Sanger sequencing methodologies, sequence data generated using our pipeline increases yield and sequencing efficiency without reducing the number of unique genes amplified. A cloning step is not required, therefore shortening data generation time. The novel downstream methodologies and workflows described provide a tool to be utilized by many fields of biology, to access and analyze the vast quantities of data generated. By combining laboratory and in silico methods, we provide a means of extracting genomic information for multigene families without complete genome sequencing.
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Affiliation(s)
- Graham M Hughes
- UCD School of Biological and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
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58
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Groussin M, Boussau B, Gouy M. A branch-heterogeneous model of protein evolution for efficient inference of ancestral sequences. Syst Biol 2013; 62:523-38. [PMID: 23475623 PMCID: PMC3676677 DOI: 10.1093/sysbio/syt016] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Most models of nucleotide or amino acid substitution used in phylogenetic studies assume that the evolutionary process has been homogeneous across lineages and that composition of nucleotides or amino acids has remained the same throughout the tree. These oversimplified assumptions are refuted by the observation that compositional variability characterizes extant biological sequences. Branch-heterogeneous models of protein evolution that account for compositional variability have been developed, but are not yet in common use because of the large number of parameters required, leading to high computational costs and potential overparameterization. Here, we present a new branch-nonhomogeneous and nonstationary model of protein evolution that captures more accurately the high complexity of sequence evolution. This model, henceforth called Correspondence and likelihood analysis (COaLA), makes use of a correspondence analysis to reduce the number of parameters to be optimized through maximum likelihood, focusing on most of the compositional variation observed in the data. The model was thoroughly tested on both simulated and biological data sets to show its high performance in terms of data fitting and CPU time. COaLA efficiently estimates ancestral amino acid frequencies and sequences, making it relevant for studies aiming at reconstructing and resurrecting ancestral amino acid sequences. Finally, we applied COaLA on a concatenate of universal amino acid sequences to confirm previous results obtained with a nonhomogeneous Bayesian model regarding the early pattern of adaptation to optimal growth temperature, supporting the mesophilic nature of the Last Universal Common Ancestor.
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Affiliation(s)
- M Groussin
- Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, Université Lyon 1, CNRS, UMR5558, Villeurbanne, France.
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59
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Backström N, Zhang Q, Edwards SV. Evidence from a House Finch (Haemorhous mexicanus) Spleen Transcriptome for Adaptive Evolution and Biased Gene Conversion in Passerine Birds. Mol Biol Evol 2013; 30:1046-50. [DOI: 10.1093/molbev/mst033] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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60
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Rands CM, Darling A, Fujita M, Kong L, Webster MT, Clabaut C, Emes RD, Heger A, Meader S, Hawkins MB, Eisen MB, Teiling C, Affourtit J, Boese B, Grant PR, Grant BR, Eisen JA, Abzhanov A, Ponting CP. Insights into the evolution of Darwin's finches from comparative analysis of the Geospiza magnirostris genome sequence. BMC Genomics 2013; 14:95. [PMID: 23402223 PMCID: PMC3575239 DOI: 10.1186/1471-2164-14-95] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Accepted: 01/23/2013] [Indexed: 01/01/2023] Open
Abstract
Background A classical example of repeated speciation coupled with ecological diversification is the evolution of 14 closely related species of Darwin’s (Galápagos) finches (Thraupidae, Passeriformes). Their adaptive radiation in the Galápagos archipelago took place in the last 2–3 million years and some of the molecular mechanisms that led to their diversification are now being elucidated. Here we report evolutionary analyses of genome of the large ground finch, Geospiza magnirostris. Results 13,291 protein-coding genes were predicted from a 991.0 Mb G. magnirostris genome assembly. We then defined gene orthology relationships and constructed whole genome alignments between the G. magnirostris and other vertebrate genomes. We estimate that 15% of genomic sequence is functionally constrained between G. magnirostris and zebra finch. Genic evolutionary rate comparisons indicate that similar selective pressures acted along the G. magnirostris and zebra finch lineages suggesting that historical effective population size values have been similar in both lineages. 21 otherwise highly conserved genes were identified that each show evidence for positive selection on amino acid changes in the Darwin's finch lineage. Two of these genes (Igf2r and Pou1f1) have been implicated in beak morphology changes in Darwin’s finches. Five of 47 genes showing evidence of positive selection in early passerine evolution have cilia related functions, and may be examples of adaptively evolving reproductive proteins. Conclusions These results provide insights into past evolutionary processes that have shaped G. magnirostris genes and its genome, and provide the necessary foundation upon which to build population genomics resources that will shed light on more contemporaneous adaptive and non-adaptive processes that have contributed to the evolution of the Darwin’s finches.
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Affiliation(s)
- Chris M Rands
- Department of Physiology, Anatomy, and Genetics, MRC Functional Genomics Unit, University of Oxford, Oxford, OX1 3PT, UK
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61
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McCormack JE, Hird SM, Zellmer AJ, Carstens BC, Brumfield RT. Applications of next-generation sequencing to phylogeography and phylogenetics. Mol Phylogenet Evol 2013; 66:526-38. [DOI: 10.1016/j.ympev.2011.12.007] [Citation(s) in RCA: 445] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Revised: 12/02/2011] [Accepted: 12/05/2011] [Indexed: 01/09/2023]
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62
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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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63
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Matsubara K, Kuraku S, Tarui H, Nishimura O, Nishida C, Agata K, Kumazawa Y, Matsuda Y. Intra-genomic GC heterogeneity in sauropsids: evolutionary insights from cDNA mapping and GC(3) profiling in snake. BMC Genomics 2012; 13:604. [PMID: 23140509 PMCID: PMC3549455 DOI: 10.1186/1471-2164-13-604] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2012] [Accepted: 10/24/2012] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Extant sauropsids (reptiles and birds) are divided into two major lineages, the lineage of Testudines (turtles) and Archosauria (crocodilians and birds) and the lineage of Lepidosauria (tuatara, lizards, worm lizards and snakes). Karyotypes of these sauropsidan groups generally consist of macrochromosomes and microchromosomes. In chicken, microchromosomes exhibit a higher GC-content than macrochromosomes. To examine the pattern of intra-genomic GC heterogeneity in lepidosaurian genomes, we constructed a cytogenetic map of the Japanese four-striped rat snake (Elaphe quadrivirgata) with 183 cDNA clones by fluorescence in situ hybridization, and examined the correlation between the GC-content of exonic third codon positions (GC3) of the genes and the size of chromosomes on which the genes were localized. RESULTS Although GC3 distribution of snake genes was relatively homogeneous compared with those of the other amniotes, microchromosomal genes showed significantly higher GC3 than macrochromosomal genes as in chicken. Our snake cytogenetic map also identified several conserved segments between the snake macrochromosomes and the chicken microchromosomes. Cross-species comparisons revealed that GC3 of most snake orthologs in such macrochromosomal segments were GC-poor (GC3 < 50%) whereas those of chicken orthologs in microchromosomes were relatively GC-rich (GC3 ≥ 50%). CONCLUSION Our results suggest that the chromosome size-dependent GC heterogeneity had already occurred before the lepidosaur-archosaur split, 275 million years ago. This character was probably present in the common ancestor of lepidosaurs and but lost in the lineage leading to Anolis during the diversification of lepidosaurs. We also identified several genes whose GC-content might have been influenced by the size of the chromosomes on which they were harbored over the course of sauropsid evolution.
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Affiliation(s)
- Kazumi Matsubara
- Department of Information and Biological Sciences, Graduate School of Natural Sciences, Nagoya City University, 1 Yamanohata, Mizuho-cho, Mizuho-ku, Nagoya, Aichi 467-8501, Japan.
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64
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Romiguier J, Ranwez V, Douzery EJP, Galtier N. Genomic evidence for large, long-lived ancestors to placental mammals. Mol Biol Evol 2012; 30:5-13. [PMID: 22949523 DOI: 10.1093/molbev/mss211] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
It is widely assumed that our mammalian ancestors, which lived in the Cretaceous era, were tiny animals that survived massive asteroid impacts in shelters and evolved into modern forms after dinosaurs went extinct, 65 Ma. The small size of most Mesozoic mammalian fossils essentially supports this view. Paleontology, however, is not conclusive regarding the ancestry of extant mammals, because Cretaceous and Paleocene fossils are not easily linked to modern lineages. Here, we use full-genome data to estimate the longevity and body mass of early placental mammals. Analyzing 36 fully sequenced mammalian genomes, we reconstruct two aspects of the ancestral genome dynamics, namely GC-content evolution and nonsynonymous over synonymous rate ratio. Linking these molecular evolutionary processes to life-history traits in modern species, we estimate that early placental mammals had a life span above 25 years and a body mass above 1 kg. This is similar to current primates, cetartiodactyls, or carnivores, but markedly different from mice or shrews, challenging the dominant view about mammalian origin and evolution. Our results imply that long-lived mammals existed in the Cretaceous era and were the most successful in evolution, opening new perspectives about the conditions for survival to the Cretaceous-Tertiary crisis.
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Affiliation(s)
- J Romiguier
- CNRS, Université Montpellier 2, UMR 5554, ISEM, Montpellier, France
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65
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Pessia E, Popa A, Mousset S, Rezvoy C, Duret L, Marais GAB. Evidence for widespread GC-biased gene conversion in eukaryotes. Genome Biol Evol 2012; 4:675-82. [PMID: 22628461 PMCID: PMC5635611 DOI: 10.1093/gbe/evs052] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
GC-biased gene conversion (gBGC) is a process that tends to increase the GC content of recombining DNA over evolutionary time and is thought to explain the evolution of GC content in mammals and yeasts. Evidence for gBGC outside these two groups is growing but is still limited. Here, we analyzed 36 completely sequenced genomes representing four of the five major groups in eukaryotes (Unikonts, Excavates, Chromalveolates and Plantae). gBGC was investigated by directly comparing GC content and recombination rates in species where recombination data are available, that is, half of them. To study all species of our dataset, we used chromosome size as a proxy for recombination rate and compared it with GC content. Among the 17 species showing a significant relationship between GC content and chromosome size, 15 are consistent with the predictions of the gBGC model. Importantly, the species showing a pattern consistent with gBGC are found in all the four major groups of eukaryotes studied, which suggests that gBGC may be widespread in eukaryotes.
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Affiliation(s)
- Eugénie Pessia
- Université Lyon 1, Centre National de la Recherche Scientifique, UMR5558, Laboratoire de Biométrie et Biologie évolutive, Villeurbanne, Cedex, France
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66
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Nam K, Ellegren H. Recombination drives vertebrate genome contraction. PLoS Genet 2012; 8:e1002680. [PMID: 22570634 PMCID: PMC3342960 DOI: 10.1371/journal.pgen.1002680] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2011] [Accepted: 03/15/2012] [Indexed: 11/19/2022] Open
Abstract
Selective and/or neutral processes may govern variation in DNA content and, ultimately, genome size. The observation in several organisms of a negative correlation between recombination rate and intron size could be compatible with a neutral model in which recombination is mutagenic for length changes. We used whole-genome data on small insertions and deletions within transposable elements from chicken and zebra finch to demonstrate clear links between recombination rate and a number of attributes of reduced DNA content. Recombination rate was negatively correlated with the length of introns, transposable elements, and intergenic spacer and with the rate of short insertions. Importantly, it was positively correlated with gene density, the rate of short deletions, the deletion bias, and the net change in sequence length. All these observations point at a pattern of more condensed genome structure in regions of high recombination. Based on the observed rates of small insertions and deletions and assuming that these rates are representative for the whole genome, we estimate that the genome of the most recent common ancestor of birds and lizards has lost nearly 20% of its DNA content up until the present. Expansion of transposable elements can counteract the effect of deletions in an equilibrium mutation model; however, since the activity of transposable elements has been low in the avian lineage, the deletion bias is likely to have had a significant effect on genome size evolution in dinosaurs and birds, contributing to the maintenance of a small genome. We also demonstrate that most of the observed correlations between recombination rate and genome contraction parameters are seen in the human genome, including for segregating indel polymorphisms. Our data are compatible with a neutral model in which recombination drives vertebrate genome size evolution and gives no direct support for a role of natural selection in this process. One major implication from genetic work done several decades ago is that the genome contains a lot of sequences that do not constitute genes or other functional elements. The total amount of DNA—the genome size—is thus not necessarily an indicator of DNA complexity or organismal complexity, an observation often referred to as the C-value paradox (C-value being a measure of DNA content). What then is it that determines genome size? One model posits that the evolution of genome size is not a consequence of natural selection but is instead governed by the incidence and character of naturally occurring mutations that affect the length of DNA, a process that is not affected by selection. Here we present the results of an analysis of how recombination affects the size of avian and human genomes. We find strong evidence that the rate of recombination is a driving force of genome size evolution. In regions of the genome where recombination occurs frequently, the loss of DNA caused by small deletions is particularly pronounced. Our simulations show that the effect of such recombination-driven genome contraction can be profound over evolutionary time scales. These observations lead to a model in which recombination is mutagenic for length changes and that the incidence of deletions increases with increasing recombination rate. Although we cannot formally exclude that natural selection contributes to the observed relationship between recombination and genome contraction, we find no evidence to support such a scenario.
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Affiliation(s)
| | - Hans Ellegren
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
- * E-mail:
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Serres-Giardi L, Belkhir K, David J, Glémin S. Patterns and evolution of nucleotide landscapes in seed plants. THE PLANT CELL 2012; 24:1379-97. [PMID: 22492812 PMCID: PMC3398553 DOI: 10.1105/tpc.111.093674] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Nucleotide landscapes, which are the way base composition is distributed along a genome, strongly vary among species. The underlying causes of these variations have been much debated. Though mutational bias and selection were initially invoked, GC-biased gene conversion (gBGC), a recombination-associated process favoring the G and C over A and T bases, is increasingly recognized as a major factor. As opposed to vertebrates, evolution of GC content is less well known in plants. Most studies have focused on the GC-poor and homogeneous Arabidopsis thaliana genome and the much more GC-rich and heterogeneous rice (Oryza sativa) genome and have often been generalized as a dicot/monocot dichotomy. This vision is clearly phylogenetically biased and does not allow understanding the mechanisms involved in GC content evolution in plants. To tackle these issues, we used EST data from more than 200 species and provided the most comprehensive description of gene GC content across the seed plant phylogeny so far available. As opposed to the classically assumed dicot/monocot dichotomy, we found continuous variations in GC content from the probably ancestral GC-poor and homogeneous genomes to the more derived GC-rich and highly heterogeneous ones, with several independent enrichment episodes. Our results suggest that gBGC could play a significant role in the evolution of GC content in plant genomes.
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Affiliation(s)
- Laurana Serres-Giardi
- Institut des Sciences de l’Evolution de Montpellier, Unité Mixte de Recherche 5554, Centre National de la Recherche Scientifique, Université Montpellier 2, F-34095 Montpellier, France
- Montpellier SupAgro, Unité Mixte de Recherche 1334, Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, F-34398 Montpellier, France
| | - Khalid Belkhir
- Institut des Sciences de l’Evolution de Montpellier, Unité Mixte de Recherche 5554, Centre National de la Recherche Scientifique, Université Montpellier 2, F-34095 Montpellier, France
| | - Jacques David
- Montpellier SupAgro, Unité Mixte de Recherche 1334, Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, F-34398 Montpellier, France
| | - Sylvain Glémin
- Institut des Sciences de l’Evolution de Montpellier, Unité Mixte de Recherche 5554, Centre National de la Recherche Scientifique, Université Montpellier 2, F-34095 Montpellier, France
- Address correspondence to
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Däumer C, Greve C, Hutterer R, Misof B, Haase M. Phylogeography of an invasive land snail: natural range expansion versus anthropogenic dispersal in Theba pisana pisana. Biol Invasions 2012. [DOI: 10.1007/s10530-012-0179-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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St John JA, Braun EL, Isberg SR, Miles LG, Chong AY, Gongora J, Dalzell P, Moran C, Bed'hom B, Abzhanov A, Burgess SC, Cooksey AM, Castoe TA, Crawford NG, Densmore LD, Drew JC, Edwards SV, Faircloth BC, Fujita MK, Greenwold MJ, Hoffmann FG, Howard JM, Iguchi T, Janes DE, Khan SY, Kohno S, de Koning AJ, Lance SL, McCarthy FM, McCormack JE, Merchant ME, Peterson DG, Pollock DD, Pourmand N, Raney BJ, Roessler KA, Sanford JR, Sawyer RH, Schmidt CJ, Triplett EW, Tuberville TD, Venegas-Anaya M, Howard JT, Jarvis ED, Guillette LJ, Glenn TC, Green RE, Ray DA. Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes. Genome Biol 2012; 13:415. [PMID: 22293439 PMCID: PMC3334581 DOI: 10.1186/gb-2012-13-1-415] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The International Crocodilian Genomes Working Group (ICGWG) will sequence and assemble the American alligator (Alligator mississippiensis), saltwater crocodile (Crocodylus porosus) and Indian gharial (Gavialis gangeticus) genomes. The status of these projects and our planned analyses are described.
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