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Yan Z, Cao Z, Liu Y, Ogilvie HA, Nakhleh L. Maximum Parsimony Inference of Phylogenetic Networks in the Presence of Polyploid Complexes. Syst Biol 2021; 71:706-720. [PMID: 34605924 PMCID: PMC9017653 DOI: 10.1093/sysbio/syab081] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 09/26/2021] [Accepted: 09/29/2021] [Indexed: 12/18/2022] Open
Abstract
Phylogenetic networks provide a powerful framework for modeling and analyzing reticulate
evolutionary histories. While polyploidy has been shown to be prevalent not only in plants
but also in other groups of eukaryotic species, most work done thus far on phylogenetic
network inference assumes diploid hybridization. These inference methods have been
applied, with varying degrees of success, to data sets with polyploid species, even though
polyploidy violates the mathematical assumptions underlying these methods. Statistical
methods were developed recently for handling specific types of polyploids and so were
parsimony methods that could handle polyploidy more generally yet while excluding
processes such as incomplete lineage sorting. In this article, we introduce a new method
for inferring most parsimonious phylogenetic networks on data that include polyploid
species. Taking gene tree topologies as input, the method seeks a phylogenetic network
that minimizes deep coalescences while accounting for polyploidy. We demonstrate the
performance of the method on both simulated and biological data. The inference method as
well as a method for evaluating evolutionary hypotheses in the form of phylogenetic
networks are implemented and publicly available in the PhyloNet software package.
[Incomplete lineage sorting; minimizing deep coalescences; multilabeled trees;
multispecies network coalescent; phylogenetic networks; polyploidy.]
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Affiliation(s)
- Zhi Yan
- Department of Computer Science, Rice University, Houston, 6100 Main Street, Houston, TX 77005, USA
| | - Zhen Cao
- Department of Computer Science, Rice University, Houston, 6100 Main Street, Houston, TX 77005, USA
| | - Yushu Liu
- Department of Computer Science, Rice University, Houston, 6100 Main Street, Houston, TX 77005, USA
| | - Huw A Ogilvie
- Department of Computer Science, Rice University, Houston, 6100 Main Street, Houston, TX 77005, USA
| | - Luay Nakhleh
- Department of Computer Science, Rice University, Houston, 6100 Main Street, Houston, TX 77005, USA
- Department of Biosciences, Rice University, Houston, 6100 Main Street, Houston, TX 77005, USA
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Reconstruction of proto-vertebrate, proto-cyclostome and proto-gnathostome genomes provides new insights into early vertebrate evolution. Nat Commun 2021; 12:4489. [PMID: 34301952 PMCID: PMC8302630 DOI: 10.1038/s41467-021-24573-z] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 06/25/2021] [Indexed: 02/07/2023] Open
Abstract
Ancient polyploidization events have had a lasting impact on vertebrate genome structure, organization and function. Some key questions regarding the number of ancient polyploidization events and their timing in relation to the cyclostome-gnathostome divergence have remained contentious. Here we generate de novo long-read-based chromosome-scale genome assemblies for the Japanese lamprey and elephant shark. Using these and other representative genomes and developing algorithms for the probabilistic macrosynteny model, we reconstruct high-resolution proto-vertebrate, proto-cyclostome and proto-gnathostome genomes. Our reconstructions resolve key questions regarding the early evolutionary history of vertebrates. First, cyclostomes diverged from the lineage leading to gnathostomes after a shared tetraploidization (1R) but before a gnathostome-specific tetraploidization (2R). Second, the cyclostome lineage experienced an additional hexaploidization. Third, 2R in the gnathostome lineage was an allotetraploidization event, and biased gene loss from one of the subgenomes shaped the gnathostome genome by giving rise to remarkably conserved microchromosomes. Thus, our reconstructions reveal the major evolutionary events and offer new insights into the origin and evolution of vertebrate genomes.
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Sacerdot C, Louis A, Bon C, Berthelot C, Roest Crollius H. Chromosome evolution at the origin of the ancestral vertebrate genome. Genome Biol 2018; 19:166. [PMID: 30333059 PMCID: PMC6193309 DOI: 10.1186/s13059-018-1559-1] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 10/04/2018] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND It has been proposed that more than 450 million years ago, two successive whole genome duplications took place in a marine chordate lineage before leading to the common ancestor of vertebrates. A precise reconstruction of these founding events would provide a framework to better understand the impact of these early whole genome duplications on extant vertebrates. RESULTS We reconstruct the evolution of chromosomes at the beginning of vertebrate evolution. We first compare 61 extant animal genomes to reconstruct the highly contiguous order of genes in a 326-million-year-old ancestral Amniota genome. In this genome, we establish a well-supported list of duplicated genes originating from the two whole genome duplications to identify tetrads of duplicated chromosomes. From this, we reconstruct a chronology in which a pre-vertebrate genome composed of 17 chromosomes duplicated to 34 chromosomes and was subject to seven chromosome fusions before duplicating again into 54 chromosomes. After the separation of the lineage of Gnathostomata (jawed vertebrates) from Cyclostomata (extant jawless fish), four more fusions took place to form the ancestral Euteleostomi (bony vertebrates) genome of 50 chromosomes. CONCLUSIONS These results firmly establish the occurrence of two whole genome duplications in the lineage that precedes the ancestor of vertebrates, resolving in particular the ambiguity raised by the analysis of the lamprey genome. This work provides a foundation for studying the evolution of vertebrate chromosomes from the standpoint of a common ancestor and particularly the pattern of duplicate gene retention and loss that resulted in the gene composition of extant vertebrate genomes.
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Affiliation(s)
- Christine Sacerdot
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, 75005, Paris, France
| | - Alexandra Louis
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, 75005, Paris, France
| | - Céline Bon
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, 75005, Paris, France
- Present Address: Laboratoire Éco-Anthropologie et Ethnobiologie, UMR 7206 CNRS - Muséum National d'Histoire Naturelle, Université Paris Diderot, Sorbonne Paris Cité, F-75016, Paris, France
| | | | - Hugues Roest Crollius
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, 75005, Paris, France.
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Nakatani Y, McLysaght A. Genomes as documents of evolutionary history: a probabilistic macrosynteny model for the reconstruction of ancestral genomes. Bioinformatics 2018; 33:i369-i378. [PMID: 28881993 PMCID: PMC5870716 DOI: 10.1093/bioinformatics/btx259] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Motivation It has been argued that whole-genome duplication (WGD) exerted a profound influence on the course of evolution. For the purpose of fully understanding the impact of WGD, several formal algorithms have been developed for reconstructing pre-WGD gene order in yeast and plant. However, to the best of our knowledge, those algorithms have never been successfully applied to WGD events in teleost and vertebrate, impeded by extensive gene shuffling and gene losses. Results Here, we present a probabilistic model of macrosynteny (i.e. conserved linkage or chromosome-scale distribution of orthologs), develop a variational Bayes algorithm for inferring the structure of pre-WGD genomes, and study estimation accuracy by simulation. Then, by applying the method to the teleost WGD, we demonstrate effectiveness of the algorithm in a situation where gene-order reconstruction algorithms perform relatively poorly due to a high rate of rearrangement and extensive gene losses. Our high-resolution reconstruction reveals previously overlooked small-scale rearrangements, necessitating a revision to previous views on genome structure evolution in teleost and vertebrate. Conclusions We have reconstructed the structure of a pre-WGD genome by employing a variational Bayes approach that was originally developed for inferring topics from millions of text documents. Interestingly, comparison of the macrosynteny and topic model algorithms suggests that macrosynteny can be regarded as documents on ancestral genome structure. From this perspective, the present study would seem to provide a textbook example of the prevalent metaphor that genomes are documents of evolutionary history. Availability and implementation The analysis data are available for download at http://www.gen.tcd.ie/molevol/supp_data/MacrosyntenyTGD.zip, and the software written in Java is available upon request. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yoichiro Nakatani
- Department of Genetics, Smurfit Institute of Genetics, Trinity College Dublin, University of Dublin, Dublin 2, Ireland
| | - Aoife McLysaght
- Department of Genetics, Smurfit Institute of Genetics, Trinity College Dublin, University of Dublin, Dublin 2, Ireland
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Anselmetti Y, Luhmann N, Bérard S, Tannier E, Chauve C. Comparative Methods for Reconstructing Ancient Genome Organization. Methods Mol Biol 2018; 1704:343-362. [PMID: 29277873 DOI: 10.1007/978-1-4939-7463-4_13] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Comparative genomics considers the detection of similarities and differences between extant genomes, and, based on more or less formalized hypotheses regarding the involved evolutionary processes, inferring ancestral states explaining the similarities and an evolutionary history explaining the differences. In this chapter, we focus on the reconstruction of the organization of ancient genomes into chromosomes. We review different methodological approaches and software, applied to a wide range of datasets from different kingdoms of life and at different evolutionary depths. We discuss relations with genome assembly, and potential approaches to validate computational predictions on ancient genomes that are almost always only accessible through these predictions.
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Affiliation(s)
- Yoann Anselmetti
- Institut des Sciences de l'Évolution, Université Montpellier 2, Montpellier, France
| | - Nina Luhmann
- Faculty of Technology, Bielefeld University, Bielefeld, Germany.,Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany.,International Research Training Group1906, Bielefeld University, Bielefeld, Germany
| | - Sèverine Bérard
- Institut des Sciences de l'Évolution, Université Montpellier 2, Montpellier, France
| | - Eric Tannier
- UMR CNRS 5558 - LBBE "Biométrie et Biologie Évolutive", Inria Grenoble Rhône-Alpes and University of Lyon, Lyon, France
| | - Cedric Chauve
- Department of Mathematics, Simon Fraser University, 8888 University Drive, Burnaby, BC, Canada, V5A 1S6.
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Rajaraman A, Ma J. Reconstructing ancestral gene orders with duplications guided by synteny level genome reconstruction. BMC Bioinformatics 2016; 17:414. [PMID: 28185565 PMCID: PMC5123302 DOI: 10.1186/s12859-016-1262-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Background Reconstructing ancestral gene orders in the presence of duplications is important for a better understanding of genome evolution. Current methods for ancestral reconstruction are limited by either computational constraints or the availability of reliable gene trees, and often ignore duplications altogether. Recently, methods that consider duplications in ancestral reconstructions have been developed, but the quality of reconstruction, counted as the number of contiguous ancestral regions found, decreases rapidly with the number of duplicated genes, complicating the application of such approaches to mammalian genomes. However, such high fragmentation is not encountered when reconstructing mammalian genomes at the synteny-block level, although the relative positions of genes in such reconstruction cannot be recovered. Results We propose a new heuristic method, MultiRes, to reconstruct ancestral gene orders with duplications guided by homologous synteny blocks for a set of related descendant genomes. The method uses a synteny-level reconstruction to break the gene-order problem into several subproblems, which are then combined in order to disambiguate duplicated genes. We applied this method to both simulated and real data. Our results showed that MultiRes outperforms other methods in terms of gene content, gene adjacency, and common interval recovery. Conclusions This work demonstrates that the inclusion of synteny-level information can help us obtain better gene-level reconstructions. Our algorithm provides a basic toolbox for reconstructing ancestral gene orders with duplications. The source code of MultiRes is available on https://github.com/ma-compbio/MultiRes. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-1262-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ashok Rajaraman
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, 15213, USA
| | - Jian Ma
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, 15213, USA.
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Vakirlis N, Sarilar V, Drillon G, Fleiss A, Agier N, Meyniel JP, Blanpain L, Carbone A, Devillers H, Dubois K, Gillet-Markowska A, Graziani S, Huu-Vang N, Poirel M, Reisser C, Schott J, Schacherer J, Lafontaine I, Llorente B, Neuvéglise C, Fischer G. Reconstruction of ancestral chromosome architecture and gene repertoire reveals principles of genome evolution in a model yeast genus. Genome Res 2016; 26:918-32. [PMID: 27247244 PMCID: PMC4937564 DOI: 10.1101/gr.204420.116] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 04/28/2016] [Indexed: 12/22/2022]
Abstract
Reconstructing genome history is complex but necessary to reveal quantitative principles governing genome evolution. Such reconstruction requires recapitulating into a single evolutionary framework the evolution of genome architecture and gene repertoire. Here, we reconstructed the genome history of the genus Lachancea that appeared to cover a continuous evolutionary range from closely related to more diverged yeast species. Our approach integrated the generation of a high-quality genome data set; the development of AnChro, a new algorithm for reconstructing ancestral genome architecture; and a comprehensive analysis of gene repertoire evolution. We found that the ancestral genome of the genus Lachancea contained eight chromosomes and about 5173 protein-coding genes. Moreover, we characterized 24 horizontal gene transfers and 159 putative gene creation events that punctuated species diversification. We retraced all chromosomal rearrangements, including gene losses, gene duplications, chromosomal inversions and translocations at single gene resolution. Gene duplications outnumbered losses and balanced rearrangements with 1503, 929, and 423 events, respectively. Gene content variations between extant species are mainly driven by differential gene losses, while gene duplications remained globally constant in all lineages. Remarkably, we discovered that balanced chromosomal rearrangements could be responsible for up to 14% of all gene losses by disrupting genes at their breakpoints. Finally, we found that nonsynonymous substitutions reached fixation at a coordinated pace with chromosomal inversions, translocations, and duplications, but not deletions. Overall, we provide a granular view of genome evolution within an entire eukaryotic genus, linking gene content, chromosome rearrangements, and protein divergence into a single evolutionary framework.
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Affiliation(s)
- Nikolaos Vakirlis
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, F-75005, Paris, France
| | - Véronique Sarilar
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Guénola Drillon
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, F-75005, Paris, France
| | - Aubin Fleiss
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, F-75005, Paris, France
| | - Nicolas Agier
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, F-75005, Paris, France
| | - Jean-Philippe Meyniel
- ISoft, Route de l'Orme, Parc "Les Algorithmes" Bâtiment Euclide, 91190 Saint-Aubin, France
| | - Lou Blanpain
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Alessandra Carbone
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, F-75005, Paris, France
| | - Hugo Devillers
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Kenny Dubois
- CRCM, CNRS, UMR7258, Inserm, U1068; Institut Paoli-Calmettes, Aix-Marseille Université, UM 105, F-13009, Marseille, France
| | - Alexandre Gillet-Markowska
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, F-75005, Paris, France
| | - Stéphane Graziani
- ISoft, Route de l'Orme, Parc "Les Algorithmes" Bâtiment Euclide, 91190 Saint-Aubin, France
| | - Nguyen Huu-Vang
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Marion Poirel
- ISoft, Route de l'Orme, Parc "Les Algorithmes" Bâtiment Euclide, 91190 Saint-Aubin, France
| | - Cyrielle Reisser
- Department of Genetics, Genomics and Microbiology, University of Strasbourg/CNRS, UMR 7156, 67083 Strasbourg, France
| | - Jonathan Schott
- CRCM, CNRS, UMR7258, Inserm, U1068; Institut Paoli-Calmettes, Aix-Marseille Université, UM 105, F-13009, Marseille, France
| | - Joseph Schacherer
- Department of Genetics, Genomics and Microbiology, University of Strasbourg/CNRS, UMR 7156, 67083 Strasbourg, France
| | - Ingrid Lafontaine
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, F-75005, Paris, France
| | - Bertrand Llorente
- CRCM, CNRS, UMR7258, Inserm, U1068; Institut Paoli-Calmettes, Aix-Marseille Université, UM 105, F-13009, Marseille, France
| | - Cécile Neuvéglise
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Gilles Fischer
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, F-75005, Paris, France
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The lineage-specific evolution of aquaporin gene clusters facilitated tetrapod terrestrial adaptation. PLoS One 2014; 9:e113686. [PMID: 25426855 PMCID: PMC4245216 DOI: 10.1371/journal.pone.0113686] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 10/27/2014] [Indexed: 01/02/2023] Open
Abstract
A major physiological barrier for aquatic organisms adapting to terrestrial life is dessication in the aerial environment. This barrier was nevertheless overcome by the Devonian ancestors of extant Tetrapoda, but the origin of specific molecular mechanisms that solved this water problem remains largely unknown. Here we show that an ancient aquaporin gene cluster evolved specifically in the sarcopterygian lineage, and subsequently diverged into paralogous forms of AQP2, -5, or -6 to mediate water conservation in extant Tetrapoda. To determine the origin of these apomorphic genomic traits, we combined aquaporin sequencing from jawless and jawed vertebrates with broad taxon assembly of >2,000 transcripts amongst 131 deuterostome genomes and developed a model based upon Bayesian inference that traces their convergent roots to stem subfamilies in basal Metazoa and Prokaryota. This approach uncovered an unexpected diversity of aquaporins in every lineage investigated, and revealed that the vertebrate superfamily consists of 17 classes of aquaporins (Aqp0 - Aqp16). The oldest orthologs associated with water conservation in modern Tetrapoda are traced to a cluster of three aqp2-like genes in Actinistia that likely arose >500 Ma through duplication of an aqp0-like gene present in a jawless ancestor. In sea lamprey, we show that aqp0 first arose in a protocluster comprised of a novel aqp14 paralog and a fused aqp01 gene. To corroborate these findings, we conducted phylogenetic analyses of five syntenic nuclear receptor subfamilies, which, together with observations of extensive genome rearrangements, support the coincident loss of ancestral aqp2-like orthologs in Actinopterygii. We thus conclude that the divergence of sarcopterygian-specific aquaporin gene clusters was permissive for the evolution of water conservation mechanisms that facilitated tetrapod terrestrial adaptation.
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Wendland J, Walther A. Chromosome number reduction in Eremothecium coryli by two telomere-to-telomere fusions. Genome Biol Evol 2014; 6:1186-98. [PMID: 24803574 PMCID: PMC4040997 DOI: 10.1093/gbe/evu089] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/27/2014] [Indexed: 11/16/2022] Open
Abstract
The genus Eremothecium belongs to the Saccharomyces complex of pre-whole-genome duplication (WGD) yeasts and contains both dimorphic and filamentous species. We established the 9.1-Mb draft genome of Eremothecium coryli, which encodes 4,682 genes, 186 tRNA genes, and harbors several Ty3 transposons as well as more than 60 remnants of transposition events (LTRs). The initial de novo assembly resulted in 19 scaffolds, which were assembled based on synteny to other Eremothecium genomes into six chromosomes. Interestingly, we identified eight E. coryli loci that bear centromeres in the closely related species E. cymbalariae. Two of these E. coryli loci, CEN1 and CEN8, however, lack conserved DNA elements and did not convey centromere function in a plasmid stability assay. Correspondingly, using a comparative genomics approach we identified two telomere-to-telomere fusion events in E. coryli as the cause of chromosome number reduction from eight to six chromosomes. Finally, with the genome sequences of E. coryli, E. cymbalariae, and Ashbya gossypii a reconstruction of three complete chromosomes of an Eremothecium ancestor revealed that E. coryli is more syntenic to this ancestor than the other Eremothecium species.
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Affiliation(s)
| | - Andrea Walther
- Carlsberg Laboratory, Yeast Biology, Copenhagen, Denmark
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10
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Schranz ME, Mohammadin S, Edger PP. Ancient whole genome duplications, novelty and diversification: the WGD Radiation Lag-Time Model. CURRENT OPINION IN PLANT BIOLOGY 2012; 15:147-53. [PMID: 22480429 DOI: 10.1016/j.pbi.2012.03.011] [Citation(s) in RCA: 178] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Revised: 03/12/2012] [Accepted: 03/14/2012] [Indexed: 05/18/2023]
Abstract
Many large and economically important plant groups (e.g. Brassicaceae, Poaceae, Asteraceae, Fabaceae and Solanaceae) have had ancient whole genome duplications (WGDs) occurring near or at the time of their origins, suggesting that WGD contributed to the origin of novel key traits and drove species diversification. However, these large clades show phylogenetic asymmetries with a species-rich crown group and a species-poor sister clade, suggesting significant 'lag-times' between WGDs and radiations. The species-poor sister groups share many key traits, but are often restricted to the hypothesized center of origin for the larger clade. Thus, the ultimate success of the crown group does not only involve the WGD and novel key traits, but largely subsequent evolutionary phenomena including later migration events, changing environmental conditions and/or differential extinction rates.
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Affiliation(s)
- M Eric Schranz
- Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090 GE Amsterdam, The Netherlands.
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11
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Yegorov S, Good S. Using paleogenomics to study the evolution of gene families: origin and duplication history of the relaxin family hormones and their receptors. PLoS One 2012; 7:e32923. [PMID: 22470432 PMCID: PMC3310001 DOI: 10.1371/journal.pone.0032923] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2011] [Accepted: 02/05/2012] [Indexed: 11/28/2022] Open
Abstract
Recent progress in the analysis of whole genome sequencing data has resulted in the emergence of paleogenomics, a field devoted to the reconstruction of ancestral genomes. Ancestral karyotype reconstructions have been used primarily to illustrate the dynamic nature of genome evolution. In this paper, we demonstrate how they can also be used to study individual gene families by examining the evolutionary history of relaxin hormones (RLN/INSL) and relaxin family peptide receptors (RXFP). Relaxin family hormones are members of the insulin superfamily, and are implicated in the regulation of a variety of primarily reproductive and neuroendocrine processes. Their receptors are G-protein coupled receptors (GPCR's) and include members of two distinct evolutionary groups, an unusual characteristic. Although several studies have tried to elucidate the origins of the relaxin peptide family, the evolutionary origin of their receptors and the mechanisms driving the diversification of the RLN/INSL-RXFP signaling systems in non-placental vertebrates has remained elusive. Here we show that the numerous vertebrate RLN/INSL and RXFP genes are products of an ancestral receptor-ligand system that originally consisted of three genes, two of which apparently trace their origins to invertebrates. Subsequently, diversification of the system was driven primarily by whole genome duplications (WGD, 2R and 3R) followed by almost complete retention of the ligand duplicates in most vertebrates but massive loss of receptor genes in tetrapods. Interestingly, the majority of 3R duplicates retained in teleosts are potentially involved in neuroendocrine regulation. Furthermore, we infer that the ancestral AncRxfp3/4 receptor may have been syntenically linked to the AncRln-like ligand in the pre-2R genome, and show that syntenic linkages among ligands and receptors have changed dynamically in different lineages. This study ultimately shows the broad utility, with some caveats, of incorporating paleogenomics data into understanding the evolution of gene families.
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Affiliation(s)
- Sergey Yegorov
- Department of Biology, University of Winnipeg, Winnipeg, Manitoba, Canada
| | - Sara Good
- Department of Biology, University of Winnipeg, Winnipeg, Manitoba, Canada
- * E-mail:
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12
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Ouangraoua A, Tannier E, Chauve C. Reconstructing the architecture of the ancestral amniote genome. Bioinformatics 2011; 27:2664-71. [DOI: 10.1093/bioinformatics/btr461] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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13
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Zapater C, Chauvigné F, Norberg B, Finn RN, Cerdà J. Dual neofunctionalization of a rapidly evolving aquaporin-1 paralog resulted in constrained and relaxed traits controlling channel function during meiosis resumption in teleosts. Mol Biol Evol 2011; 28:3151-69. [PMID: 21653921 DOI: 10.1093/molbev/msr146] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The preovulatory hydration of teleost oocytes is a unique process among vertebrates. The hydration mechanism is most pronounced in marine acanthomorph teleosts that spawn pelagic (floating) eggs; however, the molecular pathway for water influx remains poorly understood. Recently, we revealed that whole-genome duplication (WGD) resulted in teleosts harboring the largest repertoire of molecular water channels in the vertebrate lineage and that a duplicated aquaporin-1 paralog is implicated in the oocyte hydration process. However, the origin and function of the aquaporin-1 paralogs remain equivocal. By integrating the molecular phylogeny with synteny and structural analyses, we show here that the teleost aqp1aa and -1ab paralogs (previously annotated as aqp1a and -1b, respectively) arose by tandem duplication rather than WGD and that the Aqp1ab C-terminus is the most rapidly evolving subdomain within the vertebrate aquaporin superfamily. The functional role of Aqp1ab was investigated in Atlantic halibut, a marine acanthomorph teleost that spawns one of the largest pelagic eggs known. We demonstrate that Aqp1ab is required for full hydration of oocytes undergoing meiotic maturation. We further show that the rapid structural divergence of the C-terminal regulatory domain causes ex vivo loss of function of halibut Aqp1ab when expressed in amphibian oocytes but not in zebrafish or native oocytes. However, by using chimeric constructs of halibut Aqp1aa and -1ab and antisera specifically raised against the C-terminus of Aqp1ab, we found that this cytoplasmic domain regulates in vivo trafficking to the microvillar portion of the oocyte plasma membrane when intraoocytic osmotic pressure is at a maximum. Interestingly, by coinjecting polyA(+) mRNA from postvitellogenic halibut follicles, ex vivo intracellular trafficking of Aqp1ab is rescued in amphibian oocytes. These data reveal that the physiological role of Aqp1ab during meiosis resumption is conserved in teleosts, but the remarkable degeneracy of the cytoplasmic domain has resulted in alternative regulation of the trafficking mechanism.
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Affiliation(s)
- Cinta Zapater
- Laboratory of Institut de Recerca i Tecnologia Agroalimentàries, Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas, Barcelona, Spain
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Cerdà J, Finn RN. Piscine aquaporins: an overview of recent advances. ACTA ACUST UNITED AC 2010; 313:623-50. [PMID: 20717996 DOI: 10.1002/jez.634] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2010] [Revised: 06/15/2010] [Accepted: 06/29/2010] [Indexed: 11/08/2022]
Abstract
Aquaporins are a superfamily of integral membrane proteins that facilitate the rapid and yet highly selective flux of water and other small solutes across biological membranes. Since their discovery, they have been documented throughout the living biota, with the majority of research focusing on mammals and plants. Here, we review available data for piscine aquaporins, including Agnatha (jawless fish), Chondrichthyes (chimaeras, sharks, and rays), Dipnoi (lungfishes), and Teleostei (ray-finned bony fishes). Recent evidence suggests that the aquaporin superfamily has specifically expanded in the chordate lineage consequent to serial rounds of whole genome duplication, with teleost genomes harboring the largest number of paralogs. The selective retention and dichotomous clustering of most duplicated paralogs in Teleostei, with differential tissue expression profiles, implies that novel or specialized physiological functions may have evolved in this clade. The recently proposed new nomenclature of the piscine aquaporin superfamily is discussed in relation to the phylogenetic signal and genomic synteny, with the teleost aquaporin-8 paralogs used as a case study to illustrate disparities between the underlying codons, molecular phylogeny, and physical locus. Structural data indicate that piscine aquaporins display similar channel restriction residues found in the tetrapod counterparts, and hence their functional properties seem to be conserved. However, emerging evidence suggests that regulation of aquaporin function in teleosts may have diverged in some cases. Cell localization and experimental studies imply that the physiological roles of piscine aquaporins extend at least to osmoregulation, reproduction, and early development, although in most cases their specific functions remain to be elucidated.
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Affiliation(s)
- Joan Cerdà
- Laboratory of Institut de Recerca i Tecnologia Agroalimentàries (IRTA)- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain.
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15
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Genomes as documents of evolutionary history. Trends Ecol Evol 2010; 25:224-32. [DOI: 10.1016/j.tree.2009.09.007] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2009] [Revised: 09/18/2009] [Accepted: 09/21/2009] [Indexed: 02/02/2023]
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Navratilova P, Fredman D, Lenhard B, Becker TS. Regulatory divergence of the duplicated chromosomal loci sox11a/b by subpartitioning and sequence evolution of enhancers in zebrafish. Mol Genet Genomics 2009; 283:171-84. [DOI: 10.1007/s00438-009-0503-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2009] [Accepted: 12/01/2009] [Indexed: 01/05/2023]
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Feiner N, Begemann G, Renz AJ, Meyer A, Kuraku S. The origin of bmp16, a novel Bmp2/4 relative, retained in teleost fish genomes. BMC Evol Biol 2009; 9:277. [PMID: 19951429 PMCID: PMC2801517 DOI: 10.1186/1471-2148-9-277] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2009] [Accepted: 12/01/2009] [Indexed: 11/29/2022] Open
Abstract
Background Whole genome sequences have allowed us to have an overview of the evolution of gene repertoires. The target of the present study, the TGFβ superfamily, contains many genes involved in vertebrate development, and provides an ideal system to explore the relationships between evolution of gene repertoires and that of developmental programs. Results As a result of a bioinformatic survey of sequenced vertebrate genomes, we identified an uncharacterized member of the TGFβ superfamily, designated bmp16, which is confined to teleost fish species. Our molecular phylogenetic study revealed a high affinity of bmp16 to the Bmp2/4 subfamily. Importantly, further analyses based on the maximum-likelihood method unambiguously ruled out the possibility that this teleost-specific gene is a product of teleost-specific genome duplication. This suggests that the absence of a bmp16 ortholog in tetrapods is due to a secondary loss. In situ hybridization showed embryonic expression of the zebrafish bmp16 in the developing swim bladder, heart, tail bud, and ectoderm of pectoral and median fin folds in pharyngula stages, as well as gut-associated expression in 5-day embryos. Conclusion Comparisons of expression patterns revealed (1) the redundancy of bmp16 expression with its homologs in presumably plesiomorphic expression domains, such as the fin fold, heart, and tail bud, which might have permitted its loss in the tetrapod lineage, and (2) the loss of craniofacial expression and gain of swim bladder expression of bmp16 after the gene duplication between Bmp2, -4 and -16. Our findings highlight the importance of documenting secondary changes of gene repertoires and expression patterns in other gene families.
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Affiliation(s)
- Nathalie Feiner
- Laboratory for Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Universitätsstrasse 10, 78464 Konstanz, Germany.
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Jaillon O, Aury JM, Wincker P. “Changing by doubling”, the impact of Whole Genome Duplications in the evolution of eukaryotes. C R Biol 2009; 332:241-53. [DOI: 10.1016/j.crvi.2008.07.007] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2008] [Accepted: 07/21/2008] [Indexed: 12/17/2022]
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Finn RN, Kolarevic J, Kongshaug H, Nilsen F. Evolution and differential expression of a vertebrate vitellogenin gene cluster. BMC Evol Biol 2009; 9:2. [PMID: 19123940 PMCID: PMC2632621 DOI: 10.1186/1471-2148-9-2] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2008] [Accepted: 01/05/2009] [Indexed: 02/01/2023] Open
Abstract
Background The multiplicity or loss of the vitellogenin (vtg) gene family in vertebrates has been argued to have broad implications for the mode of reproduction (placental or non-placental), cleavage pattern (meroblastic or holoblastic) and character of the egg (pelagic or benthic). Earlier proposals for the existence of three forms of vertebrate vtgs present conflicting models for their origin and subsequent duplication. Results By integrating phylogenetics of novel vtg transcripts from old and modern teleosts with syntenic analyses of all available genomic variants of non-metatherian vertebrates we identify the gene orthologies between the Sarcopterygii (tetrapod branch) and Actinopterygii (fish branch). We argue that the vertebrate vtg gene cluster originated in proto-chromosome m, but that vtg genes have subsequently duplicated and rearranged following whole genome duplications. Sequencing of a novel fourth vtg transcript in labrid species, and the presence of duplicated paralogs in certain model organisms supports the notion that lineage-specific gene duplications frequently occur in teleosts. The data show that the vtg gene cluster is more conserved between acanthomorph teleosts and tetrapods, than in ostariophysan teleosts such as the zebrafish. The differential expression of the labrid vtg genes are further consistent with the notion that neofunctionalized Aa-type vtgs are important determinants of the pelagic or benthic character of the eggs in acanthomorph teleosts. Conclusion The vertebrate vtg gene cluster existed prior to the separation of Sarcopterygii from Actinopterygii >450 million years ago, a period associated with the second round of whole genome duplication. The presence of higher copy numbers in a more highly expressed subcluster is particularly prevalent in teleosts. The differential expression and latent neofunctionalization of vtg genes in acanthomorph teleosts is an adaptive feature associated with oocyte hydration and spawning in the marine environment.
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Affiliation(s)
- Roderick Nigel Finn
- Department of Biology, University of Bergen, Bergen High Technology Center, Postbox 7803, N-5020, Bergen, Norway.
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Soltis DE, Albert VA, Leebens-Mack J, Bell CD, Paterson AH, Zheng C, Sankoff D, Depamphilis CW, Wall PK, Soltis PS. Polyploidy and angiosperm diversification. AMERICAN JOURNAL OF BOTANY 2009; 96:336-48. [PMID: 21628192 DOI: 10.3732/ajb.0800079] [Citation(s) in RCA: 665] [Impact Index Per Article: 44.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Polyploidy has long been recognized as a major force in angiosperm evolution. Recent genomic investigations not only indicate that polyploidy is ubiquitous among angiosperms, but also suggest several ancient genome-doubling events. These include ancient whole genome duplication (WGD) events in basal angiosperm lineages, as well as a proposed paleohexaploid event that may have occurred close to the eudicot divergence. However, there is currently no evidence for WGD in Amborella, the putative sister species to other extant angiosperms. The question is no longer "What proportion of angiosperms are polyploid?", but "How many episodes of polyploidy characterize any given lineage?" New algorithms provide promise that ancestral genomes can be reconstructed for deep divergences (e.g., it may be possible to reconstruct the ancestral eudicot or even the ancestral angiosperm genome). Comparisons of diversification rates suggest that genome doubling may have led to a dramatic increase in species richness in several angiosperm lineages, including Poaceae, Solanaceae, Fabaceae, and Brassicaceae. However, additional genomic studies are needed to pinpoint the exact phylogenetic placement of the ancient polyploidy events within these lineages and to determine when novel genes resulting from polyploidy have enabled adaptive radiations.
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Affiliation(s)
- Douglas E Soltis
- Department of Botany, University of Florida, Gainesville, Florida 32611 USA
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Chauve C, Tannier E. A methodological framework for the reconstruction of contiguous regions of ancestral genomes and its application to mammalian genomes. PLoS Comput Biol 2008; 4:e1000234. [PMID: 19043541 PMCID: PMC2580819 DOI: 10.1371/journal.pcbi.1000234] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2008] [Accepted: 10/17/2008] [Indexed: 01/07/2023] Open
Abstract
The reconstruction of ancestral genome architectures and gene orders from homologies between extant species is a long-standing problem, considered by both cytogeneticists and bioinformaticians. A comparison of the two approaches was recently investigated and discussed in a series of papers, sometimes with diverging points of view regarding the performance of these two approaches. We describe a general methodological framework for reconstructing ancestral genome segments from conserved syntenies in extant genomes. We show that this problem, from a computational point of view, is naturally related to physical mapping of chromosomes and benefits from using combinatorial tools developed in this scope. We develop this framework into a new reconstruction method considering conserved gene clusters with similar gene content, mimicking principles used in most cytogenetic studies, although on a different kind of data. We implement and apply it to datasets of mammalian genomes. We perform intensive theoretical and experimental comparisons with other bioinformatics methods for ancestral genome segments reconstruction. We show that the method that we propose is stable and reliable: it gives convergent results using several kinds of data at different levels of resolution, and all predicted ancestral regions are well supported. The results come eventually very close to cytogenetics studies. It suggests that the comparison of methods for ancestral genome reconstruction should include the algorithmic aspects of the methods as well as the disciplinary differences in data aquisition. No DNA molecule is preserved after a few hundred thousand years, so inferring the DNA sequence organization of ancient living organisms beyond several million years can only be achieved by computational estimations, using the similarities and differences between chromosomes of extant species. This is the scope of “paleogenomics”, and it can help to better understand how genomes have evolved until today. We propose here a computational framework to estimate contiguous segments of ancestral chromosomes, based on techniques of physical mapping that are used to infer chromosome maps of extant species when their genome is not sequenced. This framework is not guided by possible evolutionary events such as rearrangements but only proposes ancestral genome architectures. We developed a method following this framework and applied it to mammalian genomes. We inferred ancestral chromosomal regions that are stable and well supported at different levels of resolution. These ancestral chromosomal regions agree with previous cytogenetics studies and were very probably part of the genome of the common ancestor of humans, macaca, mice, dogs, and cows, living 120 million years ago. We illustrate, through comparison with other bioinformatics methods, the importance of a formal methodological background when comparing ancestral genome architecture proposals obtained from different methods.
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Affiliation(s)
- Cedric Chauve
- Department of Mathematics, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Eric Tannier
- INRIA, Rhône-Alpes, France
- Université de Lyon, Lyon, France
- Université Lyon 1, Lyon, France
- Laboratoire de Biométrie et Biologie Évolutive, CNRS, UMR5558, Villeurbanne, France
- * E-mail:
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Ruiz-Herrera A, Robinson TJ. Evolutionary plasticity and cancer breakpoints in human chromosome 3. Bioessays 2008; 30:1126-37. [DOI: 10.1002/bies.20829] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Markov GV, Paris M, Bertrand S, Laudet V. The evolution of the ligand/receptor couple: a long road from comparative endocrinology to comparative genomics. Mol Cell Endocrinol 2008; 293:5-16. [PMID: 18634845 DOI: 10.1016/j.mce.2008.06.011] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2008] [Revised: 05/14/2008] [Accepted: 06/11/2008] [Indexed: 12/16/2022]
Abstract
Comparative endocrinology considers the evolution of bioregulatory systems and the anatomical structures and molecules that constitute the neuroendocrine and endocrine systems. One aim of comparative endocrinology is to trace the origins of the main endocrine systems. The understanding of the evolution of the ligand/receptor couple is central to this objective. One classical approach to tackle this question is the characterization of receptors and ligands in various types of non-model organisms using as a starting point the knowledge accumulated on classical models such as mammals (mainly human and mouse) and arthropods (with Drosophila among other insects). In this review we discuss the potential caveats associated to this two-by-two comparison between a classical model and non-model organisms. We suggest that the use of an evolutionary approach involving comparisons of several organisms in a coherent framework permits reconstruction of the most probable scenarios. The use of the vast amount of genomic data now available, coupled to functional experiments, offers unprecedented possibilities to trace back the origins of the main ligand/receptor couples.
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Omland KE, Cook LG, Crisp MD. Tree thinking for all biology: the problem with reading phylogenies as ladders of progress. Bioessays 2008; 30:854-67. [PMID: 18693264 DOI: 10.1002/bies.20794] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Phylogenies are increasingly prominent across all of biology, especially as DNA sequencing makes more and more trees available. However, their utility is compromised by widespread misconceptions about what phylogenies can tell us, and improved "tree thinking" is crucial. The most-serious problem comes from reading trees as ladders from "left to right"--many biologists assume that species-poor lineages that appear "early branching" or "basal" are ancestral--we call this the "primitive lineage fallacy". This mistake causes misleading inferences about changes in individual characteristics and leads to misrepresentation of the evolutionary process. The problem can be rectified by considering that modern phylogenies of present-day species and genes show relationships among evolutionary cousins. Emphasizing that these are extant entities in the 21(st) century will help correct inferences about ancestral characteristics, and will enable us to leave behind 19(th) century notions about the ladder of progress driving evolution.
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Affiliation(s)
- Kevin E Omland
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore MD 21250, USA.
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