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Arbore R, Barbosa S, Brejcha J, Ogawa Y, Liu Y, Nicolaï MPJ, Pereira P, Sabatino SJ, Cloutier A, Poon ESK, Marques CI, Andrade P, Debruyn G, Afonso S, Afonso R, Roy SG, Abdu U, Lopes RJ, Mojzeš P, Maršík P, Sin SYW, White MA, Araújo PM, Corbo JC, Carneiro M. A molecular mechanism for bright color variation in parrots. Science 2024; 386:eadp7710. [PMID: 39480920 PMCID: PMC7617403 DOI: 10.1126/science.adp7710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Accepted: 09/05/2024] [Indexed: 11/02/2024]
Abstract
Parrots produce stunning plumage colors through unique pigments called psittacofulvins. However, the mechanism underlying their ability to generate a spectrum of vibrant yellows, reds, and greens remains enigmatic. We uncover a unifying chemical basis for a wide range of parrot plumage colors, which result from the selective deposition of red aldehyde- and yellow carboxyl-containing psittacofulvin molecules in developing feathers. Through genetic mapping, biochemical assays, and single-cell genomics, we identified a critical player in this process, the aldehyde dehydrogenase ALDH3A2, which oxidizes aldehyde psittacofulvins into carboxyl forms in late-differentiating keratinocytes during feather development. The simplicity of the underlying molecular mechanism, in which a single enzyme influences the balance of red and yellow pigments, offers an explanation for the exceptional evolutionary lability of parrot coloration.
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Affiliation(s)
- Roberto Arbore
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Soraia Barbosa
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Jindřich Brejcha
- Department of Philosophy and History of Science, Faculty of Science, Charles University in Prague, Praha, Czech Republic
| | - Yohey Ogawa
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Yu Liu
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Michaël P. J. Nicolaï
- Evolution and Optics of Nanostructures Group, Biology Department, Ghent University, Ghent, Belgium
| | - Paulo Pereira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
| | - Stephen J. Sabatino
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Alison Cloutier
- School of Biological Sciences, The University of Hong Kong, Hong Kong
| | | | - Cristiana I. Marques
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
| | - Pedro Andrade
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Gerben Debruyn
- Evolution and Optics of Nanostructures Group, Biology Department, Ghent University, Ghent, Belgium
| | - Sandra Afonso
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Rita Afonso
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
| | - Shatadru Ghosh Roy
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva84105, Israel
| | - Uri Abdu
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva84105, Israel
| | - Ricardo J. Lopes
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
- MHNC-UP, Natural History and Science Museum of the University of Porto, Porto, Portugal
- cE3c – Center for Ecology, Evolution and Environmental Change & CHANGE, Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Peter Mojzeš
- Institute of Physics, Faculty of Mathematics and Physics, Charles University, Prague, Czech Republic
| | - Petr Maršík
- Department of Food Science, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Simon Yung Wa Sin
- School of Biological Sciences, The University of Hong Kong, Hong Kong
| | - Michael A. White
- Edison Family Center for Systems Biology and Genome Sciences, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Pedro M. Araújo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
- University of Coimbra, MARE – Marine and Environmental Sciences Centre, Department of Life Sciences, Coimbra, Portugal
| | - Joseph C. Corbo
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Miguel Carneiro
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
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2
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Griffin DK, Kretschmer R, Srikulnath K, Singchat W, O'Connor RE, Romanov MN. Insights into avian molecular cytogenetics-with reptilian comparisons. Mol Cytogenet 2024; 17:24. [PMID: 39482771 PMCID: PMC11526677 DOI: 10.1186/s13039-024-00696-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2024] [Accepted: 10/24/2024] [Indexed: 11/03/2024] Open
Abstract
In last 100 years or so, much information has been accumulated on avian karyology, genetics, physiology, biochemistry and evolution. The chicken genome project generated genomic resources used in comparative studies, elucidating fundamental evolutionary processes, much of it funded by the economic importance of domestic fowl (which are also excellent model species in many areas). Studying karyotypes and whole genome sequences revealed population processes, evolutionary biology, and genome function, uncovering the role of repetitive sequences, transposable elements and gene family expansion. Knowledge of the function of many genes and non-expressed or identified regulatory components is however still lacking. Birds (Aves) are diverse, have striking adaptations for flight, migration and survival and inhabit all continents most islands. They also have a unique karyotype with ~ 10 macrochromosomes and ~ 30 microchromosomes that are smaller than other reptiles. Classified into Palaeognathae and Neognathae they are evolutionarily close, and a subset of reptiles. Here we overview avian molecular cytogenetics with reptilian comparisons, shedding light on their karyotypes and genome structure features. We consider avian evolution, then avian (followed by reptilian) karyotypes and genomic features. We consider synteny disruptions, centromere repositioning, and repetitive elements before turning to comparative avian and reptilian genomics. In this context, we review comparative cytogenetics and genome mapping in birds as well as Z- and W-chromosomes and sex determination. Finally, we give examples of pivotal research areas in avian and reptilian cytogenomics, particularly physical mapping and map integration of sex chromosomal genes, comparative genomics of chicken, turkey and zebra finch, California condor cytogenomics as well as some peculiar cytogenetic and evolutionary examples. We conclude that comparative molecular studies and improving resources continually contribute to new approaches in population biology, developmental biology, physiology, disease ecology, systematics, evolution and phylogenetic systematics orientation. This also produces genetic mapping information for chromosomes active in rearrangements during the course of evolution. Further insights into mutation, selection and adaptation of vertebrate genomes will benefit from these studies including physical and online resources for the further elaboration of comparative genomics approaches for many fundamental biological questions.
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Affiliation(s)
- Darren K Griffin
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK.
- Faculty of Science, Animal Genomics and Bioresource Research Unit (AGB Research Unit), Kasetsart University, Chatuchak, Bangkok, 10900, Thailand.
| | - Rafael Kretschmer
- Departamento de Ecologia, Zoologia e Genética, Instituto de Biologia, Universidade Federal de Pelotas, Campus Universitário Capão do Leão, Pelotas, 96010-900, RS, Brazil
| | - Kornsorn Srikulnath
- Faculty of Science, Animal Genomics and Bioresource Research Unit (AGB Research Unit), Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
| | - Worapong Singchat
- Faculty of Science, Animal Genomics and Bioresource Research Unit (AGB Research Unit), Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
| | | | - Michael N Romanov
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK.
- Faculty of Science, Animal Genomics and Bioresource Research Unit (AGB Research Unit), Kasetsart University, Chatuchak, Bangkok, 10900, Thailand.
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk, 142132, Moscow Oblast, Russia.
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3
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Blom MP, Peona V, Prost S, Christidis L, Benz BW, Jønsson KA, Suh A, Irestedt M. Hybridization in birds-of-paradise: Widespread ancestral gene flow despite strong sexual selection in a lek-mating system. iScience 2024; 27:110300. [PMID: 39055907 PMCID: PMC11269930 DOI: 10.1016/j.isci.2024.110300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 05/08/2024] [Accepted: 06/14/2024] [Indexed: 07/28/2024] Open
Abstract
Sexual selection can directly contribute to reproductive isolation and is an important mechanism that can lead to speciation. Lek-mating is one of the most extreme forms of sexual selection, but surprisingly does not seem to preclude occasional hybridization in nature. However, hybridization among lekking species may still be trivial if selection against offspring with intermediate phenotypes prohibits introgression. Here we investigate this further by sequencing the genomes of nearly all bird-of-paradise (Paradisaeidae) species and 10 museum specimens of putative hybrid origin. We find that intergeneric hybridization indeed still takes place despite extreme differentiation in form, plumage, and behavior. In parallel, the genomes of contemporary species contain widespread signatures of past introgression, demonstrating that hybridization has repeatedly resulted in shared genetic variation despite strong sexual isolation. Our study raises important questions about extrinsic factors that modulate hybridization probability and the evolutionary consequences of introgressive hybridization between lekking species.
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Affiliation(s)
- Mozes P.K. Blom
- Department for Evolutionary Diversity Dynamics, Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Research, 10115 Berlin, Germany
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 114 18 Stockholm, Sweden
| | - Valentina Peona
- Department of Organismal Biology – Systematic Biology, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University, 752 36 Uppsala, Sweden
| | - Stefan Prost
- Ecology and Genetics Research Unit, University of Oulu, 90014 Oulu, Finland
| | - Les Christidis
- Faculty of Science and Engineering, Southern Cross University, Coffs Harbour, NSW 2450, Australia
| | - Brett W. Benz
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI 48108, USA
| | - Knud A. Jønsson
- Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 114 18 Stockholm, Sweden
| | - Alexander Suh
- Department of Organismal Biology – Systematic Biology, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University, 752 36 Uppsala, Sweden
| | - Martin Irestedt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 114 18 Stockholm, Sweden
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4
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Islam R, Rahman A. An alignment-free method for detection of missing regions for phylogenetic analysis. Heliyon 2024; 10:e32227. [PMID: 38933968 PMCID: PMC11200290 DOI: 10.1016/j.heliyon.2024.e32227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Revised: 05/17/2024] [Accepted: 05/29/2024] [Indexed: 06/28/2024] Open
Abstract
Phylogenetic tree estimation using conventional approaches usually requires pairwise or multiple sequence alignment. However, sequence alignment has difficulties related to scalability and accuracy in case of long sequences such as whole genomes, low sequence identity, and in presence of genomic rearrangements. To address these issues, alignment-free approaches have been proposed. While these methods have demonstrated promising results, many of these lead to errors when regions are missing from the sequences of one or more species that are trivially detected in alignment-based methods. Here, we present an alignment-free method for detecting missing regions in sequences of species for which phylogeny is to be estimated. It is based on counts of k-mers and can be used to filter out k-mers belonging to regions in one species that are missing in one or more of the other species. We perform experiments with real and simulated datasets containing missing regions and find that it can successfully detect a large fraction of such k-mers and can lead to improvements in the estimated phylogenies. Our method can be used in k-mer based alignment-free phylogeny estimation methods to filter out k-mers corresponding to missing regions.
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Affiliation(s)
- Rubyeat Islam
- Department of Computer Science and Engineering, Military Institute of Science and Technology, Dhaka, Bangladesh
| | - Atif Rahman
- Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka, Bangladesh
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5
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Zheng W, Gojobori J, Suh A, Satta Y. Different Host-Endogenous Retrovirus Relationships between Mammals and Birds Reflected in Genome-Wide Evolutionary Interaction Patterns. Genome Biol Evol 2024; 16:evae065. [PMID: 38527852 PMCID: PMC11005779 DOI: 10.1093/gbe/evae065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 02/25/2024] [Accepted: 03/21/2024] [Indexed: 03/27/2024] Open
Abstract
Mammals and birds differ largely in their average endogenous retrovirus loads, namely the proportion of endogenous retrovirus in the genome. The host-endogenous retrovirus relationships, including conflict and co-option, have been hypothesized among the causes of this difference. However, there has not been studies about the genomic evolutionary signal of constant host-endogenous retrovirus interactions in a long-term scale and how such interactions could lead to the endogenous retrovirus load difference. Through a phylogeny-controlled correlation analysis on ∼5,000 genes between the dN/dS ratio of each gene and the load of endogenous retrovirus in 12 mammals and 21 birds, separately, we detected genes that may have evolved in association with endogenous retrovirus loads. Birds have a higher proportion of genes with strong correlation between dN/dS and the endogenous retrovirus load than mammals. Strong evidence of association is found between the dN/dS of the coding gene for leucine-rich repeat-containing protein 23 and endogenous retrovirus load in birds. Gene set enrichment analysis shows that gene silencing rather than immunity and DNA recombination may have a larger contribution to the association between dN/dS and the endogenous retrovirus load for both mammals and birds. The above results together showing different evolutionary patterns between bird and mammal genes can partially explain the apparently lower endogenous retrovirus loads of birds, while gene silencing may be a universal mechanism that plays a remarkable role in the evolutionary interaction between the host and endogenous retrovirus. In summary, our study presents signals that the host genes might have driven or responded to endogenous retrovirus load changes in long-term evolution.
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Affiliation(s)
- Wanjing Zheng
- Department of Evolutionary Studies of Biosystems, School of Advanced Sciences, SOKENDAI (The Graduate University for Advanced Studies), Kanagawa 240-0193, Japan
- School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jun Gojobori
- Department of Evolutionary Studies of Biosystems, School of Advanced Sciences, SOKENDAI (The Graduate University for Advanced Studies), Kanagawa 240-0193, Japan
- Research Center for Integrative Evolutionary Science, SOKENDAI (The Graduate University for Advanced Studies), Kanagawa 240-0193, Japan
| | - Alexander Suh
- Department of Organismal Biology—Systematic Biology, Evolutionary Biology Centre (EBC), Uppsala University, Uppsala 75236, Sweden
- School of Biological Sciences—Organisms and the Environment, University of East Anglia, Norwich, UK
| | - Yoko Satta
- Department of Evolutionary Studies of Biosystems, School of Advanced Sciences, SOKENDAI (The Graduate University for Advanced Studies), Kanagawa 240-0193, Japan
- Research Center for Integrative Evolutionary Science, SOKENDAI (The Graduate University for Advanced Studies), Kanagawa 240-0193, Japan
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6
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Reeve AH, Kennedy JD, Pujolar JM, Petersen B, Blom MPK, Alström P, Haryoko T, Ericson PGP, Irestedt M, Nylander JAA, Jønsson KA. The formation of the Indo-Pacific montane avifauna. Nat Commun 2023; 14:8215. [PMID: 38081809 PMCID: PMC10713610 DOI: 10.1038/s41467-023-43964-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 11/24/2023] [Indexed: 12/18/2023] Open
Abstract
The processes generating the earth's montane biodiversity remain a matter of debate. Two contrasting hypotheses have been advanced to explain how montane populations form: via direct colonization from other mountains, or, alternatively, via upslope range shifts from adjacent lowland areas. We seek to reconcile these apparently conflicting hypotheses by asking whether a species' ancestral geographic origin determines its mode of mountain colonization. Island-dwelling passerine birds at the faunal crossroads between Eurasia and Australo-Papua provide an ideal study system. We recover the phylogenetic relationships of the region's montane species and reconstruct their ancestral geographic ranges, elevational ranges, and migratory behavior. We also perform genomic population studies of three super-dispersive montane species/clades with broad island distributions. Eurasian-origin species populated archipelagos via direct colonization between mountains. This mode of colonization appears related to ancestral adaptations to cold and seasonal climates, specifically short-distance migration. Australo-Papuan-origin mountain populations, by contrast, evolved from lowland ancestors, and highland distribution mostly precludes their further colonization of island mountains. Our study explains much of the distributional variation within a complex biological system, and provides a synthesis of two seemingly discordant hypotheses for montane community formation.
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Affiliation(s)
- Andrew Hart Reeve
- Natural History Museum of Denmark, University of Copenhagen, DK-2100, Copenhagen Ø, Denmark.
| | - Jonathan David Kennedy
- Natural History Museum of Denmark, University of Copenhagen, DK-2100, Copenhagen Ø, Denmark
| | - José Martín Pujolar
- Natural History Museum of Denmark, University of Copenhagen, DK-2100, Copenhagen Ø, Denmark
- Centre for Gelatinous Plankton Ecology and Evolution, DTU Aqua, Kemitorvet, Building 202, DK-2800, Kongens Lyngby, Denmark
| | - Bent Petersen
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, DK-1353, Copenhagen, Denmark
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
| | - Mozes P K Blom
- Museum für Naturkunde Berlin, Leibniz Institut für Evolutions- und Biodiversitätsforschung, 10115, Berlin, Germany
| | - Per Alström
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Tri Haryoko
- Museum Zoologicum Bogoriense, Research Center for Biosystematics and Evolution, National Research and Innovation Agency (BRIN), Cibinong, 16911, Indonesia
| | - Per G P Ericson
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, P.O. Box 50007, SE-104 05, Stockholm, Sweden
| | - Martin Irestedt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, P.O. Box 50007, SE-104 05, Stockholm, Sweden
| | - Johan A A Nylander
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, P.O. Box 50007, SE-104 05, Stockholm, Sweden
| | - Knud Andreas Jønsson
- Natural History Museum of Denmark, University of Copenhagen, DK-2100, Copenhagen Ø, Denmark
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, P.O. Box 50007, SE-104 05, Stockholm, Sweden
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7
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Liu B, Warnow T. Weighted ASTRID: fast and accurate species trees from weighted internode distances. Algorithms Mol Biol 2023; 18:6. [PMID: 37468904 PMCID: PMC10355063 DOI: 10.1186/s13015-023-00230-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 06/10/2023] [Indexed: 07/21/2023] Open
Abstract
BACKGROUND Species tree estimation is a basic step in many biological research projects, but is complicated by the fact that gene trees can differ from the species tree due to processes such as incomplete lineage sorting (ILS), gene duplication and loss (GDL), and horizontal gene transfer (HGT), which can cause different regions within the genome to have different evolutionary histories (i.e., "gene tree heterogeneity"). One approach to estimating species trees in the presence of gene tree heterogeneity resulting from ILS operates by computing trees on each genomic region (i.e., computing "gene trees") and then using these gene trees to define a matrix of average internode distances, where the internode distance in a tree T between two species x and y is the number of nodes in T between the leaves corresponding to x and y. Given such a matrix, a tree can then be computed using methods such as neighbor joining. Methods such as ASTRID and NJst (which use this basic approach) are provably statistically consistent, very fast (low degree polynomial time) and have had high accuracy under many conditions that makes them competitive with other popular species tree estimation methods. In this study, inspired by the very recent work of weighted ASTRAL, we present weighted ASTRID, a variant of ASTRID that takes the branch uncertainty on the gene trees into account in the internode distance. RESULTS Our experimental study evaluating weighted ASTRID typically shows improvements in accuracy compared to the original (unweighted) ASTRID, and shows competitive accuracy against weighted ASTRAL, the state of the art. Our re-implementation of ASTRID also improves the runtime, with marked improvements on large datasets. CONCLUSIONS Weighted ASTRID is a new and very fast method for species tree estimation that typically improves upon ASTRID and has comparable accuracy to weighted ASTRAL, while remaining much faster. Weighted ASTRID is available at https://github.com/RuneBlaze/internode .
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Affiliation(s)
- Baqiao Liu
- Department of Computer Science, University of Illinois Urbana-Champaign, Urbana, IL USA
| | - Tandy Warnow
- Department of Computer Science, University of Illinois Urbana-Champaign, Urbana, IL USA
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8
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Ferrer Obiol J, Herranz JM, Paris JR, Whiting JR, Rozas J, Riutort M, González-Solís J. Species delimitation using genomic data to resolve taxonomic uncertainties in a speciation continuum of pelagic seabirds. Mol Phylogenet Evol 2023; 179:107671. [PMID: 36442764 DOI: 10.1016/j.ympev.2022.107671] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 10/28/2022] [Accepted: 11/17/2022] [Indexed: 11/27/2022]
Abstract
Speciation is a continuous and complex process shaped by the interaction of numerous evolutionary forces. Despite the continuous nature of the speciation process, the implementation of conservation policies relies on the delimitation of species and evolutionary significant units (ESUs). Puffinus shearwaters are globally distributed and threatened pelagic seabirds. Due to remarkable morphological status the group has been under intense taxonomic debate for the past three decades. Here, we use double digest Restriction-Site Associated DNA sequencing (ddRAD-Seq) to genotype species and subspecies of North Atlantic and Mediterranean Puffinus shearwaters across their entire geographical range. We assess the phylogenetic relationships and population structure among and within the group, evaluate species boundaries, and characterise the genomic landscape of divergence. We find that current taxonomies are not supported by genomic data and propose a more accurate taxonomy by integrating genomic information with other sources of evidence. Our results show that several taxon pairs are at different stages of a speciation continuum. Our study emphasises the potential of genomic data to resolve taxonomic uncertainties, which can help to focus management actions on relevant taxa, even if they do not necessarily coincide with the taxonomic rank of species.
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Affiliation(s)
- Joan Ferrer Obiol
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), Barcelona, Catalonia, Spain; Institut de Recerca de la Biodiversitat (IRBio), Barcelona, Catalonia, Spain; Department of Environmental Science and Policy, University of Milan, Milan, Italy.
| | - Jose M Herranz
- National Institute for the Study of Liver and Gastrointestinal Diseases, CIBERehd, Carlos III Health Institute, Madrid, Spain; Program of Hepatology, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
| | - Josephine R Paris
- Department of Health, Life and Environmental Sciences, University of l'Aquila, Coppito, Italy; Department of Biosciences, University of Exeter, Exeter, UK
| | - James R Whiting
- Department of Biosciences, University of Exeter, Exeter, UK; Department of Biological Sciences, Faculty of Sciences, University of Calgary, Calgary, Canada
| | - Julio Rozas
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), Barcelona, Catalonia, Spain; Institut de Recerca de la Biodiversitat (IRBio), Barcelona, Catalonia, Spain
| | - Marta Riutort
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), Barcelona, Catalonia, Spain; Institut de Recerca de la Biodiversitat (IRBio), Barcelona, Catalonia, Spain
| | - Jacob González-Solís
- Institut de Recerca de la Biodiversitat (IRBio), Barcelona, Catalonia, Spain; Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Universitat de Barcelona (UB), Barcelona, Catalonia, Spain
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9
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Wang N, Braun EL, Liang B, Cracraft J, Smith SA. Categorical edge-based analyses of phylogenomic data reveal conflicting signals for difficult relationships in the avian tree. Mol Phylogenet Evol 2022; 174:107550. [PMID: 35691570 DOI: 10.1016/j.ympev.2022.107550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 05/13/2022] [Accepted: 06/02/2022] [Indexed: 11/28/2022]
Abstract
Phylogenetic analyses fail to yield a satisfactory resolution of some relationships in the tree of life even with genome-scale datasets, so the failure is unlikely to reflect limitations in the amount of data. Gene tree conflicts are particularly notable in studies focused on these contentious nodes, and taxon sampling, different analytical methods, and/or data type effects can further confound analyses. Although many efforts have been made to incorporate biological conflicts, few studies have curated individual genes for their efficiency in phylogenomic studies. Here, we conduct an edge-based analysis of Neoavian evolution, examining the phylogenetic efficacy of two recent phylogenomic bird datasets and three datatypes (ultraconserved elements [UCEs], introns, and coding regions). We assess the potential causes for biases in signal-resolution for three difficult nodes: the earliest divergence of Neoaves, the position of the enigmatic Hoatzin (Opisthocomus hoazin), and the position of owls (Strigiformes). We observed extensive conflict among genes for all data types and datasets even after meticulous curation. Edge-based analyses (EBA) increased congruence and provided information about the impact of data type, GC content variation (GCCV), and outlier genes on each of nodes we examined. First, outlier gene signals appeared to drive different patterns of support for the relationships among the earliest diverging Neoaves. Second, the placement of Hoatzin was highly variable, although our EBA did reveal a previously unappreciated data type effect with an impact on its position. It also revealed that the resolution with the most support here was Hoatzin + shorebirds. Finally, GCCV, rather than data type (i.e., coding vs non-coding) per se, was correlated with a signal that supports monophyly of owls + Accipitriformes (hawks, eagles, and vultures). Eliminating high GCCV loci increased the signal for owls + mousebirds. Categorical EBA was able to reveal the nature of each edge and provide a way to highlight especially problematic branches that warrant a further examination. The current study increases our understanding about the contentious parts of the avian tree, which show even greater conflicts than appreciated previously.
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Affiliation(s)
- Ning Wang
- College of Life Sciences, Inner Mongolia University, Hohhot 010070, China; Department of Ecology & Evolutionary Biology, University of Michigan, 1105 N University Ave, Ann Arbor, MI 48109-1048, USA; Department of Ornithology, American Museum of Natural History, New York, NY 10024, USA.
| | - Edward L Braun
- Department of Biology, University of Florida, Gainesville, FL 32607, USA
| | - Bin Liang
- College of Life Sciences, Inner Mongolia University, Hohhot 010070, China; Department of Ecology & Evolutionary Biology, University of Michigan, 1105 N University Ave, Ann Arbor, MI 48109-1048, USA
| | - Joel Cracraft
- Department of Ornithology, American Museum of Natural History, New York, NY 10024, USA
| | - Stephen A Smith
- Department of Ecology & Evolutionary Biology, University of Michigan, 1105 N University Ave, Ann Arbor, MI 48109-1048, USA
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10
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Ng CS, Lai CK, Ke HM, Lee HH, Chen CF, Tang PC, Cheng HC, Lu MJ, Li WH, Tsai IJ. Genome Assembly and Evolutionary Analysis of the Mandarin Duck Aix galericulata Reveal Strong Genome Conservation among Ducks. Genome Biol Evol 2022; 14:evac083. [PMID: 35640266 PMCID: PMC9189614 DOI: 10.1093/gbe/evac083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/25/2022] [Indexed: 11/13/2022] Open
Abstract
The mandarin duck, Aix galericulata, is popular in East Asian cultures and displays exaggerated sexual dimorphism, especially in feather traits during breeding seasons. We generated and annotated the first mandarin duck de novo assembly, which was 1.08 Gb in size and encoded 16,615 proteins. Using a phylogenomic approach calibrated with fossils and molecular divergences, we inferred that the last common ancestor of ducks occurred 13.3-26.7 Ma. The majority of the mandarin duck genome repetitive sequences belonged to the chicken repeat 1 (CR1) retroposon CR1-J2_Pass, which underwent a duck lineage-specific burst. Synteny analyses among ducks revealed infrequent chromosomal rearrangements in which breaks were enriched in LINE retrotransposons and DNA transposons. The calculation of the dN/dS ratio revealed that the majority of duck genes were under strong purifying selection. The expanded gene families in the mandarin duck are primarily involved in olfactory perception as well as the development and morphogenesis of feather and branching structures. This new reference genome will improve our understanding of the morphological and physiological characteristics of ducks and provide a valuable resource for functional genomics studies to investigate the feather traits of the mandarin duck.
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Affiliation(s)
- Chen Siang Ng
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan
- Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan
- Bioresource Conservation Research Center, National Tsing Hua University, Hsinchu, Taiwan
- The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
| | - Cheng-Kuo Lai
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan
| | - Huei-Mien Ke
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Hsin-Han Lee
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Chih-Feng Chen
- The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
- Department of Animal Science, National Chung Hsing University, Taichung, Taiwan
| | - Pin-Chi Tang
- The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
- Department of Animal Science, National Chung Hsing University, Taichung, Taiwan
| | - Hsu-Chen Cheng
- The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
- Department of Life Science, National Chung Hsing University, Taichung, Taiwan
| | - Meiyeh J. Lu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Wen-Hsiung Li
- The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Department of Ecology and Evolution, University of Chicago, Illinois, USA
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11
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Rahman MA, Tutul AA, Abdullah SM, Bayzid MS. CHAPAO: Likelihood and hierarchical reference-based representation of biomolecular sequences and applications to compressing multiple sequence alignments. PLoS One 2022; 17:e0265360. [PMID: 35436292 PMCID: PMC9015123 DOI: 10.1371/journal.pone.0265360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Accepted: 02/28/2022] [Indexed: 11/18/2022] Open
Abstract
Background
High-throughput experimental technologies are generating tremendous amounts of genomic data, offering valuable resources to answer important questions and extract biological insights. Storing this sheer amount of genomic data has become a major concern in bioinformatics. General purpose compression techniques (e.g. gzip, bzip2, 7-zip) are being widely used due to their pervasiveness and relatively good speed. However, they are not customized for genomic data and may fail to leverage special characteristics and redundancy of the biomolecular sequences.
Results
We present a new lossless compression method CHAPAO (COmpressing Alignments using Hierarchical and Probabilistic Approach), which is especially designed for multiple sequence alignments (MSAs) of biomolecular data and offers very good compression gain. We have introduced a novel hierarchical referencing technique to represent biomolecular sequences which combines likelihood based analyses of the sequence similarities and graph theoretic algorithms. We performed an extensive evaluation study using a collection of real biological data from the avian phylogenomics project, 1000 plants project (1KP), and 16S and 23S rRNA datasets. We report the performance of CHAPAO in comparison with general purpose compression techniques as well as with MFCompress and Nucleotide Archival Format (NAF)—two of the best known methods especially designed for FASTA files. Experimental results suggest that CHAPAO offers significant improvements in compression gain over most other alternative methods. CHAPAO is freely available as an open source software at https://github.com/ashiq24/CHAPAO.
Conclusion
CHAPAO advances the state-of-the-art in compression algorithms and represents a potential alternative to the general purpose compression techniques as well as to the existing specialized compression techniques for biomolecular sequences.
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Affiliation(s)
- Md Ashiqur Rahman
- Department of Computer Science and Engineering/Bangladesh University of Engineering and Technology, Dhaka, Bangladesh
| | - Abdullah Aman Tutul
- Department of Computer Science and Engineering/Bangladesh University of Engineering and Technology, Dhaka, Bangladesh
| | - Sifat Muhammad Abdullah
- Department of Computer Science and Engineering/Bangladesh University of Engineering and Technology, Dhaka, Bangladesh
| | - Md. Shamsuzzoha Bayzid
- Department of Computer Science and Engineering/Bangladesh University of Engineering and Technology, Dhaka, Bangladesh
- * E-mail:
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12
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Hansen CCR, Westfall KM, Pálsson S. Evaluation of four methods to identify the homozygotic sex chromosome in small populations. BMC Genomics 2022; 23:160. [PMID: 35209843 PMCID: PMC8867824 DOI: 10.1186/s12864-022-08393-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 02/15/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Whole genomes are commonly assembled into a collection of scaffolds and often lack annotations of autosomes, sex chromosomes, and organelle genomes (i.e., mitochondrial and chloroplast). As these chromosome types differ in effective population size and can have highly disparate evolutionary histories, it is imperative to take this information into account when analysing genomic variation. Here we assessed the accuracy of four methods for identifying the homogametic sex chromosome in a small population using two whole genome sequences (WGS) and 133 RAD sequences of white-tailed eagles (Haliaeetus albicilla): i) difference in read depth per scaffold in a male and a female, ii) heterozygosity per scaffold in a male and a female, iii) mapping to the reference genome of a related species (chicken) with annotated sex chromosomes, and iv) analysis of SNP-loadings from a principal components analysis (PCA), based on the low-depth RADseq data. RESULTS The best performing approach was the reference mapping (method iii), which identified 98.12% of the expected homogametic sex chromosome (Z). Read depth per scaffold (method i) identified 86.41% of the homogametic sex chromosome with few false positives. SNP-loading scores (method iv) identified 78.6% of the Z-chromosome and had a false positive discovery rate of more than 10%. Heterozygosity per scaffold (method ii) did not provide clear results due to a lack of diversity in both the Z and autosomal chromosomes, and potential interference from the heterogametic sex chromosome (W). The evaluation of these methods also revealed 10 Mb of putative PAR and gametologous regions. CONCLUSION Identification of the homogametic sex chromosome in a small population is best accomplished by reference mapping or examining differences in read depth between sexes.
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Affiliation(s)
| | - Kristen M Westfall
- Department of Life and Environmental Sciences, University of Iceland, Reykjavik, Iceland.,Current: Fisheries and Oceans Canada, Pacific Biological Station, Nanaimo, BC, Canada
| | - Snæbjörn Pálsson
- Department of Life and Environmental Sciences, University of Iceland, Reykjavik, Iceland
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13
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Sin SYW, Cloutier A, Nevitt G, Edwards SV. Olfactory receptor subgenome and expression in a highly olfactory procellariiform seabird. Genetics 2021; 220:6458329. [PMID: 34888634 DOI: 10.1093/genetics/iyab210] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 10/04/2021] [Indexed: 11/13/2022] Open
Abstract
Procellariiform seabirds rely on their sense of smell for foraging and homing. Both genomes and transcriptomes yield important clues about how olfactory receptor (OR) subgenomes are shaped by natural and sexual selection, yet no transcriptomes have been made of any olfactory epithelium of any bird species thus far. Here we assembled a high-quality genome and nasal epithelium transcriptome of the Leach's storm-petrel (Oceanodroma leucorhoa) to extensively characterize their OR repertoire. Using a depth-of-coverage-assisted counting method, we estimated over 160 intact OR genes (∼500 including OR fragments). This method reveals the highest number of intact OR genes and the lowest proportion of pseudogenes compared to other waterbirds studied, and suggests that rates of OR gene duplication vary between major clades of birds, with particularly high rates in passerines. OR expression patterns reveal two OR genes (OR6-6 and OR5-11) highly expressed in adults, and four OR genes (OR14-14, OR14-12, OR10-2, and OR14-9) differentially expressed between age classes of storm-petrels. All four genes differentially expressed between age classes were more highly expressed in chicks compared to adults, suggesting that ORs genes may exhibit ontogenetic specializations. Three highly differentially expressed OR genes also had high copy number ratios, suggesting that expression variation may be linked to copy number in the genome. We provide better estimates of OR gene number by using a copy number-assisted counting method, and document ontogenetic changes in OR gene expression that may be linked to olfactory specialization. These results provide valuable insight into the expression, development, and macroevolution of olfaction in seabirds.
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Affiliation(s)
- Simon Yung Wa Sin
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA.,School of Biological Sciences, The University of Hong Kong, Pok Fu Lam Road, Hong Kong SAR, China
| | - Alison Cloutier
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Gabrielle Nevitt
- Department of Neurobiology, Physiology and Behavior and the Graduate Group in Ecology, University of California, Davis, CA 95616, USA
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
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14
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Ferrer Obiol J, James HF, Chesser RT, Bretagnolle V, González-Solís J, Rozas J, Riutort M, Welch AJ. Integrating Sequence Capture and Restriction Site-Associated DNA Sequencing to Resolve Recent Radiations of Pelagic Seabirds. Syst Biol 2021; 70:976-996. [PMID: 33512506 PMCID: PMC8357341 DOI: 10.1093/sysbio/syaa101] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 11/13/2020] [Accepted: 12/15/2020] [Indexed: 01/01/2023] Open
Abstract
The diversification of modern birds has been shaped by a number of radiations. Rapid diversification events make reconstructing the evolutionary relationships among taxa challenging due to the convoluted effects of incomplete lineage sorting (ILS) and introgression. Phylogenomic data sets have the potential to detect patterns of phylogenetic incongruence, and to address their causes. However, the footprints of ILS and introgression on sequence data can vary between different phylogenomic markers at different phylogenetic scales depending on factors such as their evolutionary rates or their selection pressures. We show that combining phylogenomic markers that evolve at different rates, such as paired-end double-digest restriction site-associated DNA (PE-ddRAD) and ultraconserved elements (UCEs), allows a comprehensive exploration of the causes of phylogenetic discordance associated with short internodes at different timescales. We used thousands of UCE and PE-ddRAD markers to produce the first well-resolved phylogeny of shearwaters, a group of medium-sized pelagic seabirds that are among the most phylogenetically controversial and endangered bird groups. We found that phylogenomic conflict was mainly derived from high levels of ILS due to rapid speciation events. We also documented a case of introgression, despite the high philopatry of shearwaters to their breeding sites, which typically limits gene flow. We integrated state-of-the-art concatenated and coalescent-based approaches to expand on previous comparisons of UCE and RAD-Seq data sets for phylogenetics, divergence time estimation, and inference of introgression, and we propose a strategy to optimize RAD-Seq data for phylogenetic analyses. Our results highlight the usefulness of combining phylogenomic markers evolving at different rates to understand the causes of phylogenetic discordance at different timescales. [Aves; incomplete lineage sorting; introgression; PE-ddRAD-Seq; phylogenomics; radiations; shearwaters; UCEs.].
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Affiliation(s)
- Joan Ferrer Obiol
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalonia, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Barcelona, Catalonia, Spain
| | - Helen F James
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - R Terry Chesser
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
- U.S. Geological Survey, Patuxent Wildlife Research Center, Laurel, MD, USA
| | - Vincent Bretagnolle
- Centre d’Études Biologiques de Chizé, CNRS & La Rochelle Université, 79360, Villiers en Bois, France
| | - Jacob González-Solís
- Institut de Recerca de la Biodiversitat (IRBio), Barcelona, Catalonia, Spain
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Julio Rozas
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalonia, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Barcelona, Catalonia, Spain
| | - Marta Riutort
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalonia, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Barcelona, Catalonia, Spain
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15
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Vanamamalai VK, Garg P, Kolluri G, Gandham RK, Jali I, Sharma S. Transcriptomic analysis to infer key molecular players involved during host response to NDV challenge in Gallus gallus (Leghorn & Fayoumi). Sci Rep 2021; 11:8486. [PMID: 33875770 PMCID: PMC8055681 DOI: 10.1038/s41598-021-88029-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 03/22/2021] [Indexed: 11/09/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are the transcripts of length longer than 200 nucleotides. They are involved in the regulation of various biological activities. Leghorn and Fayoumi breeds of Gallus gallus were known to be having differential resistance against Newcastle Disease Virus (NDV) infection. Differentially expressed genes which were thought to be involved in this pattern of resistance were already studied. Here we report the analysis of the transcriptomic data of Harderian gland of Gallus gallus for studying the lncRNAs involved in regulation of these genes. Using bioinformatics approaches, a total of 37,411 lncRNAs were extracted and 359 lncRNAs were differentially expressing. Functional annotation using co-expression analysis revealed the involvement of lncRNAs in the regulation of various pathways. We also identified 1232 quantitative trait loci (QTLs) associated with the genes interacting with lncRNA. Additionally, we identified the role of lncRNAs as putative micro RNA precursors, and the interaction of differentially expressed Genes with transcription factors and micro RNAs. Our study revealed the role of lncRNAs during host response against NDV infection which would facilitate future experiments in unravelling regulatory mechanisms of development in the genetic improvement of the susceptible breeds of Gallus gallus.
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Affiliation(s)
- Venkata Krishna Vanamamalai
- National Institute of Animal Biotechnology (NIAB), Opposite Journalist Colony, Near Gowlidoddi Extended Q City Road, Gachibowli, Hyderabad, Telangana, 500032, India
| | - Priyanka Garg
- National Institute of Animal Biotechnology (NIAB), Opposite Journalist Colony, Near Gowlidoddi Extended Q City Road, Gachibowli, Hyderabad, Telangana, 500032, India
| | - Gautham Kolluri
- ICAR-Central Avian Research Institute, Izatnagar, Bareilly, Uttar Pradesh, 243122, India
| | - Ravi Kumar Gandham
- National Institute of Animal Biotechnology (NIAB), Opposite Journalist Colony, Near Gowlidoddi Extended Q City Road, Gachibowli, Hyderabad, Telangana, 500032, India
| | - Itishree Jali
- National Institute of Animal Biotechnology (NIAB), Opposite Journalist Colony, Near Gowlidoddi Extended Q City Road, Gachibowli, Hyderabad, Telangana, 500032, India
| | - Shailesh Sharma
- National Institute of Animal Biotechnology (NIAB), Opposite Journalist Colony, Near Gowlidoddi Extended Q City Road, Gachibowli, Hyderabad, Telangana, 500032, India.
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16
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Minh BQ, Hahn MW, Lanfear R. New Methods to Calculate Concordance Factors for Phylogenomic Datasets. Mol Biol Evol 2021; 37:2727-2733. [PMID: 32365179 PMCID: PMC7475031 DOI: 10.1093/molbev/msaa106] [Citation(s) in RCA: 313] [Impact Index Per Article: 78.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
We implement two measures for quantifying genealogical concordance in phylogenomic data sets: the gene concordance factor (gCF) and the novel site concordance factor (sCF). For every branch of a reference tree, gCF is defined as the percentage of "decisive" gene trees containing that branch. This measure is already in wide usage, but here we introduce a package that calculates it while accounting for variable taxon coverage among gene trees. sCF is a new measure defined as the percentage of decisive sites supporting a branch in the reference tree. gCF and sCF complement classical measures of branch support in phylogenetics by providing a full description of underlying disagreement among loci and sites. An easy to use implementation and tutorial is freely available in the IQ-TREE software package (http://www.iqtree.org/doc/Concordance-Factor, last accessed May 13, 2020).
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Affiliation(s)
- Bui Quang Minh
- Research School of Computer Science, Australian National University, Canberra, ACT, Australia.,Department of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Matthew W Hahn
- Department of Biology, Indiana University, Bloomington, IN.,Department of Computer Science, Indiana University, Bloomington, IN
| | - Robert Lanfear
- Department of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, ACT, Australia
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17
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Recuerda M, Vizueta J, Cuevas-Caballé C, Blanco G, Rozas J, Milá B. Chromosome-Level Genome Assembly of the Common Chaffinch (Aves: Fringilla coelebs): A Valuable Resource for Evolutionary Biology. Genome Biol Evol 2021; 13:evab034. [PMID: 33616654 PMCID: PMC8046334 DOI: 10.1093/gbe/evab034] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/16/2021] [Indexed: 12/26/2022] Open
Abstract
The common chaffinch, Fringilla coelebs, is one of the most common, widespread, and well-studied passerines in Europe, with a broad distribution encompassing Western Europe and parts of Asia, North Africa, and the Macaronesian archipelagos. We present a high-quality genome assembly of the common chaffinch generated using Illumina shotgun sequencing in combination with Chicago and Hi-C libraries. The final genome is a 994.87-Mb chromosome-level assembly, with 98% of the sequence data located in chromosome scaffolds and a N50 statistic of 69.73 Mb. Our genome assembly shows high completeness, with a complete BUSCO score of 93.9% using the avian data set. Around 7.8% of the genome contains interspersed repetitive elements. The structural annotation yielded 17,703 genes, 86.5% of which have a functional annotation, including 7,827 complete universal single-copy orthologs out of 8,338 genes represented in the BUSCO avian data set. This new annotated genome assembly will be a valuable resource as a reference for comparative and population genomic analyses of passerine, avian, and vertebrate evolution.
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Affiliation(s)
- María Recuerda
- National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, Spain
| | - Joel Vizueta
- National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, Spain
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Cristian Cuevas-Caballé
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Guillermo Blanco
- National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, Spain
| | - Julio Rozas
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Borja Milá
- National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, Spain
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18
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Minh BQ, Dang CC, Vinh LS, Lanfear R. QMaker: Fast and accurate method to estimate empirical models of protein evolution. Syst Biol 2021; 70:1046-1060. [PMID: 33616668 PMCID: PMC8357343 DOI: 10.1093/sysbio/syab010] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 12/25/2020] [Accepted: 02/10/2021] [Indexed: 11/29/2022] Open
Abstract
Amino acid substitution models play a crucial role in phylogenetic analyses. Maximum likelihood (ML) methods have been proposed to estimate amino acid substitution models; however, they are typically complicated and slow. In this article, we propose QMaker, a new ML method to estimate a general time-reversible \documentclass[12pt]{minimal}
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}{}$Q$\end{document} matrix from a large protein data set consisting of multiple sequence alignments. QMaker combines an efficient ML tree search algorithm, a model selection for handling the model heterogeneity among alignments, and the consideration of rate mixture models among sites. We provide QMaker as a user-friendly function in the IQ-TREE software package (http://www.iqtree.org) supporting the use of multiple CPU cores so that biologists can easily estimate amino acid substitution models from their own protein alignments. We used QMaker to estimate new empirical general amino acid substitution models from the current Pfam database as well as five clade-specific models for mammals, birds, insects, yeasts, and plants. Our results show that the new models considerably improve the fit between model and data and in some cases influence the inference of phylogenetic tree topologies.[Amino acid replacement matrices; amino acid substitution models; maximum likelihood estimation; phylogenetic inferences.]
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Affiliation(s)
- Bui Quang Minh
- School of Computing, Australian National University, 145 Science Road, Acton, ACT 2601, Canberra, Australia
- Department of Ecology and Evolution, Research School of Biology, Australian National University, 145 Science Road, Acton, ACT 2601, Canberra, Australia
| | - Cuong Cao Dang
- Faculty of Information Technology, University of Engineering and Technology, Vietnam National University, Hanoi, 144 Xuan Thuy, Cau Giay, 10000 Hanoi, Vietnam Bui Quang Minh and Cuong Cao Dang contributed equally to this article
| | - Le Sy Vinh
- Faculty of Information Technology, University of Engineering and Technology, Vietnam National University, Hanoi, 144 Xuan Thuy, Cau Giay, 10000 Hanoi, Vietnam Bui Quang Minh and Cuong Cao Dang contributed equally to this article
- Correspondence to be sent to: University of Engineering and Technology, Vietnam National University, Hanoi, 144 Xuan Thuy, Cau Giay, 10000 Hanoi, Vietnam; E-mail: and Department of Ecology and Evolution, Research School of Biology, Australian National University, 145 Science Road, Acton, ACT 2601, Canberra, Australia; E-mail:
| | - Robert Lanfear
- Department of Ecology and Evolution, Research School of Biology, Australian National University, 145 Science Road, Acton, ACT 2601, Canberra, Australia
- Correspondence to be sent to: University of Engineering and Technology, Vietnam National University, Hanoi, 144 Xuan Thuy, Cau Giay, 10000 Hanoi, Vietnam; E-mail: and Department of Ecology and Evolution, Research School of Biology, Australian National University, 145 Science Road, Acton, ACT 2601, Canberra, Australia; E-mail:
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De Mendoza RS, Gómez RO, Tambussi CP. The lacrimal/ectethmoid region of waterfowl (Aves, Anseriformes): Phylogenetic signal and major evolutionary patterns. J Morphol 2020; 281:1486-1500. [PMID: 32936967 DOI: 10.1002/jmor.21265] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 08/02/2020] [Accepted: 09/02/2020] [Indexed: 11/08/2022]
Abstract
Waterfowl (Aves, Anseriformes) constitute an ancient global radiation, and understanding the pattern and timing of their evolution requires a well-corroborated phylogeny including extant species and fossils. Following the molecular advances in avian systematics, however, morphology has often been held as misleading, yet congruence with molecular data has been shown to vary considerably among different skeletal parts. Here, we explore phylogenetic signal in discrete characters of the lacrimal/ectethmoid region of waterfowl, which is highly variable among species and constitutes a rich source of data. We do so by combining cladistic and multivariate approaches, and using phylogenetic comparative methods. We quantitatively recognize three major morphological types among lacrimal bones, and discuss homoplasy and potential synapomorphies of major clades using a molecular backbone tree. Our results clearly indicate that the lacrimal bone carries substantial phylogenetic signal and could be of systematic value at different levels of the phylogeny of waterfowl, feeding the exploration of other regions of the skull with this combined approach.
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Affiliation(s)
- Ricardo S De Mendoza
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina.,División Paleontología Vertebrados, Museo de La Plata, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, La Plata, Argentina
| | - Raúl O Gómez
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina.,Departamento de Biodiversidad y Biología Experimental, Facultad de Ciencias Exactas, Físicas y Naturales, Universidad de Buenos Aires, Pabellón 2, Ciudad Universitaria, Buenos Aires, Argentina
| | - Claudia P Tambussi
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina.,Centro de Investigaciones en Ciencias de la Tierra (CICTERRA), Universidad Nacional de Córdoba, Ciudad Universitaria, Córdoba, X5016GCA, Argentina
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20
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Wang S, Chang WL, Zhang Q, Ma M, Yang F, Zhuo D, Hans HIC, Yang R, Wu P, Habib M, Juan WT, Chuong CM. Variations of Mesozoic feathers: Insights from the morphogenesis of extant feather rachises. Evolution 2020; 74:2121-2133. [PMID: 32614075 DOI: 10.1111/evo.14051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 06/21/2020] [Accepted: 06/27/2020] [Indexed: 12/14/2022]
Abstract
The rachises of extant feathers, composed of dense cortex and spongy internal medulla, are flexible and light, yet stiff enough to withstand the load required for flight, among other functions. Incomplete knowledge of early feathers prevents a full understanding of how cylindrical rachises have evolved. Bizarre feathers with unusually wide and flattened rachises, known as "rachis-dominated feathers" (RDFs), have been observed in fossil nonavian and avian theropods. Newly discovered RDFs embedded in early Late Cretaceous Burmese ambers (about 99 million year ago) suggest the unusually wide and flattened rachises mainly consist of a dorsal cortex, lacking a medulla and a ventral cortex. Coupled with findings on extant feather morphogenesis, known fossil RDFs were categorized into three morphotypes based on their rachidial configurations. For each morphotype, potential developmental scenarios were depicted by referring to the rachidial development in chickens, and relative stiffness of each morphotype was estimated through functional simulations. The results suggest rachises of RDFs are developmentally equivalent to a variety of immature stages of cylindrical rachises. Similar rachidial morphotypes documented in extant penguins suggest that the RDFs are not unique to Mesozoic theropods, although they are likely to have evolved independently in extant penguins.
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Affiliation(s)
- Shuo Wang
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, California, 90033
| | - Wei-Ling Chang
- Integrative Stem Cell Center, China Medical University Hospital, Taichung, 40447, Taiwan
| | - Qiyue Zhang
- College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Menglu Ma
- Laboratory of Vertebrate Evolution, College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Feng Yang
- Beijing Advanced Innovation Center for Imaging Technology, Capital Normal University, Beijing, 100048, China
| | - De Zhuo
- Beijing Xiachong Amber Museum, Beijing, 100083, China
| | - Harn I-Chen Hans
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, California, 90033
- International Research Center of Wound Repair and Regeneration, National Cheng Kung University, Tainan, 70101, Taiwan
| | - Rui Yang
- Laboratory of Vertebrate Evolution, College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Ping Wu
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, California, 90033
| | - Michael Habib
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, California, 90033
- Los Angeles County Museum of Natural History, Los Angeles, California, 90007
| | - Wen-Tau Juan
- Integrative Stem Cell Center, China Medical University Hospital, Taichung, 40447, Taiwan
- Department of Biomedical Imaging and Radiological Science, China Medical University, Taichung, 40402, Taiwan
| | - Cheng-Ming Chuong
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, California, 90033
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21
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Degrandi TM, Barcellos SA, Costa AL, Garnero ADV, Hass I, Gunski RJ. Introducing the Bird Chromosome Database: An Overview of Cytogenetic Studies in Birds. Cytogenet Genome Res 2020; 160:199-205. [PMID: 32369809 DOI: 10.1159/000507768] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 03/26/2020] [Indexed: 11/19/2022] Open
Abstract
Bird chromosomes, which have been investigated scientifically for more than a century, present a number of unique features. In general, bird karyotypes have a high diploid number (2n) of typically around 80 chromosomes that are divided into macro- and microchromosomes. In recent decades, FISH studies using whole chromosome painting probes have shown that the macrochromosomes evolved through both inter- and intrachromosomal rearrangements. However, chromosome painting data are available for only a few bird species, which hinders a more systematic approach to the understanding of the evolutionary history of the enigmatic bird karyotype. Thus, we decided to create an innovative database through compilation of the cytogenetic data available for birds, including chromosome numbers and the results of chromosome painting with chicken (Gallus gallus) probes. The data were obtained through an extensive literature review, which focused on cytogenetic studies published up to 2019. In the first version of the "Bird Chromosome Database (BCD)" (https://sites.unipampa.edu.br/birdchromosomedatabase) we have compiled data on the chromosome numbers of 1,067 bird species and chromosome painting data on 96 species. We found considerable variation in the diploid numbers, which ranged from 40 to 142, although most (around 50%) of the species studied up to now have between 78 and 82 chromosomes. Despite its importance for cytogenetic research, chromosome painting has been applied to less than 1% of all bird species. The BCD will enable researchers to identify the main knowledge gaps in bird cytogenetics, including the most under-sampled groups, and make inferences on chromosomal homologies in phylogenetic studies.
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22
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Deep-Time Demographic Inference Suggests Ecological Release as Driver of Neoavian Adaptive Radiation. DIVERSITY-BASEL 2020. [DOI: 10.3390/d12040164] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Assessing the applicability of theory to major adaptive radiations in deep time represents an extremely difficult problem in evolutionary biology. Neoaves, which includes 95% of living birds, is believed to have undergone a period of rapid diversification roughly coincident with the Cretaceous–Paleogene (K-Pg) boundary. We investigate whether basal neoavian lineages experienced an ecological release in response to ecological opportunity, as evidenced by density compensation. We estimated effective population sizes (Ne) of basal neoavian lineages by combining coalescent branch lengths (CBLs) and the numbers of generations between successive divergences. We used a modified version of Accurate Species TRee Algorithm (ASTRAL) to estimate CBLs directly from insertion–deletion (indel) data, as well as from gene trees using DNA sequence and/or indel data. We found that some divergences near the K-Pg boundary involved unexpectedly high gene tree discordance relative to the estimated number of generations between speciation events. The simplest explanation for this result is an increase in Ne, despite the caveats discussed herein. It appears that at least some early neoavian lineages, similar to the ancestor of the clade comprising doves, mesites, and sandgrouse, experienced ecological release near the time of the K-Pg mass extinction.
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23
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Lee H, Kim J, Weber JA, Chung O, Cho YS, Jho S, Jun J, Kim HM, Lim J, Choi JP, Jeon S, Blazyte A, Edwards JS, Paek WK, Bhak J. Whole Genome Analysis of the Red-Crowned Crane Provides Insight into Avian Longevity. Mol Cells 2020; 43:86-95. [PMID: 31940721 PMCID: PMC6999708 DOI: 10.14348/molcells.2019.0190] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 10/31/2019] [Accepted: 12/18/2019] [Indexed: 11/29/2022] Open
Abstract
The red-crowned crane (Grus japonensis) is an endangered, large-bodied crane native to East Asia. It is a traditional symbol of longevity and its long lifespan has been confirmed both in captivity and in the wild. Lifespan in birds is known to be positively correlated with body size and negatively correlated with metabolic rate, though the genetic mechanisms for the red-crowned crane's long lifespan have not previously been investigated. Using whole genome sequencing and comparative evolutionary analyses against the grey-crowned crane and other avian genomes, including the long-lived common ostrich, we identified redcrowned crane candidate genes with known associations with longevity. Among these are positively selected genes in metabolism and immunity pathways (NDUFA5, NDUFA8, NUDT12, SOD3, CTH , RPA1, PHAX, HNMT , HS2ST1 , PPCDC , PSTK CD8B, GP9, IL-9R, and PTPRC). Our analyses provide genetic evidence for low metabolic rate and longevity, accompanied by possible convergent adaptation signatures among distantly related large and long-lived birds. Finally, we identified low genetic diversity in the red-crowned crane, consistent with its listing as an endangered species, and this genome should provide a useful genetic resource for future conservation studies of this rare and iconic species.
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Affiliation(s)
- HyeJin Lee
- Personal Genomics Institute, Genome Research Foundation, Cheongju 28160,
Korea
| | - Jungeun Kim
- Personal Genomics Institute, Genome Research Foundation, Cheongju 28160,
Korea
| | - Jessica A. Weber
- Department of Genetics, Harvard Medical School, Boston, MA 02115,
USA
| | | | | | - Sungwoong Jho
- Personal Genomics Institute, Genome Research Foundation, Cheongju 28160,
Korea
| | | | - Hak-Min Kim
- KOGIC, Ulsan National Institute of Science and Technology, Ulsan 44919,
Korea
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919,
Korea
| | - Jeongheui Lim
- National Science Museum, Ministry of Science and ICT, Daejeon 34143,
Korea
| | - Jae-Pil Choi
- Personal Genomics Institute, Genome Research Foundation, Cheongju 28160,
Korea
| | - Sungwon Jeon
- KOGIC, Ulsan National Institute of Science and Technology, Ulsan 44919,
Korea
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919,
Korea
| | - Asta Blazyte
- KOGIC, Ulsan National Institute of Science and Technology, Ulsan 44919,
Korea
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919,
Korea
| | - Jeremy S. Edwards
- Chemistry and Chemical Biology, UNM Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87131,
USA
| | - Woon Kee Paek
- National Science Museum, Ministry of Science and ICT, Daejeon 34143,
Korea
| | - Jong Bhak
- Personal Genomics Institute, Genome Research Foundation, Cheongju 28160,
Korea
- Clinomics, Ulsan 44919,
Korea
- KOGIC, Ulsan National Institute of Science and Technology, Ulsan 44919,
Korea
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919,
Korea
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24
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Dhar R, Seethy A, Pethusamy K, Singh S, Rohil V, Purkayastha K, Mukherjee I, Goswami S, Singh R, Raj A, Srivastava T, Acharya S, Rajashekhar B, Karmakar S. De novo assembly of the Indian blue peacock (Pavo cristatus) genome using Oxford Nanopore technology and Illumina sequencing. Gigascience 2019; 8:5488106. [PMID: 31077316 PMCID: PMC6511069 DOI: 10.1093/gigascience/giz038] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Revised: 09/30/2018] [Accepted: 03/18/2019] [Indexed: 01/23/2023] Open
Abstract
Background The Indian peafowl (Pavo cristanus) is native to South Asia and is the national bird of India. Here we present a draft genome sequence of the male blue peacock using Illumina and Oxford Nanopore technology (ONT). Results ONT sequencing gave ∼2.3-fold sequencing coverage, whereas Illumina generated 150–base pair paired-end sequence data at 284.6-fold coverage from 5 libraries. Subsequently, we generated a 0.915-gigabase pair de novo assembly of the peacock genome with a scaffold N50 of 0.23 megabase pairs (Mb). We predict that the peacock genome contains 23,153 protein-coding genes and 75.3 Mb (7.33%) of repetitive sequences. Conclusions We report a high-quality assembly of the peacock genome using a hybrid approach of sequences generated by both Illumina and ONT. The long-read chemistry generated by ONT was useful for addressing challenges related to de novo assembly, particularly at regions containing repetitive sequences spanning longer than the read length, and which could not be resolved with only short-read–based assembly. Contig assembly of Illumina short reads gave an N50 of 1,639 bases, whereas with ONT, the N50 increased by >9-fold to 14,749 bases. The initial contig assembly based on Illumina sequencing reads alone gave 685,241 contigs. Further scaffolding on assembled contigs using both Illumina and ONT sequencing reads resulted in a final assembly of 15,025 super-scaffolds, with an N50 of ∼0.23 Mb. Ninety-five percent of proteins predicted by homology matched with those in a public repository, verifying the completeness of our assembly. Like other phylogenetic studies of avian conserved genes, we found P. cristatus to be most closely related to Gallus gallus, followed by Meleagris gallopavo and Anas platyrhynchos. Compared with the recently published peacock genome assembly, the current, superior, hybrid assembly has greater sequencing depth, fewer non-ATGC sequences, and fewer scaffolds.
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Affiliation(s)
- Ruby Dhar
- Department of Biochemistry, Room 3020, AIIMS - All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
| | - Ashikh Seethy
- Department of Biochemistry, Room 3020, AIIMS - All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
| | - Karthikeyan Pethusamy
- Department of Biochemistry, Room 3020, AIIMS - All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
| | - Sunil Singh
- Department of Biochemistry, Room 3020, AIIMS - All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
| | - Vishwajeet Rohil
- Vallabhbhai Patel Chest Institute (VPCI), Delhi University, New Delhi 110007, India
| | - Kakali Purkayastha
- Vallabhbhai Patel Chest Institute (VPCI), Delhi University, New Delhi 110007, India
| | - Indrani Mukherjee
- Department of Biochemistry, Room 3020, AIIMS - All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
| | - Sandeep Goswami
- Department of Biochemistry, Room 3020, AIIMS - All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
| | - Rakesh Singh
- Kanpur Zoo, Hastings Ave, Azad Nagar, Nawabganj, Kanpur, Uttar Pradesh 208002, India
| | - Ankita Raj
- Department of Biochemistry, Room 3020, AIIMS - All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
| | - Tryambak Srivastava
- Department of Biochemistry, Room 3020, AIIMS - All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
| | - Sovon Acharya
- Department of Biochemistry, Room 3020, AIIMS - All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
| | - Balaji Rajashekhar
- Institute of Computer Science, University of Tartu, J. Liivi, Tartu 50409, Estonia.,Celixa, 19/1 Sankey Road, Bangalore 560020, India
| | - Subhradip Karmakar
- Department of Biochemistry, Room 3020, AIIMS - All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
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25
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Cloutier A, Sackton TB, Grayson P, Clamp M, Baker AJ, Edwards SV. Whole-Genome Analyses Resolve the Phylogeny of Flightless Birds (Palaeognathae) in the Presence of an Empirical Anomaly Zone. Syst Biol 2019; 68:937-955. [PMID: 31135914 PMCID: PMC6857515 DOI: 10.1093/sysbio/syz019] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 03/06/2019] [Accepted: 04/09/2019] [Indexed: 01/17/2023] Open
Abstract
Palaeognathae represent one of the two basal lineages in modern birds, and comprise the volant (flighted) tinamous and the flightless ratites. Resolving palaeognath phylogenetic relationships has historically proved difficult, and short internal branches separating major palaeognath lineages in previous molecular phylogenies suggest that extensive incomplete lineage sorting (ILS) might have accompanied a rapid ancient divergence. Here, we investigate palaeognath relationships using genome-wide data sets of three types of noncoding nuclear markers, together totaling 20,850 loci and over 41 million base pairs of aligned sequence data. We recover a fully resolved topology placing rheas as the sister to kiwi and emu + cassowary that is congruent across marker types for two species tree methods (MP-EST and ASTRAL-II). This topology is corroborated by patterns of insertions for 4274 CR1 retroelements identified from multispecies whole-genome screening, and is robustly supported by phylogenomic subsampling analyses, with MP-EST demonstrating particularly consistent performance across subsampling replicates as compared to ASTRAL. In contrast, analyses of concatenated data supermatrices recover rheas as the sister to all other nonostrich palaeognaths, an alternative that lacks retroelement support and shows inconsistent behavior under subsampling approaches. While statistically supporting the species tree topology, conflicting patterns of retroelement insertions also occur and imply high amounts of ILS across short successive internal branches, consistent with observed patterns of gene tree heterogeneity. Coalescent simulations and topology tests indicate that the majority of observed topological incongruence among gene trees is consistent with coalescent variation rather than arising from gene tree estimation error alone, and estimated branch lengths for short successive internodes in the inferred species tree fall within the theoretical range encompassing the anomaly zone. Distributions of empirical gene trees confirm that the most common gene tree topology for each marker type differs from the species tree, signifying the existence of an empirical anomaly zone in palaeognaths.
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Affiliation(s)
- Alison Cloutier
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
- Department of Ornithology, Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Timothy B Sackton
- Informatics Group, Harvard University, 28 Oxford Street, Cambridge, MA 02138, USA
| | - Phil Grayson
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
- Department of Ornithology, Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Michele Clamp
- Informatics Group, Harvard University, 28 Oxford Street, Cambridge, MA 02138, USA
| | - Allan J Baker
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcox Street, Toronto, Ontario M5S 3B2, Canada
- Department of Natural History, Royal Ontario Museum, 100 Queen’s Park, Toronto, Ontario M5S 2C6, Canada
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
- Department of Ornithology, Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
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26
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Braun EL. An evolutionary model motivated by physicochemical properties of amino acids reveals variation among proteins. Bioinformatics 2019; 34:i350-i356. [PMID: 29950007 PMCID: PMC6022633 DOI: 10.1093/bioinformatics/bty261] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Motivation The relative rates of amino acid interchanges over evolutionary time are likely to vary among proteins. Variation in those rates has the potential to reveal information about constraints on proteins. However, the most straightforward model that could be used to estimate relative rates of amino acid substitution is parameter-rich and it is therefore impractical to use for this purpose. Results A six-parameter model of amino acid substitution that incorporates information about the physicochemical properties of amino acids was developed. It showed that amino acid side chain volume, polarity and aromaticity have major impacts on protein evolution. It also revealed variation among proteins in the relative importance of those properties. The same general approach can be used to improve the fit of empirical models such as the commonly used PAM and LG models. Availability and implementation Perl code and test data are available from https://github.com/ebraun68/sixparam. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Edward L Braun
- Department of Biology and Genetics Institute, University of Florida, Gainesville, FL, USA
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27
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A Multireference-Based Whole Genome Assembly for the Obligate Ant-Following Antbird, Rhegmatorhina melanosticta (Thamnophilidae). DIVERSITY-BASEL 2019. [DOI: 10.3390/d11090144] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Current generation high-throughput sequencing technology has facilitated the generation of more genomic-scale data than ever before, thus greatly improving our understanding of avian biology across a range of disciplines. Recent developments in linked-read sequencing (Chromium 10×) and reference-based whole-genome assembly offer an exciting prospect of more accessible chromosome-level genome sequencing in the near future. We sequenced and assembled a genome of the Hairy-crested Antbird (Rhegmatorhina melanosticta), which represents the first publicly available genome for any antbird (Thamnophilidae). Our objectives were to (1) assemble scaffolds to chromosome level based on multiple reference genomes, and report on differences relative to other genomes, (2) assess genome completeness and compare content to other related genomes, and (3) assess the suitability of linked-read sequencing technology for future studies in comparative phylogenomics and population genomics studies. Our R. melanosticta assembly was both highly contiguous (de novo scaffold N50 = 3.3 Mb, reference based N50 = 53.3 Mb) and relatively complete (contained close to 90% of evolutionarily conserved single-copy avian genes and known tetrapod ultraconserved elements). The high contiguity and completeness of this assembly enabled the genome to be successfully mapped to the chromosome level, which uncovered a consistent structural difference between R. melanosticta and other avian genomes. Our results are consistent with the observation that avian genomes are structurally conserved. Additionally, our results demonstrate the utility of linked-read sequencing for non-model genomics. Finally, we demonstrate the value of our R. melanosticta genome for future researchers by mapping reduced representation sequencing data, and by accurately reconstructing the phylogenetic relationships among a sample of thamnophilid species.
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28
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Abstract
The early radiation of Neoaves has been hypothesized to be an intractable “hard polytomy”. We explore the fundamental properties of insertion/deletion alleles (indels), an under-utilized form of genomic data with the potential to help solve this. We scored >5 million indels from >7000 pan-genomic intronic and ultraconserved element (UCE) loci in 48 representatives of all neoavian orders. We found that intronic and UCE indels exhibited less homoplasy than nucleotide (nt) data. Gene trees estimated using indel data were less resolved than those estimated using nt data. Nevertheless, Accurate Species TRee Algorithm (ASTRAL) species trees estimated using indels were generally similar to nt-based ASTRAL trees, albeit with lower support. However, the power of indel gene trees became clear when we combined them with nt gene trees, including a striking result for UCEs. The individual UCE indel and nt ASTRAL trees were incongruent with each other and with the intron ASTRAL trees; however, the combined indel+nt ASTRAL tree was much more congruent with the intronic trees. Finally, combining indel and nt data for both introns and UCEs provided sufficient power to reduce the scope of the polytomy that was previously proposed for several supraordinal lineages of Neoaves.
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29
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Weber CC, Whelan S. Physicochemical Amino Acid Properties Better Describe Substitution Rates in Large Populations. Mol Biol Evol 2019; 36:679-690. [PMID: 30668757 DOI: 10.1093/molbev/msz003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Substitutions between chemically distant amino acids are known to occur less frequently than those between more similar amino acids. This knowledge, however, is not reflected in most codon substitution models, which treat all nonsynonymous changes as if they were equivalent in terms of impact on the protein. A variety of methods for integrating chemical distances into models have been proposed, with a common approach being to divide substitutions into radical or conservative categories. Nevertheless, it remains unclear whether the resulting models describe sequence evolution better than their simpler counterparts. We propose a parametric codon model that distinguishes between radical and conservative substitutions, allowing us to assess if radical substitutions are preferentially removed by selection. Applying our new model to a range of phylogenomic data, we find differentiating between radical and conservative substitutions provides significantly better fit for large populations, but see no equivalent improvement for smaller populations. Comparing codon and amino acid models using these same data shows that alignments from large populations tend to select phylogenetic models containing information about amino acid exchangeabilities, whereas the structure of the genetic code is more important for smaller populations. Our results suggest selection against radical substitutions is, on average, more pronounced in large populations than smaller ones. The reduced observable effect of selection in smaller populations may be due to stronger genetic drift making it more challenging to detect preferences. Our results imply an important connection between the life history of a phylogenetic group and the model that best describes its evolution.
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Affiliation(s)
- Claudia C Weber
- Center for Computational Genetics and Genomics, Department of Biology, Temple University, Philadelphia, PA.,European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Simon Whelan
- Evolutionary Biology Center, Uppsala University, Uppsala, Sweden
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30
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Statistical binning leads to profound model violation due to gene tree error incurred by trying to avoid gene tree error. Mol Phylogenet Evol 2019; 134:164-171. [DOI: 10.1016/j.ympev.2019.02.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 11/30/2018] [Accepted: 02/14/2019] [Indexed: 11/19/2022]
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31
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Sarmashghi S, Bohmann K, P. Gilbert MT, Bafna V, Mirarab S. Skmer: assembly-free and alignment-free sample identification using genome skims. Genome Biol 2019; 20:34. [PMID: 30760303 PMCID: PMC6374904 DOI: 10.1186/s13059-019-1632-4] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Accepted: 01/16/2019] [Indexed: 01/10/2023] Open
Abstract
The ability to inexpensively describe taxonomic diversity is critical in this era of rapid climate and biodiversity changes. The recent genome-skimming approach extends current barcoding practices beyond short markers by applying low-pass sequencing and recovering whole organelle genomes computationally. This approach discards the nuclear DNA, which constitutes the vast majority of the data. In contrast, we suggest using all unassembled reads. We introduce an assembly-free and alignment-free tool, Skmer, to compute genomic distances between the query and reference genome skims. Skmer shows excellent accuracy in estimating distances and identifying the closest match in reference datasets.
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Affiliation(s)
- Shahab Sarmashghi
- Department of Electrical & Computer Engineering, University of California, San Diego, La Jolla, 92093 CA USA
| | - Kristine Bohmann
- Evolutionary Genomics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- School of Biological Sciences, University of East Anglia, Norwich, Norfolk UK
| | - M. Thomas P. Gilbert
- Evolutionary Genomics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- Norwegian University of Science and Technology, Trondheim, 7491 Norway
| | - Vineet Bafna
- Department of Computer Science & Engineering, University of California, San Diego, La Jolla, 92093 CA USA
| | - Siavash Mirarab
- Department of Electrical & Computer Engineering, University of California, San Diego, La Jolla, 92093 CA USA
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32
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Tambussi CP, Degrange FJ, De Mendoza RS, Sferco E, Santillana S. A stem anseriform from the early Palaeocene of Antarctica provides new key evidence in the early evolution of waterfowl. Zool J Linn Soc 2019. [DOI: 10.1093/zoolinnean/zly085] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Claudia P Tambussi
- Centro de Investigaciones en Ciencias de la Tierra (CICTERRA), Universidad Nacional de Córdoba, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Universitaria, Córdoba, Argentina
| | - Federico J Degrange
- Centro de Investigaciones en Ciencias de la Tierra (CICTERRA), Universidad Nacional de Córdoba, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Universitaria, Córdoba, Argentina
| | - Ricardo S De Mendoza
- Universidad Nacional de La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), División Paleontología Vertebrados, Facultad de Ciencias Naturales y Museo de La Plata, La Plata, Argentina
| | - Emilia Sferco
- Centro de Investigaciones en Ciencias de la Tierra (CICTERRA), Universidad Nacional de Córdoba, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Universitaria, Córdoba, Argentina
| | - Sergrio Santillana
- Instituto Antártico Argentino (IAA), General San Martín, Buenos Aires, Argentina
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Hieronymus TL, Waugh DA, Clarke JA. A new zygodactylid species indicates the persistence of stem passerines into the early Oligocene in North America. BMC Evol Biol 2019; 19:3. [PMID: 30611195 PMCID: PMC6321701 DOI: 10.1186/s12862-018-1319-6] [Citation(s) in RCA: 5] [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] [Received: 06/13/2018] [Accepted: 12/04/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The lake deposits of the informal Ruby Paper Shale unit, part of the Renova Formation of Montana, have yielded abundant plant fossils that document Late Eocene - Early Oligocene global cooling in western North America. A nearly complete small bird with feather impressions was recovered from this unit in in 1959, but has only been informally mentioned. RESULTS Here we describe this fossil and identify it as a new species of Zygodactylus, a stem lineage passerine with a zygodactyl foot. The new taxon shows morphological traits that are convergent on crown Passeriformes, including an elongate hallux, reduced body size, and a comparative shortening of proximal limb elements. The fossil documents the persistence of this lineage into the earliest Oligocene (~ 33 Ma) in North America. It is the latest occurring North American species of a group that persists in Europe until the Miocene. CONCLUSIONS Eocene-Oligocene global cooling is known to have significantly remodeled both Palearctic and Nearctic mammal faunas but its impact on related avifaunas has remained poorly understood. The geographic and temporal range expansion provided by the new taxon together with avian other taxa with limited fossil records suggests a similar pattern of retraction in North America followed by Europe.
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Affiliation(s)
- Tobin L. Hieronymus
- Department of Anatomy and Neurobiology, Northeast Ohio Medical University, 4209 State Rt 44, Rootstown, OH 44272 USA
| | - David A. Waugh
- Department of Anatomy and Neurobiology, Northeast Ohio Medical University, 4209 State Rt 44, Rootstown, OH 44272 USA
| | - Julia A. Clarke
- University of Texas at Austin, Jackson School of Geosciences, Austin, TX USA
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Formenti G, Chiara M, Poveda L, Francoijs KJ, Bonisoli-Alquati A, Canova L, Gianfranceschi L, Horner DS, Saino N. SMRT long reads and Direct Label and Stain optical maps allow the generation of a high-quality genome assembly for the European barn swallow (Hirundo rustica rustica). Gigascience 2019; 8:5202456. [PMID: 30496513 PMCID: PMC6324554 DOI: 10.1093/gigascience/giy142] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 10/06/2018] [Accepted: 11/14/2018] [Indexed: 11/12/2022] Open
Abstract
Background The barn swallow (Hirundo rustica) is a migratory bird that has been the focus of a large number of ecological, behavioral, and genetic studies. To facilitate further population genetics and genomic studies, we present a reference genome assembly for the European subspecies (H. r. rustica). Findings As part of the Genome10K effort on generating high-quality vertebrate genomes (Vertebrate Genomes Project), we have assembled a highly contiguous genome assembly using single molecule real-time (SMRT) DNA sequencing and several Bionano optical map technologies. We compared and integrated optical maps derived from both the Nick, Label, Repair, and Stain technology and from the Direct Label and Stain (DLS) technology. As proposed by Bionano, DLS more than doubled the scaffold N50 with respect to the nickase. The dual enzyme hybrid scaffold led to a further marginal increase in scaffold N50 and an overall increase of confidence in the scaffolds. After removal of haplotigs, the final assembly is approximately 1.21 Gbp in size, with a scaffold N50 value of more than 25.95 Mbp. Conclusions This high-quality genome assembly represents a valuable resource for future studies of population genetics and genomics in the barn swallow and for studies concerning the evolution of avian genomes. It also represents one of the very first genomes assembled by combining SMRT long-read sequencing with the new Bionano DLS technology for scaffolding. The quality of this assembly demonstrates the potential of this methodology to substantially increase the contiguity of genome assemblies.
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Affiliation(s)
- Giulio Formenti
- Department of Environmental Science and Policy, University of Milan, via celoria 2, Milan, 20133, Italy
| | - Matteo Chiara
- Department of Biosciences, University of Milan, via celoria 26, Milan, 20133, Italy
| | - Lucy Poveda
- Functional Genomics Center of Zurich, University of Zurich, Winterthurerstrasse 190, Zürich, 8057, Switzerland
| | | | - Andrea Bonisoli-Alquati
- Department of Biological Sciences, California State Polytechnic University, 3801 West Temple Avenue, Pomona, California, 91768, USA
| | - Luca Canova
- Department of Biochemistry, University of Pavia, Via Taramelli 12, Pavia, 27100, Italy
| | - Luca Gianfranceschi
- Department of Biosciences, University of Milan, via celoria 26, Milan, 20133, Italy
| | - David Stephen Horner
- Department of Biosciences, University of Milan, via celoria 26, Milan, 20133, Italy
| | - Nicola Saino
- Department of Environmental Science and Policy, University of Milan, via celoria 2, Milan, 20133, Italy
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Adams RH, Castoe TA. Supergene validation: A model-based protocol for assessing the accuracy of non-model-based supergene methods. MethodsX 2019; 6:2181-2188. [PMID: 31667118 PMCID: PMC6812401 DOI: 10.1016/j.mex.2019.09.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 09/19/2019] [Indexed: 11/16/2022] Open
Abstract
Genome-scale species tree inference is largely restricted to heuristic approaches that use estimated gene trees to reconstruct species-level relationships. Central to these heuristic species tree methods is the assumption that the gene trees are estimated without error. To increase the accuracy of input gene trees used to infer species trees, several techniques have recently been developed for constructing longer “supergenes” that represent sets of loci inferred to share the same genealogical history. While these supergene methods are designed to increase the amount of data for gene tree estimation by concatenating several loci into “supergenes” to increase gene tree accuracy, no formal protocols have been proposed to validate this key “supergene” concatenation step. In a recent study, we developed several supergene validation strategies for assessing the accuracy of a popular supergene method: the so-called “statistical binning” pipeline. In this article, we describe a more generalizable and model-based “supergene validation” protocol for assessing the accuracy of supergenes and supergene methods using model-based tests of phylogenetic congruency. Supergenes are validated by adopting model-based tests of topological congruence These model-based procedures out preform non-model based methods for supergene construction The results of this protocol can be used to assess the overall performance of a supergene method across a phylogenomic dataset
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Workman RE, Myrka AM, Wong GW, Tseng E, Welch KC, Timp W. Single-molecule, full-length transcript sequencing provides insight into the extreme metabolism of the ruby-throated hummingbird Archilochus colubris. Gigascience 2018; 7:1-12. [PMID: 29618047 PMCID: PMC5869288 DOI: 10.1093/gigascience/giy009] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 02/07/2018] [Indexed: 01/09/2023] Open
Abstract
Background Hummingbirds oxidize ingested nectar sugars directly to fuel foraging but cannot sustain this fuel use during fasting periods, such as during the night or during long-distance migratory flights. Instead, fasting hummingbirds switch to oxidizing stored lipids that are derived from ingested sugars. The hummingbird liver plays a key role in moderating energy homeostasis and this remarkable capacity for fuel switching. Additionally, liver is the principle location of de novo lipogenesis, which can occur at exceptionally high rates, such as during premigratory fattening. Yet understanding how this tissue and whole organism moderates energy turnover is hampered by a lack of information regarding how relevant enzymes differ in sequence, expression, and regulation. Findings We generated a de novo transcriptome of the hummingbird liver using PacBio full-length cDNA sequencing (Iso-Seq), yielding 8.6Gb of sequencing data, or 2.6M reads from 4 different size fractions. We analyzed data using the SMRTAnalysis v3.1 Iso-Seq pipeline, then clustered isoforms into gene families to generate de novo gene contigs using Cogent. We performed orthology analysis to identify closely related sequences between our transcriptome and other avian and human gene sets. Finally, we closely examined homology of critical lipid metabolism genes between our transcriptome data and avian and human genomes. Conclusions We confirmed high levels of sequence divergence within hummingbird lipogenic enzymes, suggesting a high probability of adaptive divergent function in the hepatic lipogenic pathways. Our results leverage cutting-edge technology and a novel bioinformatics pipeline to provide a first direct look at the transcriptome of this incredible organism.
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Affiliation(s)
- Rachael E Workman
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Alexander M Myrka
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada and Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - G William Wong
- Department of Physiology and Center for Metabolism and Obesity Research, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | - Kenneth C Welch
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada and Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Winston Timp
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland
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Gilbert PS, Wu J, Simon MW, Sinsheimer JS, Alfaro ME. Filtering nucleotide sites by phylogenetic signal to noise ratio increases confidence in the Neoaves phylogeny generated from ultraconserved elements. Mol Phylogenet Evol 2018; 126:116-128. [PMID: 29626666 PMCID: PMC6217972 DOI: 10.1016/j.ympev.2018.03.033] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 03/20/2018] [Accepted: 03/29/2018] [Indexed: 02/06/2023]
Abstract
Despite genome scale analyses, high-level relationships among Neoaves birds remain contentious. The placements of the Neoaves superorders are notoriously difficult to resolve because they involve deep splits followed by short internodes. Using our approach, we investigate whether filtering UCE loci on their phylogenetic signal to noise ratio helps to resolve key nodes in the Neoaves tree of life. We find that our analysis of data sets filtered for high signal to noise ratio results in topologies that are inconsistent with unfiltered results but that are congruent with whole-genome analyses. These relationships include the Columbea + Passerea sister relationship and the Phaethontimorphae + Aequornithia sister relationship. We also find increased statistical support for more recent nodes (i.e. the Pelecanidae + Ardeidae sister relationship, the Eucavitaves clade, and the Otidiformes + Musophagiformes sister relationship). We also find instances where support is reduced for well-established clades, possibly due to the removal of sites with moderate signal-to-noise ratio. Our results suggest that filtering on the basis of signal to noise ratio is a useful tool for resolving problematic splits in phylogenomic data sets.
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Affiliation(s)
- Princess S Gilbert
- Department of Ecology & Evolutionary Biology, University of California, Los Angeles, CA, USA.
| | - Jing Wu
- Henry Samueli School of Engineering and Applied Science, Department of Computer Science, University of California, Los Angeles, CA, USA
| | - Margaret W Simon
- Department of Ecology & Evolutionary Biology, University of California, Los Angeles, CA, USA
| | - Janet S Sinsheimer
- Department of Biomathematics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA; Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, CA, USA
| | - Michael E Alfaro
- Department of Ecology & Evolutionary Biology, University of California, Los Angeles, CA, USA.
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So many genes, so little time: A practical approach to divergence-time estimation in the genomic era. PLoS One 2018; 13:e0197433. [PMID: 29772020 PMCID: PMC5957400 DOI: 10.1371/journal.pone.0197433] [Citation(s) in RCA: 131] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 05/02/2018] [Indexed: 11/24/2022] Open
Abstract
Phylogenomic datasets have been successfully used to address questions involving evolutionary relationships, patterns of genome structure, signatures of selection, and gene and genome duplications. However, despite the recent explosion in genomic and transcriptomic data, the utility of these data sources for efficient divergence-time inference remains unexamined. Phylogenomic datasets pose two distinct problems for divergence-time estimation: (i) the volume of data makes inference of the entire dataset intractable, and (ii) the extent of underlying topological and rate heterogeneity across genes makes model mis-specification a real concern. “Gene shopping”, wherein a phylogenomic dataset is winnowed to a set of genes with desirable properties, represents an alternative approach that holds promise in alleviating these issues. We implemented an approach for phylogenomic datasets (available in SortaDate) that filters genes by three criteria: (i) clock-likeness, (ii) reasonable tree length (i.e., discernible information content), and (iii) least topological conflict with a focal species tree (presumed to have already been inferred). Such a winnowing procedure ensures that errors associated with model (both clock and topology) mis-specification are minimized, therefore reducing error in divergence-time estimation. We demonstrated the efficacy of this approach through simulation and applied it to published animal (Aves, Diplopoda, and Hymenoptera) and plant (carnivorous Caryophyllales, broad Caryophyllales, and Vitales) phylogenomic datasets. By quantifying rate heterogeneity across both genes and lineages we found that every empirical dataset examined included genes with clock-like, or nearly clock-like, behavior. Moreover, many datasets had genes that were clock-like, exhibited reasonable evolutionary rates, and were mostly compatible with the species tree. We identified overlap in age estimates when analyzing these filtered genes under strict clock and uncorrelated lognormal (UCLN) models. However, this overlap was often due to imprecise estimates from the UCLN model. We find that “gene shopping” can be an efficient approach to divergence-time inference for phylogenomic datasets that may otherwise be characterized by extensive gene tree heterogeneity.
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Schiavo G, Strillacci MG, Ribani A, Bovo S, Roman-Ponce SI, Cerolini S, Bertolini F, Bagnato A, Fontanesi L. Few mitochondrial DNA sequences are inserted into the turkey (Meleagris gallopavo) nuclear genome: evolutionary analyses and informativity in the domestic lineage. Anim Genet 2018. [PMID: 29521475 DOI: 10.1111/age.12648] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mitochondrial DNA (mtDNA) insertions have been detected in the nuclear genome of many eukaryotes. These sequences are pseudogenes originated by horizontal transfer of mtDNA fragments into the nuclear genome, producing nuclear DNA sequences of mitochondrial origin (numt). In this study we determined the frequency and distribution of mtDNA-originated pseudogenes in the turkey (Meleagris gallopavo) nuclear genome. The turkey reference genome (Turkey_2.01) was aligned with the reference linearized mtDNA sequence using last. A total of 32 numt sequences (corresponding to 18 numt regions derived by unique insertional events) were identified in the turkey nuclear genome (size ranging from 66 to 1415 bp; identity against the modern turkey mtDNA corresponding region ranging from 62% to 100%). Numts were distributed in nine chromosomes and in one scaffold. They derived from parts of 10 mtDNA protein-coding genes, ribosomal genes, the control region and 10 tRNA genes. Seven numt regions reported in the turkey genome were identified in orthologues positions in the Gallus gallus genome and therefore were present in the ancestral genome that in the Cretaceous originated the lineages of the modern crown Galliformes. Five recently integrated turkey numts were validated by PCR in 168 turkeys of six different domestic populations. None of the analysed numts were polymorphic (i.e. absence of the inserted sequence, as reported in numts of recent integration in other species), suggesting that the reticulate speciation model is not useful for explaining the origin of the domesticated turkey lineage.
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Affiliation(s)
- G Schiavo
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale G. Fanin 46, 40127, Bologna, Italy
| | - M G Strillacci
- Department of Veterinary Medicine, University of Milan, Via Celoria 10, 20133, Milano, Italy
| | - A Ribani
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale G. Fanin 46, 40127, Bologna, Italy
| | - S Bovo
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale G. Fanin 46, 40127, Bologna, Italy.,Biocomputing Group, Department of Biological, Geological, and Environmental Sciences, University of Bologna, Via San Giacomo 9/2, 40126, Bologna, Italy
| | - S I Roman-Ponce
- Centro Nacional de Investigación en Fisiología y Mejoramiento Animal, Instituto Nacional de Investigaciones Forestales, Agricola y Pecuarias (INIFAP), Km.1 Carretera a Colón, Auchitlán, 76280, Querétaro, Mexico
| | - S Cerolini
- Department of Veterinary Medicine, University of Milan, Via Celoria 10, 20133, Milano, Italy
| | - F Bertolini
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale G. Fanin 46, 40127, Bologna, Italy.,Department of Animal Science, Iowa State University, 2255 Kildee Hall, 50011, Ames, IA, USA
| | - A Bagnato
- Department of Veterinary Medicine, University of Milan, Via Celoria 10, 20133, Milano, Italy
| | - L Fontanesi
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale G. Fanin 46, 40127, Bologna, Italy
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40
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Edwards SV, Cloutier A, Baker AJ. Conserved Nonexonic Elements: A Novel Class of Marker for Phylogenomics. Syst Biol 2017; 66:1028-1044. [PMID: 28637293 PMCID: PMC5790140 DOI: 10.1093/sysbio/syx058] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 06/03/2017] [Accepted: 06/06/2017] [Indexed: 01/12/2023] Open
Abstract
Noncoding markers have a particular appeal as tools for phylogenomic analysis because, at least in vertebrates, they appear less subject to strong variation in GC content among lineages. Thus far, ultraconserved elements (UCEs) and introns have been the most widely used noncoding markers. Here we analyze and study the evolutionary properties of a new type of noncoding marker, conserved nonexonic elements (CNEEs), which consists of noncoding elements that are estimated to evolve slower than the neutral rate across a set of species. Although they often include UCEs, CNEEs are distinct from UCEs because they are not ultraconserved, and, most importantly, the core region alone is analyzed, rather than both the core and its flanking regions. Using a data set of 16 birds plus an alligator outgroup, and ∼3600-∼3800 loci per marker type, we found that although CNEEs were less variable than bioinformatically derived UCEs or introns and in some cases exhibited a slower approach to branch resolution as determined by phylogenomic subsampling, the quality of CNEE alignments was superior to those of the other markers, with fewer gaps and missing species. Phylogenetic resolution using coalescent approaches was comparable among the three marker types, with most nodes being fully and congruently resolved. Comparison of phylogenetic results across the three marker types indicated that one branch, the sister group to the passerine + falcon clade, was resolved differently and with moderate (>70%) bootstrap support between CNEEs and UCEs or introns. Overall, CNEEs appear to be promising as phylogenomic markers, yielding phylogenetic resolution as high as for UCEs and introns but with fewer gaps, less ambiguity in alignments and with patterns of nucleotide substitution more consistent with the assumptions of commonly used methods of phylogenetic analysis.
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Affiliation(s)
- Scott V. Edwards
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, 26 Oxford Street, Harvard University, Cambridge, MA 02138 USA
| | - Alison Cloutier
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, 26 Oxford Street, Harvard University, Cambridge, MA 02138 USA
- Department of Natural History, Royal Ontario Museum, 100 Queen’s Park, Toronto, Ontario, M5S 2C6 Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcox Street, Toronto, Ontario, M5S 3B2 Canada
| | - Allan J. Baker
- Department of Natural History, Royal Ontario Museum, 100 Queen’s Park, Toronto, Ontario, M5S 2C6 Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcox Street, Toronto, Ontario, M5S 3B2 Canada
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Dyomin A, Volodkina V, Koshel E, Galkina S, Saifitdinova A, Gaginskaya E. Evolution of ribosomal internal transcribed spacers in Deuterostomia. Mol Phylogenet Evol 2017; 116:87-96. [PMID: 28860009 DOI: 10.1016/j.ympev.2017.08.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 08/11/2017] [Accepted: 08/25/2017] [Indexed: 11/30/2022]
Abstract
Sequences of ribosomal internal transcribed spacers (ITSs) are of great importance to molecular phylogenetics and DNA barcoding, but remain unstudied in some large taxa of Deuterostomia. We have analyzed complete ITS1 and ITS2 sequences in 62 species from 16 Deuterostomia classes, with ITS sequences in 24 species from 11 classes initially obtained using unannotated contigs and raw read sequences. A general tendency for both ITS length and GC-content increase from interior to superior Deuterostomia taxa, a uniform GC-content in both ITSs within the same species, thymine content decrease in sense DNA sequences of both ITSs are shown. A possible role of GC-based gene conversion in Deuterostomia ITS evolutionary changes is hypothesized. The first example of non-LTR retrotransposon insertion into ITS sequence in Deuterostomia is described in turtle Geochelone nigra. The roles of mobile genetic element insertions in the evolution of ITS sequences in some Sauropsida taxa are discussed as well.
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Affiliation(s)
- Alexander Dyomin
- Biological Faculty of Saint-Petersburg State University, Universitetskaya emb. 7/9, Saint-Petersburg 199034, Russia.
| | - Valeria Volodkina
- Biological Faculty of Saint-Petersburg State University, Universitetskaya emb. 7/9, Saint-Petersburg 199034, Russia.
| | - Elena Koshel
- Biological Faculty of Saint-Petersburg State University, Universitetskaya emb. 7/9, Saint-Petersburg 199034, Russia.
| | - Svetlana Galkina
- Biological Faculty of Saint-Petersburg State University, Universitetskaya emb. 7/9, Saint-Petersburg 199034, Russia.
| | - Alsu Saifitdinova
- Biological Faculty of Saint-Petersburg State University, Universitetskaya emb. 7/9, Saint-Petersburg 199034, Russia.
| | - Elena Gaginskaya
- Biological Faculty of Saint-Petersburg State University, Universitetskaya emb. 7/9, Saint-Petersburg 199034, Russia.
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42
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Indrischek H, Prohaska SJ, Gurevich VV, Gurevich EV, Stadler PF. Uncovering missing pieces: duplication and deletion history of arrestins in deuterostomes. BMC Evol Biol 2017; 17:163. [PMID: 28683816 PMCID: PMC5501109 DOI: 10.1186/s12862-017-1001-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 06/19/2017] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The cytosolic arrestin proteins mediate desensitization of activated G protein-coupled receptors (GPCRs) via competition with G proteins for the active phosphorylated receptors. Arrestins in active, including receptor-bound, conformation are also transducers of signaling. Therefore, this protein family is an attractive therapeutic target. The signaling outcome is believed to be a result of structural and sequence-dependent interactions of arrestins with GPCRs and other protein partners. Here we elucidated the detailed evolution of arrestins in deuterostomes. RESULTS Identity and number of arrestin paralogs were determined searching deuterostome genomes and gene expression data. In contrast to standard gene prediction methods, our strategy first detects exons situated on different scaffolds and then solves the problem of assigning them to the correct gene. This increases both the completeness and the accuracy of the annotation in comparison to conventional database search strategies applied by the community. The employed strategy enabled us to map in detail the duplication- and deletion history of arrestin paralogs including tandem duplications, pseudogenizations and the formation of retrogenes. The two rounds of whole genome duplications in the vertebrate stem lineage gave rise to four arrestin paralogs. Surprisingly, visual arrestin ARR3 was lost in the mammalian clades Afrotheria and Xenarthra. Duplications in specific clades, on the other hand, must have given rise to new paralogs that show signatures of diversification in functional elements important for receptor binding and phosphate sensing. CONCLUSION The current study traces the functional evolution of deuterostome arrestins in unprecedented detail. Based on a precise re-annotation of the exon-intron structure at nucleotide resolution, we infer the gain and loss of paralogs and patterns of conservation, co-variation and selection.
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Affiliation(s)
- Henrike Indrischek
- Computational EvoDevo Group, Department of Computer Science, Universität Leipzig, Härtelstraße 16-18, Leipzig, D-04107, Germany.
- Bioinformatics Group, Department of Computer Science, Universität Leipzig, Härtelstraße 16-18, Leipzig, D-04107, Germany.
- Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstraße 16-18, Leipzig, D-04107, Germany.
| | - Sonja J Prohaska
- Computational EvoDevo Group, Department of Computer Science, Universität Leipzig, Härtelstraße 16-18, Leipzig, D-04107, Germany
- Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstraße 16-18, Leipzig, D-04107, Germany
| | - Vsevolod V Gurevich
- Department of Pharmacology, Vanderbilt University, 2200 Pierce Ave, Nashville, TN 37232, USA
| | - Eugenia V Gurevich
- Department of Pharmacology, Vanderbilt University, 2200 Pierce Ave, Nashville, TN 37232, USA
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science, Universität Leipzig, Härtelstraße 16-18, Leipzig, D-04107, Germany
- Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstraße 16-18, Leipzig, D-04107, Germany
- Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, Leipzig, D-04103, Germany
- Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, Leipzig, D-04103, Germany
- Department of Theoretical Chemistry, University of Vienna, Währinger Straße 17, Vienna, A-1090, Austria
- Center for non-coding RNA in Technology and Health, Grønegårdsvej 3, Frederiksberg C, DK-1870, Denmark
- Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA
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43
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Raven N, Lisovski S, Klaassen M, Lo N, Madsen T, Ho SYW, Ujvari B. Purifying selection and concerted evolution of RNA-sensing toll-like receptors in migratory waders. INFECTION GENETICS AND EVOLUTION 2017; 53:135-145. [PMID: 28528860 DOI: 10.1016/j.meegid.2017.05.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Revised: 05/15/2017] [Accepted: 05/17/2017] [Indexed: 01/05/2023]
Abstract
Migratory birds encounter a broad range of pathogens during their journeys, making them ideal models for studying immune gene evolution. Despite the potential value of these species to immunoecology and disease epidemiology, previous studies have typically focused on their adaptive immune gene repertoires. In this study, we examined the evolution of innate immune genes in three long-distance migratory waders (order Charadriiformes). We analysed two parts of the extracellular domains of two Toll-like receptors (TLR3 and TLR7) involved in virus recognition in the Sanderling (Calidris alba), Red-necked Stint (Calidris ruficollis), and Ruddy Turnstone (Arenaria interpres). Our analysis was extended to 50 avian species for which whole-genome sequences were available, including two additional waders. We found that the inferred relationships among avian TLR3 and TLR7 do not match the whole-genome phylogeny of birds. Further analyses showed that although both loci are predominantly under purifying selection, the evolution of the extracellular domain of avian TLR3 has also been driven by episodic diversifying selection. TLR7 was found to be duplicated in all five wader species and in two other orders of birds, Cuculiformes and Passeriformes. The duplication is likely to have occurred in the ancestor of each order, and the duplicated copies appear to be undergoing concerted evolution. The phylogenetic relationships of wader TLR7 matched those of the five wader species, but that of TLR3 did not. Instead, the tree inferred from TLR3 showed potential associations with the species' ecology, including migratory behaviour and exposure to pathogens. Our study demonstrates the importance of combining immunological and ecological knowledge to understand the impact of immune gene polymorphism on the evolutionary ecology of infectious diseases.
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Affiliation(s)
- Nynke Raven
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Waurn Ponds, VIC 3216, Australia
| | - Simeon Lisovski
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Waurn Ponds, VIC 3216, Australia
| | - Marcel Klaassen
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Waurn Ponds, VIC 3216, Australia
| | - Nathan Lo
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Thomas Madsen
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Waurn Ponds, VIC 3216, Australia
| | - Simon Y W Ho
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Beata Ujvari
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Waurn Ponds, VIC 3216, Australia.
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44
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Sarver BA, Keeble S, Cosart T, Tucker PK, Dean MD, Good JM. Phylogenomic Insights into Mouse Evolution Using a Pseudoreference Approach. Genome Biol Evol 2017; 9:726-739. [PMID: 28338821 PMCID: PMC5381554 DOI: 10.1093/gbe/evx034] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/20/2017] [Indexed: 12/15/2022] Open
Abstract
Comparative genomic studies are now possible across a broad range of evolutionary timescales, but the generation and analysis of genomic data across many different species still present a number of challenges. The most sophisticated genotyping and down-stream analytical frameworks are still predominantly based on comparisons to high-quality reference genomes. However, established genomic resources are often limited within a given group of species, necessitating comparisons to divergent reference genomes that could restrict or bias comparisons across a phylogenetic sample. Here, we develop a scalable pseudoreference approach to iteratively incorporate sample-specific variation into a genome reference and reduce the effects of systematic mapping bias in downstream analyses. To characterize this framework, we used targeted capture to sequence whole exomes (∼54 Mbp) in 12 lineages (ten species) of mice spanning the Mus radiation. We generated whole exome pseudoreferences for all species and show that this iterative reference-based approach improved basic genomic analyses that depend on mapping accuracy while preserving the associated annotations of the mouse reference genome. We then use these pseudoreferences to resolve evolutionary relationships among these lineages while accounting for phylogenetic discordance across the genome, contributing an important resource for comparative studies in the mouse system. We also describe patterns of genomic introgression among lineages and compare our results to previous studies. Our general approach can be applied to whole or partitioned genomic data and is easily portable to any system with sufficient genomic resources, providing a useful framework for phylogenomic studies in mice and other taxa.
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Affiliation(s)
- Brice A.J. Sarver
- Division of Biological Sciences, University of Montana, Missoula, MT
| | - Sara Keeble
- Division of Biological Sciences, University of Montana, Missoula, MT
| | - Ted Cosart
- Division of Biological Sciences, University of Montana, Missoula, MT
| | - Priscilla K. Tucker
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI
| | - Matthew D. Dean
- Molecular and Computational Biology, University of Southern California, Los Angeles, CA
| | - Jeffrey M. Good
- Division of Biological Sciences, University of Montana, Missoula, MT
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45
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Suh A. The phylogenomic forest of bird trees contains a hard polytomy at the root of Neoaves. ZOOL SCR 2016. [DOI: 10.1111/zsc.12213] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Alexander Suh
- Department of Evolutionary Biology Evolutionary Biology Centre (EBC) Uppsala University SE ‐ 752 36 Uppsala Sweden
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46
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Mason AS, Fulton JE, Hocking PM, Burt DW. A new look at the LTR retrotransposon content of the chicken genome. BMC Genomics 2016; 17:688. [PMID: 27577548 PMCID: PMC5006616 DOI: 10.1186/s12864-016-3043-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 08/24/2016] [Indexed: 11/23/2022] Open
Abstract
Background LTR retrotransposons contribute approximately 10 % of the mammalian genome, but it has been previously reported that there is a deficit of these elements in the chicken relative to both mammals and other birds. A novel LTR retrotransposon classification pipeline, LocaTR, was developed and subsequently utilised to re-examine the chicken LTR retrotransposon annotation, and determine if the proposed chicken deficit is biologically accurate or simply a technical artefact. Results Using LocaTR 3.01 % of the chicken galGal4 genome assembly was annotated as LTR retrotransposon-derived elements (nearly double the previous annotation), including 1,073 that were structurally intact. Element distribution is significantly correlated with chromosome size and is non-random within each chromosome. Elements are significantly depleted within coding regions and enriched in gene sparse areas of the genome. Over 40 % of intact elements are found in clusters, unrelated by age or genera, generally in poorly recombining regions. The transcription of most LTR retrotransposons were suppressed or incomplete, but individual domain and full length retroviral transcripts were produced in some cases, although mostly with regularly interspersed stop codons in all reading frames. Furthermore, RNAseq data from 23 diverse tissues enabled greater characterisation of the co-opted endogenous retrovirus Ovex1. This gene was shown to be expressed ubiquitously but at variable levels across different tissues. LTR retrotransposon content was found to be very variable across the avian lineage and did not correlate with either genome size or phylogenetic position. However, the extent of previous, species-specific LTR retrotransposon annotation appears to be a confounding factor. Conclusions Use of the novel LocaTR pipeline has nearly doubled the annotated LTR retrotransposon content of the chicken genome compared to previous estimates. Further analysis has described element distribution, clustering patterns and degree of expression in a variety of adult tissues, as well as in three embryonic stages. This study also enabled better characterisation of the co-opted gamma retroviral envelope gene Ovex1. Additionally, this work suggests that there is no deficit of LTR retrotransposons within the Galliformes relative to other birds, or to mammalian genomes when scaled for the three-fold difference in genome size. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3043-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andrew S Mason
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK.
| | - Janet E Fulton
- Hy-Line International, 1915 Sugar Grove Avenue, Dallas Grove, IA, 50063, USA
| | - Paul M Hocking
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - David W Burt
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK.
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47
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Edmunds SC, Li P, Hunter CI, Xiao SZ, Davidson RL, Nogoy N, Goodman L. Experiences in integrated data and research object publishing using GigaDB. INTERNATIONAL JOURNAL ON DIGITAL LIBRARIES 2016. [DOI: 10.1007/s00799-016-0174-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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48
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Suh A, Witt CC, Menger J, Sadanandan KR, Podsiadlowski L, Gerth M, Weigert A, McGuire JA, Mudge J, Edwards SV, Rheindt FE. Ancient horizontal transfers of retrotransposons between birds and ancestors of human pathogenic nematodes. Nat Commun 2016; 7:11396. [PMID: 27097561 PMCID: PMC4844689 DOI: 10.1038/ncomms11396] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 03/21/2016] [Indexed: 02/08/2023] Open
Abstract
Parasite host switches may trigger disease emergence, but prehistoric host ranges are often unknowable. Lymphatic filariasis and loiasis are major human diseases caused by the insect-borne filarial nematodes Brugia, Wuchereria and Loa. Here we show that the genomes of these nematodes and seven tropical bird lineages exclusively share a novel retrotransposon, AviRTE, resulting from horizontal transfer (HT). AviRTE subfamilies exhibit 83–99% nucleotide identity between genomes, and their phylogenetic distribution, paleobiogeography and invasion times suggest that HTs involved filarial nematodes. The HTs between bird and nematode genomes took place in two pantropical waves, >25–22 million years ago (Myr ago) involving the Brugia/Wuchereria lineage and >20–17 Myr ago involving the Loa lineage. Contrary to the expectation from the mammal-dominated host range of filarial nematodes, we hypothesize that these major human pathogens may have independently evolved from bird endoparasites that formerly infected the global breadth of avian biodiversity. Lymphatic filariasis and loiasis are diseases caused by insect-borne filarial nematodes. Here, Suh et al. identify a retrotransposon that is present in the genomes of these nematodes and seven tropical bird lineages, indicating two waves of horizontal gene transfer around 17–25 million years ago.
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Affiliation(s)
- Alexander Suh
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, SE-752 36 Uppsala, Sweden
| | - Christopher C Witt
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico 87131, USA
| | - Juliana Menger
- Department of Conservation Biology, Helmholtz Centre for Environmental Research (UFZ), D-04318 Leipzig, Germany.,Molecular Evolution and Systematics of Animals, Institute of Biology, University of Leipzig, D-04103 Leipzig, Germany.,Instituto Nacional de Pesquisas da Amazônia (INPA), AM 69067-375 Manaus, Brazil
| | - Keren R Sadanandan
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Lars Podsiadlowski
- Institute of Evolutionary Biology and Ecology, University of Bonn, D-53121 Bonn, Germany
| | - Michael Gerth
- Molecular Evolution and Systematics of Animals, Institute of Biology, University of Leipzig, D-04103 Leipzig, Germany
| | - Anne Weigert
- Molecular Evolution and Systematics of Animals, Institute of Biology, University of Leipzig, D-04103 Leipzig, Germany.,Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Jimmy A McGuire
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, California 94720, USA
| | - Joann Mudge
- National Center for Genome Resources, Santa Fe, New Mexico 87505, USA
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Frank E Rheindt
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
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49
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Kobert K, Salichos L, Rokas A, Stamatakis A. Computing the Internode Certainty and Related Measures from Partial Gene Trees. Mol Biol Evol 2016; 33:1606-17. [PMID: 26915959 PMCID: PMC4868120 DOI: 10.1093/molbev/msw040] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
We present, implement, and evaluate an approach to calculate the internode certainty (IC) and tree certainty (TC) on a given reference tree from a collection of partial gene trees. Previously, the calculation of these values was only possible from a collection of gene trees with exactly the same taxon set as the reference tree. An application to sets of partial gene trees requires mathematical corrections in the IC and TC calculations. We implement our methods in RAxML and test them on empirical datasets. These tests imply that the inclusion of partial trees does matter. However, in order to provide meaningful measurements, any dataset should also include trees containing the full species set.
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Affiliation(s)
- Kassian Kobert
- Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Leonidas Salichos
- Department of Molecular Biophysics and Biochemistry, Yale University Department of Biological Sciences, Vanderbilt University
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University Department of Biomedical Informatics, Vanderbilt University Medical Center
| | - Alexandros Stamatakis
- Heidelberg Institute for Theoretical Studies, Heidelberg, Germany Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Postfach 6980, Karlsruhe, 76128, Germany
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50
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Borowiec ML. AMAS: a fast tool for alignment manipulation and computing of summary statistics. PeerJ 2016; 4:e1660. [PMID: 26835189 DOI: 10.7287/peerj.preprints.1355] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 01/13/2016] [Indexed: 05/26/2023] Open
Abstract
The amount of data used in phylogenetics has grown explosively in the recent years and many phylogenies are inferred with hundreds or even thousands of loci and many taxa. These modern phylogenomic studies often entail separate analyses of each of the loci in addition to multiple analyses of subsets of genes or concatenated sequences. Computationally efficient tools for handling and computing properties of thousands of single-locus or large concatenated alignments are needed. Here I present AMAS (Alignment Manipulation And Summary), a tool that can be used either as a stand-alone command-line utility or as a Python package. AMAS works on amino acid and nucleotide alignments and combines capabilities of sequence manipulation with a function that calculates basic statistics. The manipulation functions include conversions among popular formats, concatenation, extracting sites and splitting according to a pre-defined partitioning scheme, creation of replicate data sets, and removal of taxa. The statistics calculated include the number of taxa, alignment length, total count of matrix cells, overall number of undetermined characters, percent of missing data, AT and GC contents (for DNA alignments), count and proportion of variable sites, count and proportion of parsimony informative sites, and counts of all characters relevant for a nucleotide or amino acid alphabet. AMAS is particularly suitable for very large alignments with hundreds of taxa and thousands of loci. It is computationally efficient, utilizes parallel processing, and performs better at concatenation than other popular tools. AMAS is a Python 3 program that relies solely on Python's core modules and needs no additional dependencies. AMAS source code and manual can be downloaded from http://github.com/marekborowiec/AMAS/ under GNU General Public License.
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Affiliation(s)
- Marek L Borowiec
- Department of Entomology and Nematology, UC Davis , Davis , United States
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