1
|
Knief U, Müller IA, Stryjewski KF, Metzler D, Sorenson MD, Wolf JBW. Evolution of chromosomal inversions across an avian radiation. Mol Biol Evol 2024:msae092. [PMID: 38743589 DOI: 10.1093/molbev/msae092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 04/05/2024] [Accepted: 05/03/2024] [Indexed: 05/16/2024] Open
Abstract
Chromosomal inversions are structural mutations that can play a prominent role in adaptation and speciation. Inversions segregating across species boundaries (trans-species inversions) are often taken as evidence for ancient balancing selection or adaptive introgression but can also be due to incomplete lineage sorting (ILS). Using whole-genome resequencing data from 18 populations of 11 recognized munia species in the genus Lonchura (N = 176 individuals), we identify four large para- and pericentric inversions ranging in size from 4 to 20 Mb. All four inversions co-segregate across multiple species and predate the numerous speciation events associated with the rapid radiation of this clade across the prehistoric Sahul (Australia, New Guinea) and Bismarck Archipelago. Using coalescent theory, we infer that trans-specificity is improbable for neutrally segregating variation despite substantial ILS characterizing this young radiation. Instead, maintenance of all three autosomal inversions (chr1, chr5, chr6) is best explained by selection acting along eco-geographic clines not observed for the collinear parts of the genome. In addition, the large sex chromosome inversion largely aligns with species boundaries and shows signatures of repeated positive selection for both alleles. This study provides evidence for trans-species inversion polymorphisms involved in both adaptation and speciation. It further highlights the importance of informing selection inference using a null model of neutral evolution derived from the collinear part of the genome.
Collapse
Affiliation(s)
- Ulrich Knief
- Division of Evolutionary Biology, Faculty of Biology, Ludwig Maximilian University of Munich, 82152 Planegg-Martinsried, Germany
- Evolutionary Biology & Ecology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Ingo A Müller
- Division of Evolutionary Biology, Faculty of Biology, Ludwig Maximilian University of Munich, 82152 Planegg-Martinsried, Germany
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 11418 Stockholm, Sweden
- Division of Systematics and Evolution, Department of Zoology, Stockholm University, 11418 Stockholm, Sweden
| | | | - Dirk Metzler
- Division of Evolutionary Biology, Faculty of Biology, Ludwig Maximilian University of Munich, 82152 Planegg-Martinsried, Germany
| | | | - Jochen B W Wolf
- Division of Evolutionary Biology, Faculty of Biology, Ludwig Maximilian University of Munich, 82152 Planegg-Martinsried, Germany
| |
Collapse
|
2
|
Merondun J, Marques CI, Andrade P, Meshcheryagina S, Galván I, Afonso S, Alves JM, Araújo PM, Bachurin G, Balacco J, Bán M, Fedrigo O, Formenti G, Fossøy F, Fülöp A, Golovatin M, Granja S, Hewson C, Honza M, Howe K, Larson G, Marton A, Moskát C, Mountcastle J, Procházka P, Red’kin Y, Sims Y, Šulc M, Tracey A, Wood JMD, Jarvis ED, Hauber ME, Carneiro M, Wolf JBW. Evolution and genetic architecture of sex-limited polymorphism in cuckoos. Sci Adv 2024; 10:eadl5255. [PMID: 38657058 PMCID: PMC11042743 DOI: 10.1126/sciadv.adl5255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 03/20/2024] [Indexed: 04/26/2024]
Abstract
Sex-limited polymorphism has evolved in many species including our own. Yet, we lack a detailed understanding of the underlying genetic variation and evolutionary processes at work. The brood parasitic common cuckoo (Cuculus canorus) is a prime example of female-limited color polymorphism, where adult males are monochromatic gray and females exhibit either gray or rufous plumage. This polymorphism has been hypothesized to be governed by negative frequency-dependent selection whereby the rarer female morph is protected against harassment by males or from mobbing by parasitized host species. Here, we show that female plumage dichromatism maps to the female-restricted genome. We further demonstrate that, consistent with balancing selection, ancestry of the rufous phenotype is shared with the likewise female dichromatic sister species, the oriental cuckoo (Cuculus optatus). This study shows that sex-specific polymorphism in trait variation can be resolved by genetic variation residing on a sex-limited chromosome and be maintained across species boundaries.
Collapse
Affiliation(s)
- Justin Merondun
- Division of Evolutionary Biology, LMU Munich, Planegg-Martinsried, Germany
- Department of Ornithology, Max Planck Institute for Biological Intelligence, Seewiesen, Germany
| | - Cristiana I. Marques
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, 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
| | - Swetlana Meshcheryagina
- Institute of Plant and Animal Ecology, Ural Branch, Russian Academy of Sciences, Yekaterinburg, Russia
| | - Ismael Galván
- Departamento de Ecología Evolutiva, Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain
| | - 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
| | - Joel M. Alves
- 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 Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
- Palaeogenomics and Bio-Archaeology Research Network, School of Archaeology, University of Oxford, Oxford, OX1 3QY, UK
| | - 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
- Department of Life Sciences, MARE–Marine and Environmental Sciences Centre/ARNET–Aquatic Research Network, University of Coimbra, Coimbra, Portugal
| | | | - Jennifer Balacco
- The Vertebrate Genome Lab, Rockefeller University, New York, NY 10065, USA
| | - Miklós Bán
- HUN-REN-UD Behavioral Ecology Research Group, Department of Evolutionary Zoology and Human Biology, University of Debrecen, Debrecen, Hungary
| | - Olivier Fedrigo
- The Vertebrate Genome Lab, Rockefeller University, New York, NY 10065, USA
| | - Giulio Formenti
- The Vertebrate Genome Lab, Rockefeller University, New York, NY 10065, USA
| | - Frode Fossøy
- Centre for Biodiversity Genetics, Norwegian Institute for Nature Research, Trondheim, Norway
| | - Attila Fülöp
- HUN-REN-UD Behavioral Ecology Research Group, Department of Evolutionary Zoology and Human Biology, University of Debrecen, Debrecen, Hungary
- Evolutionary Ecology Group, Hungarian Department of Biology and Ecology, Babeş-Bolyai University, Cluj-Napoca, Romania
- STAR-UBB Institute of Advanced Studies in Science and Technology, Babeş-Bolyai University, Cluj-Napoca, Romania
| | - Mikhail Golovatin
- Institute of Plant and Animal Ecology, Ural Branch, Russian Academy of Sciences, Yekaterinburg, Russia
| | - Sofia Granja
- 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
- Palaeogenomics and Bio-Archaeology Research Network, School of Archaeology, University of Oxford, Oxford, OX1 3QY, UK
| | | | - Marcel Honza
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Kerstin Howe
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Greger Larson
- Palaeogenomics and Bio-Archaeology Research Network, School of Archaeology, University of Oxford, Oxford, OX1 3QY, UK
| | - Attila Marton
- Evolutionary Ecology Group, Faculty of Biology and Geology, Babeș-Bolyai University, Cluj-Napoca, Romania
- Department of Evolutionary Zoology and Human Biology, University of Debrecen, Debrecen, Hungary
| | - Csaba Moskát
- Hungarian Natural History Museum, Budapest, Hungary
| | | | - Petr Procházka
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | | | - Ying Sims
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Michal Šulc
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Alan Tracey
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | | | - Erich D. Jarvis
- The Vertebrate Genome Lab, Rockefeller University, New York, NY 10065, USA
| | - Mark E. Hauber
- Advanced Science Research Center and Program in Psychology, Graduate Center of the City University of New York, New York, NY 10031, 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
| | - Jochen B. W. Wolf
- Division of Evolutionary Biology, LMU Munich, Planegg-Martinsried, Germany
| |
Collapse
|
3
|
Mirarab S, Rivas-González I, Feng S, Stiller J, Fang Q, Mai U, Hickey G, Chen G, Brajuka N, Fedrigo O, Formenti G, Wolf JBW, Howe K, Antunes A, Schierup MH, Paten B, Jarvis ED, Zhang G, Braun EL. A region of suppressed recombination misleads neoavian phylogenomics. Proc Natl Acad Sci U S A 2024; 121:e2319506121. [PMID: 38557186 PMCID: PMC11009670 DOI: 10.1073/pnas.2319506121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 02/07/2024] [Indexed: 04/04/2024] Open
Abstract
Genomes are typically mosaics of regions with different evolutionary histories. When speciation events are closely spaced in time, recombination makes the regions sharing the same history small, and the evolutionary history changes rapidly as we move along the genome. When examining rapid radiations such as the early diversification of Neoaves 66 Mya, typically no consistent history is observed across segments exceeding kilobases of the genome. Here, we report an exception. We found that a 21-Mb region in avian genomes, mapped to chicken chromosome 4, shows an extremely strong and discordance-free signal for a history different from that of the inferred species tree. Such a strong discordance-free signal, indicative of suppressed recombination across many millions of base pairs, is not observed elsewhere in the genome for any deep avian relationships. Although long regions with suppressed recombination have been documented in recently diverged species, our results pertain to relationships dating circa 65 Mya. We provide evidence that this strong signal may be due to an ancient rearrangement that blocked recombination and remained polymorphic for several million years prior to fixation. We show that the presence of this region has misled previous phylogenomic efforts with lower taxon sampling, showing the interplay between taxon and locus sampling. We predict that similar ancient rearrangements may confound phylogenetic analyses in other clades, pointing to a need for new analytical models that incorporate the possibility of such events.
Collapse
Affiliation(s)
- Siavash Mirarab
- Electrical and Computer Engineering Department, University of California, San Diego, CA95032
| | | | - Shaohong Feng
- Center for Evolutionary & Organismal Biology, Zhejiang University School of Medicine, Hangzhou310058, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou311121, China
| | - Josefin Stiller
- Section for Ecology & Evolution, Department of Biology, University of Copenhagen, København2100, Denmark
| | - Qi Fang
- BGI-Research, Shenzhen518083, China
| | - Uyen Mai
- Electrical and Computer Engineering Department, University of California, San Diego, CA95032
| | - Glenn Hickey
- Genomics Institute, University of California, Santa Cruz, CA96064
| | - Guangji Chen
- Center for Evolutionary & Organismal Biology, Zhejiang University School of Medicine, Hangzhou310058, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou311121, China
| | - Nadolina Brajuka
- Vertebrate Genome Lab, Rockefeller University, New York, NY10065
| | - Olivier Fedrigo
- Vertebrate Genome Lab, Rockefeller University, New York, NY10065
| | - Giulio Formenti
- Vertebrate Genome Lab, Rockefeller University, New York, NY10065
| | - Jochen B. W. Wolf
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximillians-Universität, Munich82152, Germany
| | - Kerstin Howe
- Tree of Life Division, Wellcome Sanger Institute, CambridgeCB10 1RQ, United Kingdom
| | - Agostinho Antunes
- Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto4099-002, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Porto4099-002, Portugal
| | | | - Benedict Paten
- Genomics Institute, University of California, Santa Cruz, CA96064
| | - Erich D. Jarvis
- Vertebrate Genome Lab, Rockefeller University, New York, NY10065
| | - Guojie Zhang
- Center for Evolutionary & Organismal Biology, Zhejiang University School of Medicine, Hangzhou310058, China
| | - Edward L. Braun
- Department of Biology, University of Florida, Gainesville, FL32611
| |
Collapse
|
4
|
Catalán A, Merondun J, Knief U, Wolf JBW. Chromatin accessibility, not 5mC methylation covaries with partial dosage compensation in crows. PLoS Genet 2023; 19:e1010901. [PMID: 37747941 PMCID: PMC10575545 DOI: 10.1371/journal.pgen.1010901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 10/13/2023] [Accepted: 08/07/2023] [Indexed: 09/27/2023] Open
Abstract
The evolution of genetic sex determination is often accompanied by degradation of the sex-limited chromosome. Male heterogametic systems have evolved convergent, epigenetic mechanisms restoring the resulting imbalance in gene dosage between diploid autosomes (AA) and the hemizygous sex chromosome (X). Female heterogametic systems (AAf Zf, AAm ZZm) tend to only show partial dosage compensation (0.5 < Zf:AAf < 1) and dosage balance (0.5
Collapse
Affiliation(s)
- Ana Catalán
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Uppsala, Sweden
- Division of Evolutionary Biology, LMU Munich, Planegg-Martinsried, Germany
| | - Justin Merondun
- Division of Evolutionary Biology, LMU Munich, Planegg-Martinsried, Germany
| | - Ulrich Knief
- Division of Evolutionary Biology, LMU Munich, Planegg-Martinsried, Germany
- Evolutionary Biology & Ecology,Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Jochen B. W. Wolf
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Uppsala, Sweden
- Division of Evolutionary Biology, LMU Munich, Planegg-Martinsried, Germany
| |
Collapse
|
5
|
Lopes F, Oliveira LR, Beux Y, Kessler A, Cárdenas-Alayza S, Majluf P, Páez-Rosas D, Chaves J, Crespo E, Brownell RL, Baylis AMM, Sepúlveda M, Franco-Trecu V, Loch C, Robertson BC, Peart CR, Wolf JBW, Bonatto SL. Genomic evidence for homoploid hybrid speciation in a marine mammal apex predator. Sci Adv 2023; 9:eadf6601. [PMID: 37134171 PMCID: PMC10156116 DOI: 10.1126/sciadv.adf6601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Hybridization is widespread and constitutes an important source of genetic variability and evolution. In animals, its role in generating novel and independent lineages (hybrid speciation) has been strongly debated, with only a few cases supported by genomic data. The South American fur seal (SAfs) Arctocephalus australis is a marine apex predator of Pacific and Atlantic waters, with a disjunct set of populations in Peru and Northern Chile [Peruvian fur seal (Pfs)] with controversial taxonomic status. We demonstrate, using complete genome and reduced representation sequencing, that the Pfs is a genetically distinct species with an admixed genome that originated from hybridization between the SAfs and the Galapagos fur seal (Arctocephalus galapagoensis) ~400,000 years ago. Our results strongly support the origin of Pfs by homoploid hybrid speciation over alternative introgression scenarios. This study highlights the role of hybridization in promoting species-level biodiversity in large vertebrates.
Collapse
Affiliation(s)
- Fernando Lopes
- Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, PUCRS, Porto Alegre, Brazil
- Laboratório de Ecologia de Mamíferos, Universidade do Vale do Rio dos Sinos, São Leopoldo, Brazil
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Larissa R Oliveira
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
- Grupo de Estudos de Mamíferos Aquáticos do Rio Grande do Sul (GEMARS), Torres, Brazil
| | - Yago Beux
- Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, PUCRS, Porto Alegre, Brazil
| | - Amanda Kessler
- Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, PUCRS, Porto Alegre, Brazil
| | - Susana Cárdenas-Alayza
- Centro para la Sostenibilidad Ambiental, Universidad Peruana Cayetano Heredia, Lima, Peru
- Departamento de Ciencias Biológicas y Fisiológicas, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Patricia Majluf
- Centro para la Sostenibilidad Ambiental, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Diego Páez-Rosas
- Colegio de Ciencias Biológicas y Ambientales, COCIBA, Universidad San Francisco de Quito, Quito, Ecuador
- Dirección del Parque Nacional Galápagos, Oficina Técnica San Cristobal, Islas Galápagos, Ecuador
| | - Jaime Chaves
- Colegio de Ciencias Biológicas y Ambientales, COCIBA, Universidad San Francisco de Quito, Quito, Ecuador
- Galapagos Science Center, Puerto Baquerizo Moreno, Ecuador
- Department of Biology, San Francisco State University, 1800 Holloway Ave, San Francisco, CA, USA
| | - Enrique Crespo
- Laboratório de Mamíferos Marinos, CESIMAR - CCT CENPAT, CONICET, Puerto Madryn, Argentina
| | - Robert L Brownell
- Southwest Fisheries Science Center, NOAA Fisheries, La Jolla, CA, USA
| | | | - Maritza Sepúlveda
- Centro de Investigación y Gestión de Recursos Naturales (CIGREN), Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile
| | - Valentina Franco-Trecu
- Departamento de Ecología y Evolución, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Carolina Loch
- Sir John Walsh Research Institute, Faculty of Dentistry, University of Otago, Dunedin, New Zealand
| | | | - Claire R Peart
- Division of Evolutionary Biology, LMU Munich, München, Germany
| | - Jochen B W Wolf
- Division of Evolutionary Biology, LMU Munich, München, Germany
| | - Sandro L Bonatto
- Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, PUCRS, Porto Alegre, Brazil
| |
Collapse
|
6
|
Bolnick DI, Hund AK, Nosil P, Peng F, Ravinet M, Stankowski S, Subramanian S, Wolf JBW, Yukilevich R. A multivariate view of the speciation continuum. Evolution 2023; 77:318-328. [PMID: 36622661 DOI: 10.1093/evolut/qpac004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 09/26/2022] [Accepted: 10/26/2022] [Indexed: 01/10/2023]
Abstract
The concept of a "speciation continuum" has gained popularity in recent decades. It emphasizes speciation as a continuous process that may be studied by comparing contemporary population pairs that show differing levels of divergence. In their recent perspective article in Evolution, Stankowski and Ravinet provided a valuable service by formally defining the speciation continuum as a continuum of reproductive isolation, based on opinions gathered from a survey of speciation researchers. While we agree that the speciation continuum has been a useful concept to advance the understanding of the speciation process, some intrinsic limitations exist. Here, we advocate for a multivariate extension, the speciation hypercube, first proposed by Dieckmann et al. in 2004, but rarely used since. We extend the idea of the speciation cube and suggest it has strong conceptual and practical advantages over a one-dimensional model. We illustrate how the speciation hypercube can be used to visualize and compare different speciation trajectories, providing new insights into the processes and mechanisms of speciation. A key strength of the speciation hypercube is that it provides a unifying framework for speciation research, as it allows questions from apparently disparate subfields to be addressed in a single conceptual model.
Collapse
Affiliation(s)
- Daniel I Bolnick
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, United States
| | - Amanda K Hund
- Department of Biology, Carleton College, Northfield, MN, United States
| | - Patrik Nosil
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3, Montpellier, France
| | - Foen Peng
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, United States.,Department of Biology, Haverford College, Haverford, PA, United States
| | - Mark Ravinet
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | | | - Swapna Subramanian
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, United States
| | - Jochen B W Wolf
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany
| | - Roman Yukilevich
- Department of Biology, Union College, Schenectady, NY, United States
| |
Collapse
|
7
|
Westerdahl H, Mellinger S, Sigeman H, Kutschera VE, Proux-Wéra E, Lundberg M, Weissensteiner M, Churcher A, Bunikis I, Hansson B, Wolf JBW, Strandh M. The genomic architecture of the passerine MHC region: high repeat content and contrasting evolutionary histories of single copy and tandemly duplicated MHC genes. Mol Ecol Resour 2022; 22:2379-2395. [PMID: 35348299 DOI: 10.1111/1755-0998.13614] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 03/09/2022] [Accepted: 03/23/2022] [Indexed: 12/01/2022]
Abstract
The Major Histocompatibility Complex (MHC) is of central importance to the immune system, and an optimal MHC diversity is believed to maximize pathogen elimination. Birds show substantial variation in MHC diversity, ranging from few genes in most bird orders to very many genes in passerines. Our understanding of the evolutionary trajectories of the MHC in passerines is hampered by lack of data on genomic organization. Therefore, we assemble and annotate the MHC genomic region of the great reed warbler (Acrocephalus arundinaceus), using long-read sequencing and optical mapping. The MHC region is large (>5.5Mb), characterized by structural changes compared to hitherto investigated bird orders and shows higher repeat content than the genome average. These features were supported by analyses in three additional passerines. MHC genes in passerines are found in two different chromosomal arrangements, either as single copy MHC genes located among non-MHC genes, or as tandemly duplicated tightly linked MHC genes. Some single copy MHC genes are old and putative orthologs among species. In contrast tandemly duplicated MHC genes are monophyletic within species and have evolved by simultaneous gene duplication of several MHC genes. Structural differences in the MHC genomic region among bird orders seem substantial compared to mammals and have possibly been fuelled by clade-specific immune system adaptations. Our study provides methodological guidance in characterizing complex genomic regions, constitutes a resource for MHC research in birds, and calls for a revision of the general belief that avian MHC has a conserved gene order and small size compared to mammals.
Collapse
Affiliation(s)
- Helena Westerdahl
- Molecular Ecology and Evolution Lab, Department of Biology, Lund University, Sölvegatan 37, SE-223 62, Lund, Sweden
| | - Samantha Mellinger
- Molecular Ecology and Evolution Lab, Department of Biology, Lund University, Sölvegatan 37, SE-223 62, Lund, Sweden
| | - Hanna Sigeman
- Molecular Ecology and Evolution Lab, Department of Biology, Lund University, Sölvegatan 37, SE-223 62, Lund, Sweden
| | - Verena E Kutschera
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Box 1031, SE-17121, Solna, Sweden
| | - Estelle Proux-Wéra
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Box 1031, SE-17121, Solna, Sweden
| | - Max Lundberg
- Molecular Ecology and Evolution Lab, Department of Biology, Lund University, Sölvegatan 37, SE-223 62, Lund, Sweden
| | - Matthias Weissensteiner
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Grosshaderner Str. 2, 82152, Planegg-Martinsried, Germany
| | - Allison Churcher
- National Bioinformatics Infrastructure Sweden, Department of Molecular Biology, Umeå University, SE-901 87, Umeå, Sweden
| | - Ignas Bunikis
- Uppsala Genome Center, Science for Life Laboratory, Dept. of Immunology, Genetics and Pathology, Uppsala University, BMC, Box 815, SE-752 37, Uppsala, Sweden
| | - Bengt Hansson
- Molecular Ecology and Evolution Lab, Department of Biology, Lund University, Sölvegatan 37, SE-223 62, Lund, Sweden
| | - Jochen B W Wolf
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Grosshaderner Str. 2, 82152, Planegg-Martinsried, Germany
| | - Maria Strandh
- Molecular Ecology and Evolution Lab, Department of Biology, Lund University, Sölvegatan 37, SE-223 62, Lund, Sweden
| |
Collapse
|
8
|
Tusso S, Suo F, Liang Y, Du LL, Wolf JBW. Reactivation of transposable elements following hybridization in fission yeast. Genome Res 2021; 32:324-336. [PMID: 34907076 PMCID: PMC8805722 DOI: 10.1101/gr.276056.121] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 12/09/2021] [Indexed: 11/29/2022]
Abstract
Hybridization is thought to reactivate transposable elements (TEs) that were efficiently suppressed in the genomes of the parental hosts. Here, we provide evidence for this “genomic shock hypothesis” in the fission yeast Schizosaccharomyces pombe. In this species, two divergent lineages (Sp and Sk) have experienced recent, likely human-induced, hybridization. We used long-read sequencing data to assemble genomes of 37 samples derived from 31 S. pombe strains spanning a wide range of ancestral admixture proportions. A comprehensive TE inventory revealed exclusive presence of long terminal repeat (LTR) retrotransposons. Sequence analysis of active full-length elements, as well as solo LTRs, revealed a complex history of homologous recombination. Population genetic analyses of syntenic sequences placed insertion of many solo LTRs before the split of the Sp and Sk lineages. Most full-length elements were inserted more recently, after hybridization. With the exception of a single full-length element with signs of positive selection, both solo LTRs and, in particular, full-length elements carry signatures of purifying selection indicating effective removal by the host. Consistent with reactivation upon hybridization, the number of full-length LTR retrotransposons, varying extensively from zero to 87 among strains, significantly increases with the degree of genomic admixture. This study gives a detailed account of global TE diversity in S. pombe, documents complex recombination histories within TE elements, and provides evidence for the “genomic shock hypothesis.”
Collapse
Affiliation(s)
| | - Fang Suo
- National Institute of Biological Sciences
| | - Yue Liang
- National Institute of Biological Sciences
| | - Li-Lin Du
- National Institute of Biological Sciences
| | | |
Collapse
|
9
|
Schielzeth H, Wolf JBW. Community genomics: a community-wide perspective on within-species genetic diversity. Am J Bot 2021; 108:2108-2111. [PMID: 34767249 DOI: 10.1002/ajb2.1796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 09/07/2021] [Indexed: 06/13/2023]
Affiliation(s)
- Holger Schielzeth
- Institute of Ecology and Evolution, Friedrich Schiller University Jena, Germany
| | - Jochen B W Wolf
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Germany
| |
Collapse
|
10
|
Metzler D, Knief U, Peñalba JV, Wolf JBW. Assortative mating and epistatic mating-trait architecture induce complex movement of the crow hybrid zone. Evolution 2021; 75:3154-3174. [PMID: 34694633 DOI: 10.1111/evo.14386] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 10/06/2021] [Indexed: 12/20/2022]
Abstract
Hybrid zones provide a window into the evolutionary processes governing species divergence. Yet, the contribution of mate choice to the temporal and spatial stability of hybrid zones remains poorly explored. Here, we investigate the effects of assortative mating on hybrid-zone dynamics by means of a mathematical model parameterized with phenotype and genotype data from the hybrid zone between all-black carrion and gray-coated hooded crows. In the best-fit model, narrow clines of the two mating-trait loci were maintained by a moderate degree of assortative mating inducing pre- and postzygotic isolation via positive frequency-dependent selection. Epistasis between the two loci induced hybrid-zone movement in favor of alleles conveying dark plumage followed by a shift in the opposite direction favoring gray-coated phenotypes ∼ 1 200 generations after secondary contact. Unlinked neutral loci diffused near-unimpeded across the zone. These results were generally robust to the choice of matching rule (self-referencing or parental imprinting) and effects of genetic drift. Overall, this study illustrates under which conditions assortative mating can maintain steep clines in mating-trait loci without generalizing to genome-wide reproductive isolation. It further emphasizes the importance of the genetic mating-trait architecture for spatio-temporal hybrid-zone dynamics.
Collapse
Affiliation(s)
- Dirk Metzler
- Faculty of Biology, Division of Evolutionary Biology, LMU Munich, Munich, 80539, Germany
| | - Ulrich Knief
- Faculty of Biology, Division of Evolutionary Biology, LMU Munich, Munich, 80539, Germany
| | - Joshua V Peñalba
- Faculty of Biology, Division of Evolutionary Biology, LMU Munich, Munich, 80539, Germany
| | - Jochen B W Wolf
- Faculty of Biology, Division of Evolutionary Biology, LMU Munich, Munich, 80539, Germany
| |
Collapse
|
11
|
Peart CR, Williams C, Pophaly SD, Neely BA, Gulland FMD, Adams DJ, Ng BL, Cheng W, Goebel ME, Fedrigo O, Haase B, Mountcastle J, Fungtammasan A, Formenti G, Collins J, Wood J, Sims Y, Torrance J, Tracey A, Howe K, Rhie A, Hoffman JI, Johnson J, Jarvis ED, Breen M, Wolf JBW. Hi-C scaffolded short- and long-read genome assemblies of the California sea lion are broadly consistent for syntenic inference across 45 million years of evolution. Mol Ecol Resour 2021; 21:2455-2470. [PMID: 34097816 PMCID: PMC9732816 DOI: 10.1111/1755-0998.13443] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 05/06/2021] [Accepted: 05/26/2021] [Indexed: 12/13/2022]
Abstract
With the advent of chromatin-interaction maps, chromosome-level genome assemblies have become a reality for a wide range of organisms. Scaffolding quality is, however, difficult to judge. To explore this gap, we generated multiple chromosome-scale genome assemblies of an emerging wild animal model for carcinogenesis, the California sea lion (Zalophus californianus). Short-read assemblies were scaffolded with two independent chromatin interaction mapping data sets (Hi-C and Chicago), and long-read assemblies with three data types (Hi-C, optical maps and 10X linked reads) following the "Vertebrate Genomes Project (VGP)" pipeline. In both approaches, 18 major scaffolds recovered the karyotype (2n = 36), with scaffold N50s of 138 and 147 Mb, respectively. Synteny relationships at the chromosome level with other pinniped genomes (2n = 32-36), ferret (2n = 34), red panda (2n = 36) and domestic dog (2n = 78) were consistent across approaches and recovered known fissions and fusions. Comparative chromosome painting and multicolour chromosome tiling with a panel of 264 genome-integrated single-locus canine bacterial artificial chromosome probes provided independent evaluation of genome organization. Broad-scale discrepancies between the approaches were observed within chromosomes, most commonly in translocations centred around centromeres and telomeres, which were better resolved in the VGP assembly. Genomic and cytological approaches agreed on near-perfect synteny of the X chromosome, and in combination allowed detailed investigation of autosomal rearrangements between dog and sea lion. This study presents high-quality genomes of an emerging cancer model and highlights that even highly fragmented short-read assemblies scaffolded with Hi-C can yield reliable chromosome-level scaffolds suitable for comparative genomic analyses.
Collapse
Affiliation(s)
- Claire R. Peart
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Munchen, Germany
| | - Christina Williams
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
| | - Saurabh D. Pophaly
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Munchen, Germany,Max Planck institute for Plant Breeding Research, Cologne, Germany
| | - Benjamin A. Neely
- National Institute of Standards and Technology, NIST Charleston, Charleston, South Carolina, USA
| | - Frances M. D. Gulland
- Karen Dryer Wildlife Health Center, University of California Davis, Davis, California, USA
| | - David J. Adams
- Cytometry Core Facility, Wellcome Sanger Institute, Cambridge, UK
| | - Bee Ling Ng
- Cytometry Core Facility, Wellcome Sanger Institute, Cambridge, UK
| | - William Cheng
- Cytometry Core Facility, Wellcome Sanger Institute, Cambridge, UK
| | - Michael E. Goebel
- Institute of Marine Science, University of California Santa Cruz, Santa Cruz, California, USA
| | - Olivier Fedrigo
- Vertebrate Genome Lab, The Rockefeller University, New York City, New York, USA
| | - Bettina Haase
- Vertebrate Genome Lab, The Rockefeller University, New York City, New York, USA
| | | | | | - Giulio Formenti
- Vertebrate Genome Lab, The Rockefeller University, New York City, New York, USA,Laboratory of Neurogenetics of Language, The Rockefeller University, New York City, New York, USA
| | - Joanna Collins
- Tree of Life Programme, Wellcome Sanger Institute, Cambridge, UK
| | - Jonathan Wood
- Tree of Life Programme, Wellcome Sanger Institute, Cambridge, UK
| | - Ying Sims
- Tree of Life Programme, Wellcome Sanger Institute, Cambridge, UK
| | - James Torrance
- Tree of Life Programme, Wellcome Sanger Institute, Cambridge, UK
| | - Alan Tracey
- Tree of Life Programme, Wellcome Sanger Institute, Cambridge, UK
| | - Kerstin Howe
- Tree of Life Programme, Wellcome Sanger Institute, Cambridge, UK
| | - Arang Rhie
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
| | - Joseph I. Hoffman
- Department of Animal Behaviour, Bielefeld University, Bielefeld, Germany,British Antarctic Survey, Cambridge, UK
| | - Jeremy Johnson
- Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, USA
| | - Erich D. Jarvis
- Vertebrate Genome Lab, The Rockefeller University, New York City, New York, USA,Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - Matthew Breen
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA,Comparative Medicine Institute, North Carolina State University, Raleigh, North Carolina, USA
| | - Jochen B. W. Wolf
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Munchen, Germany
| |
Collapse
|
12
|
Knief U, Forstmeier W, Kempenaers B, Wolf JBW. A sex chromosome inversion is associated with copy number variation of mitochondrial DNA in zebra finch sperm. R Soc Open Sci 2021; 8:211025. [PMID: 34540261 PMCID: PMC8437020 DOI: 10.1098/rsos.211025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 07/14/2021] [Indexed: 06/13/2023]
Abstract
The propulsion of sperm cells via movement of the flagellum is of vital importance for successful fertilization. While the exact mechanism of energy production for this movement varies between species, in avian species energy is thought to come predominantly from the mitochondria located in the sperm midpiece. Larger midpieces may contain more mitochondria, which should enhance the energetic capacity and possibly promote mobility. Due to an inversion polymorphism on their sex chromosome TguZ, zebra finches (Taeniopygia guttata castanotis) exhibit large within-species variation in sperm midpiece length, and those sperm with the longest midpieces swim the fastest. Here, we test through quantitative real-time PCR in zebra finch ejaculates whether the inversion genotype has an effect on the copy number of mitochondrial DNA (mtDNA). We find that zebra finches carrying the derived allele (correlated with longer sperm midpieces) have more copies of the mtDNA in their ejaculates than those homozygous for the ancestral allele (shorter midpieces). We suggest downstream effects of mtDNA copy number variation on the rate of adenosine triphosphate production, which in turn may influence sperm swimming speed and fertilization success. Central components of gamete energy metabolism may thus be the proximate cause for a fitness-relevant genetic polymorphism, stabilizing a megabase-scale inversion at an intermediate allele frequency in the wild.
Collapse
Affiliation(s)
- Ulrich Knief
- Division of Evolutionary Biology, Faculty of Biology, Ludwig Maximilian University of Munich, Planegg-Martinsried 82152, Germany
| | - Wolfgang Forstmeier
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology, Seewiesen 82319, Germany
| | - Bart Kempenaers
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology, Seewiesen 82319, Germany
| | - Jochen B. W. Wolf
- Division of Evolutionary Biology, Faculty of Biology, Ludwig Maximilian University of Munich, Planegg-Martinsried 82152, Germany
| |
Collapse
|
13
|
Foote AD, Hooper R, Alexander A, Baird RW, Baker CS, Ballance L, Barlow J, Brownlow A, Collins T, Constantine R, Dalla Rosa L, Davison NJ, Durban JW, Esteban R, Excoffier L, Martin SLF, Forney KA, Gerrodette T, Gilbert MTP, Guinet C, Hanson MB, Li S, Martin MD, Robertson KM, Samarra FIP, de Stephanis R, Tavares SB, Tixier P, Totterdell JA, Wade P, Wolf JBW, Fan G, Zhang Y, Morin PA. Runs of homozygosity in killer whale genomes provide a global record of demographic histories. Mol Ecol 2021; 30:6162-6177. [PMID: 34416064 DOI: 10.1111/mec.16137] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 08/10/2021] [Accepted: 08/18/2021] [Indexed: 02/06/2023]
Abstract
Runs of homozygosity (ROH) occur when offspring inherit haplotypes that are identical by descent from each parent. Length distributions of ROH are informative about population history; specifically, the probability of inbreeding mediated by mating system and/or population demography. Here, we investigated whether variation in killer whale (Orcinus orca) demographic history is reflected in genome-wide heterozygosity and ROH length distributions, using a global data set of 26 genomes representative of geographic and ecotypic variation in this species, and two F1 admixed individuals with Pacific-Atlantic parentage. We first reconstructed demographic history for each population as changes in effective population size through time using the pairwise sequential Markovian coalescent (PSMC) method. We found a subset of populations declined in effective population size during the Late Pleistocene, while others had more stable demography. Genomes inferred to have undergone ancestral declines in effective population size, were autozygous at hundreds of short ROH (<1 Mb), reflecting high background relatedness due to coalescence of haplotypes deep within the pedigree. In contrast, longer and therefore younger ROH (>1.5 Mb) were found in low latitude populations, and populations of known conservation concern. These include a Scottish killer whale, for which 37.8% of the autosomes were comprised of ROH >1.5 Mb in length. The fate of this population, in which only two adult males have been sighted in the past five years, and zero fecundity over the last two decades, may be inextricably linked to its demographic history and consequential inbreeding depression.
Collapse
Affiliation(s)
- Andrew D Foote
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU, Trondheim, Norway.,Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Bangor, Gwynedd, UK.,CMPG, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Rebecca Hooper
- University of Exeter, Penryn Campus, Penryn, Cornwall, UK
| | - Alana Alexander
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | | | - Charles Scott Baker
- Marine Mammal Institute, Oregon State University, Newport, Oregon, USA.,School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Lisa Ballance
- Marine Mammal Institute, Oregon State University, Newport, Oregon, USA.,Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanographic and Atmospheric Administration, La Jolla, California, USA
| | - Jay Barlow
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanographic and Atmospheric Administration, La Jolla, California, USA
| | - Andrew Brownlow
- Scottish Marine Animal Stranding Scheme, Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - Tim Collins
- Ocean Giants Program, Wildlife Conservation Society, New York City, New York
| | | | - Luciano Dalla Rosa
- Laboratório de Ecologia e Conservação da Megafauna Marinha, Instituto de Oceanografia, Universidade Federal do Rio Grande, Rio Grande, Brazil
| | - Nicholas J Davison
- Scottish Marine Animal Stranding Scheme, Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - John W Durban
- Marine Mammal Institute, Oregon State University, Newport, Oregon, USA.,Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanographic and Atmospheric Administration, La Jolla, California, USA
| | - Ruth Esteban
- CIRCE, Conservation, Information and Research on Cetaceans, Algeciras, Spain
| | - Laurent Excoffier
- CMPG, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Sarah L Fordyce Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU, Trondheim, Norway
| | - Karin A Forney
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Moss Landing, California, USA.,Moss Landing Marine Laboratories, San Jose State University, Moss Landing, California, USA
| | - Tim Gerrodette
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanographic and Atmospheric Administration, La Jolla, California, USA
| | - M Thomas P Gilbert
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU, Trondheim, Norway.,Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Christophe Guinet
- UMR 7372 La Rochelle Université - CNRS, Centre d'Etudes Biologiques de Chizé (CEBC), Villiers-en-Bois, France
| | - M Bradley Hanson
- National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Northwest Fisheries Science Center, Seattle, Washington, USA
| | - Songhai Li
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-Sea Science and Engineering, Chinese Academy of Science, Sanya, China
| | - Michael D Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU, Trondheim, Norway
| | - Kelly M Robertson
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanographic and Atmospheric Administration, La Jolla, California, USA
| | - Filipa I P Samarra
- University of Iceland's Institute of Research Centres, Vestmannaeyjar, Iceland
| | - Renaud de Stephanis
- CIRCE, Conservation, Information and Research on Cetaceans, Algeciras, Spain
| | - Sara B Tavares
- Scottish Oceans Institute, East Sands, University of St. Andrews, St. Andrews, UK.,Cetacean Research Program, Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, Canada
| | - Paul Tixier
- UMR 7372 La Rochelle Université - CNRS, Centre d'Etudes Biologiques de Chizé (CEBC), Villiers-en-Bois, France.,MARBEC Université de Montpellier-CNRS-IFREMER-IRD, Sète, France
| | | | - Paul Wade
- National Marine Mammal Laboratory, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Alaska Fisheries Science Center, Seattle, Washington, USA
| | - Jochen B W Wolf
- Section of Evolutionary Biology, Department of Biology II, Ludwig Maximilian University of Munich, Planegg-Martinsried, Germany
| | - Guangyi Fan
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China.,BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Yaolei Zhang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China.,Translational Immunology group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Phillip A Morin
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanographic and Atmospheric Administration, La Jolla, California, USA
| |
Collapse
|
14
|
Peart CR, Tusso S, Pophaly SD, Botero-Castro F, Wu CC, Aurioles-Gamboa D, Baird AB, Bickham JW, Forcada J, Galimberti F, Gemmell NJ, Hoffman JI, Kovacs KM, Kunnasranta M, Lydersen C, Nyman T, de Oliveira LR, Orr AJ, Sanvito S, Valtonen M, Shafer ABA, Wolf JBW. Author Correction: Determinants of genetic variation across eco-evolutionary scales in pinnipeds. Nat Ecol Evol 2021; 5:1317. [PMID: 34262153 DOI: 10.1038/s41559-021-01529-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Claire R Peart
- Science of Life Laboratories and Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden.,Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany
| | - Sergio Tusso
- Science of Life Laboratories and Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden.,Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany
| | - Saurabh D Pophaly
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany.,Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Fidel Botero-Castro
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany
| | - Chi-Chih Wu
- Science of Life Laboratories and Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden
| | - David Aurioles-Gamboa
- Laboratorio de Ecología de Pinnípedos 'Burney J. Le Boeuf', Centro Interdisciplinario de Ciencias Marinas, Instituto Politécnico Nacional, Baja California Sur, México
| | - Amy B Baird
- Department of Natural Sciences, University of Houston-Downtown, Houston, TX, USA
| | - John W Bickham
- Department of Ecology and Conservation Biology, Texas A&M University, College Station, TX, USA
| | - Jaume Forcada
- British Antarctic Survey, Natural Environment Research Council, Cambridge, UK
| | | | - Neil J Gemmell
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Joseph I Hoffman
- British Antarctic Survey, Natural Environment Research Council, Cambridge, UK.,Department of Animal Behaviour, Bielefeld University, Bielefeld, Germany
| | - Kit M Kovacs
- Norwegian Polar Institute, Fram Centre, Tromsø, Norway
| | - Mervi Kunnasranta
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland.,Natural Resources Institute Finland (Luke), Joensuu, Finland
| | | | - Tommi Nyman
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland.,Department of Ecosystems in the Barents Region, Norwegian Institute of Bioeconomy Research, Svanhovd Research Station, Svanvik, Norway
| | | | - Anthony J Orr
- National Oceanic and Atmospheric Administration, National Marine Fisheries Service, Alaska Fisheries Science Center, Marine Mammal Laboratory, Seattle, WA, USA
| | - Simona Sanvito
- Elephant Seal Research Group, Sea Lion Island, Falkland Islands
| | - Mia Valtonen
- The Saimaa Ringed Seal Genome Project, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Aaron B A Shafer
- Science of Life Laboratories and Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden. .,Forensic Science & Environmental Life Sciences, Trent University, Peterborough, Ontario, Canada.
| | - Jochen B W Wolf
- Science of Life Laboratories and Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden. .,Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany.
| |
Collapse
|
15
|
Weissensteiner MH, Bunikis I, Catalán A, Francoijs KJ, Knief U, Heim W, Peona V, Pophaly SD, Sedlazeck FJ, Suh A, Warmuth VM, Wolf JBW. Author Correction: Discovery and population genomics of structural variation in a songbird genus. Nat Commun 2021; 12:3163. [PMID: 34017009 PMCID: PMC8138003 DOI: 10.1038/s41467-021-23640-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Matthias H Weissensteiner
- Department of Evolutionary Biology and Science for Life Laboratory, Uppsala University, 752 36, Uppsala, Sweden. .,Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Grosshaderner Str. 2, 82152, Planegg-Martinsried, Germany. .,Department of Biology, Pennsylvania State University, 310 Wartik Lab, PA, 16802, USA.
| | - Ignas Bunikis
- Uppsala Genome Center, Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, BMC, Box 815752 37, Uppsala, Sweden
| | - Ana Catalán
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Grosshaderner Str. 2, 82152, Planegg-Martinsried, Germany
| | | | - Ulrich Knief
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Grosshaderner Str. 2, 82152, Planegg-Martinsried, Germany
| | - Wieland Heim
- Institute of Landscsape Ecology, University of Münster, Heisenbergstrasse 2, 48149, Münster, Germany
| | - Valentina Peona
- Department of Evolutionary Biology and Science for Life Laboratory, Uppsala University, 752 36, Uppsala, Sweden.,Department of Organismal Biology - Systematic Biology, Uppsala University, 752 36, Uppsala, Sweden
| | - Saurabh D Pophaly
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Grosshaderner Str. 2, 82152, Planegg-Martinsried, Germany.,Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center at Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Alexander Suh
- Department of Evolutionary Biology and Science for Life Laboratory, Uppsala University, 752 36, Uppsala, Sweden.,Department of Organismal Biology - Systematic Biology, Uppsala University, 752 36, Uppsala, Sweden.,School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TU, UK
| | - Vera M Warmuth
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Grosshaderner Str. 2, 82152, Planegg-Martinsried, Germany
| | - Jochen B W Wolf
- Department of Evolutionary Biology and Science for Life Laboratory, Uppsala University, 752 36, Uppsala, Sweden. .,Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Grosshaderner Str. 2, 82152, Planegg-Martinsried, Germany.
| |
Collapse
|
16
|
Tusso S, Nieuwenhuis BPS, Weissensteiner B, Immler S, Wolf JBW. Experimental evolution of adaptive divergence under varying degrees of gene flow. Nat Ecol Evol 2021; 5:338-349. [PMID: 33432131 DOI: 10.1038/s41559-020-01363-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 11/12/2020] [Indexed: 01/28/2023]
Abstract
Adaptive divergence is the key evolutionary process generating biodiversity by means of natural selection. Yet, the conditions under which it can arise in the presence of gene flow remain contentious. To address this question, we subjected 132 sexually reproducing fission yeast populations, sourced from two independent genetic backgrounds, to disruptive ecological selection and manipulated the level of migration between environments. Contrary to theoretical expectations, adaptive divergence was most pronounced when migration was either absent (allopatry) or maximal (sympatry), but was much reduced at intermediate rates (parapatry and local mating). This effect was apparent across central life-history components (survival, asexual growth and mating) but differed in magnitude between ancestral genetic backgrounds. The evolution of some fitness components was constrained by pervasive negative correlations (trade-off between asexual growth and mating), while others changed direction under the influence of migration (for example, survival and mating). In allopatry, adaptive divergence was mainly conferred by standing genetic variation and resulted in ecological specialization. In sympatry, divergence was mainly mediated by novel mutations enriched in a subset of genes and was characterized by the repeated emergence of two strategies: an ecological generalist and an asexual growth specialist. Multiple loci showed consistent evidence for antagonistic pleiotropy across migration treatments providing a conceptual link between adaptation and divergence. This evolve-and-resequence experiment shows that rapid ecological differentiation can arise even under high rates of gene flow. It further highlights that adaptive trajectories are governed by complex interactions of gene flow, ancestral variation and genetic correlations.
Collapse
Affiliation(s)
- Sergio Tusso
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität Munich, Munich, Germany. .,Science for Life Laboratory, Uppsala University, Uppsala, Sweden. .,Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden.
| | - Bart P S Nieuwenhuis
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität Munich, Munich, Germany
| | - Bernadette Weissensteiner
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität Munich, Munich, Germany
| | - Simone Immler
- Science for Life Laboratory, Uppsala University, Uppsala, Sweden.,Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden.,School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Jochen B W Wolf
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität Munich, Munich, Germany. .,Science for Life Laboratory, Uppsala University, Uppsala, Sweden. .,Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden.
| |
Collapse
|
17
|
Lopes F, Oliveira LR, Kessler A, Beux Y, Crespo E, Cárdenas-Alayza S, Majluf P, Sepúlveda M, Brownell RL, Franco-Trecu V, Páez-Rosas D, Chaves J, Loch C, Robertson BC, Acevedo-Whitehouse K, Elorriaga-Verplancken FR, Kirkman SP, Peart CR, Wolf JBW, Bonatto SL. Phylogenomic Discordance in the Eared Seals is best explained by Incomplete Lineage Sorting following Explosive Radiation in the Southern Hemisphere. Syst Biol 2020; 70:786-802. [PMID: 33367817 DOI: 10.1093/sysbio/syaa099] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 12/02/2020] [Accepted: 12/08/2020] [Indexed: 12/25/2022] Open
Abstract
The phylogeny and systematics of fur seals and sea lions (Otariidae) have long been studied with diverse data types, including an increasing amount of molecular data. However, only a few phylogenetic relationships have reached acceptance because of strong gene-tree species tree discordance. Divergence times estimates in the group also vary largely between studies. These uncertainties impeded the understanding of the biogeographical history of the group, such as when and how trans-equatorial dispersal and subsequent speciation events occurred. Here, we used high-coverage genome-wide sequencing for 14 of the 15 species of Otariidae to elucidate the phylogeny of the family and its bearing on the taxonomy and biogeographical history. Despite extreme topological discordance among gene trees, we found a fully supported species tree that agrees with the few well-accepted relationships and establishes monophyly of the genus Arctocephalus. Our data support a relatively recent trans-hemispheric dispersal at the base of a southern clade, which rapidly diversified into six major lineages between 3 and 2.5 Ma. Otaria diverged first, followed by Phocarctos and then four major lineages within Arctocephalus. However, we found Zalophus to be nonmonophyletic, with California (Zalophus californianus) and Steller sea lions (Eumetopias jubatus) grouping closer than the Galapagos sea lion (Zalophus wollebaeki) with evidence for introgression between the two genera. Overall, the high degree of genealogical discordance was best explained by incomplete lineage sorting resulting from quasi-simultaneous speciation within the southern clade with introgresssion playing a subordinate role in explaining the incongruence among and within prior phylogenetic studies of the family. [Hybridization; ILS; phylogenomics; Pleistocene; Pliocene; monophyly.].
Collapse
Affiliation(s)
- Fernando Lopes
- Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, 90619-900 Porto Alegre, RS, Brazil.,Laboratório de Ecologia de Mamíferos, Universidade do Vale do Rio dos Sinos, São Leopoldo, RS, Brazil
| | - Larissa R Oliveira
- Laboratório de Ecologia de Mamíferos, Universidade do Vale do Rio dos Sinos, São Leopoldo, RS, Brazil.,GEMARS, Grupo de Estudos de Mamíferos Aquáticos do Rio Grande do Sul, 95560-000 Torres, RS, Brazil
| | - Amanda Kessler
- Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, 90619-900 Porto Alegre, RS, Brazil
| | - Yago Beux
- Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, 90619-900 Porto Alegre, RS, Brazil
| | - Enrique Crespo
- Centro Nacional Patagónico - CENPAT, CONICET, Puerto Madryn, Argentina
| | - Susana Cárdenas-Alayza
- Centro para la Sostenibilidad Ambiental, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Patricia Majluf
- Centro para la Sostenibilidad Ambiental, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Maritza Sepúlveda
- Centro de Investigación y Gestión de Recursos Naturales (CIGREN), Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile
| | - Robert L Brownell
- Southwest Fisheries Science Center, National Oceanic and Atmospheric Administration, NOAA, La Jolla, USA
| | - Valentina Franco-Trecu
- Departamento de Ecología y Evolución, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Diego Páez-Rosas
- Colegio de Ciencias Biológicas y Ambientales, COCIBA, Universidad San Francisco de Quito, Quito, Ecuador
| | - Jaime Chaves
- Colegio de Ciencias Biológicas y Ambientales, COCIBA, Universidad San Francisco de Quito, Quito, Ecuador.,Department of Biology, San Francisco State University, 1800 Holloway Ave, San Francisco, CA, USA
| | - Carolina Loch
- Sir John Walsh Research Institute, Faculty of Dentistry, University of Otago, Dunedin, New Zealand
| | | | - Karina Acevedo-Whitehouse
- Unit for Basic and Applied Microbiology, School of Natural Sciences, Universidad Autónoma de Querétaro, Querétaro, Mexico
| | | | - Stephen P Kirkman
- Department of Environmental Affairs, Oceans and Coasts, Cape Town, South Africa
| | - Claire R Peart
- Department Biologie II, Division of Evolutionary Biology, Ludwig-Maximilians-Universität München, Münich, Germany
| | - Jochen B W Wolf
- Department Biologie II, Division of Evolutionary Biology, Ludwig-Maximilians-Universität München, Münich, Germany
| | - Sandro L Bonatto
- Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, 90619-900 Porto Alegre, RS, Brazil
| |
Collapse
|
18
|
Dussex N, Kutschera VE, Wiberg RAW, Parker DJ, Hunt GR, Gray RD, Rutherford K, Abe H, Fleischer RC, Ritchie MG, Rutz C, Wolf JBW, Gemmell NJ. A genome-wide investigation of adaptive signatures in protein-coding genes related to tool behaviour in New Caledonian and Hawaiian crows. Mol Ecol 2020; 30:973-986. [PMID: 33305388 DOI: 10.1111/mec.15775] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 11/27/2020] [Accepted: 12/04/2020] [Indexed: 12/30/2022]
Abstract
Very few animals habitually manufacture and use tools. It has been suggested that advanced tool behaviour co-evolves with a suite of behavioural, morphological and life history traits. In fact, there are indications for such an adaptive complex in tool-using crows (genus Corvus species). Here, we sequenced the genomes of two habitually tool-using and ten non-tool-using crow species to search for genomic signatures associated with a tool-using lifestyle. Using comparative genomic and population genetic approaches, we screened for signals of selection in protein-coding genes in the tool-using New Caledonian and Hawaiian crows. While we detected signals of recent selection in New Caledonian crows near genes associated with bill morphology, our data indicate that genetic changes in these two lineages are surprisingly subtle, with little evidence at present for convergence. We explore the biological explanations for these findings, such as the relative roles of gene regulation and protein-coding changes, as well as the possibility that statistical power to detect selection in recently diverged lineages may have been insufficient. Our study contributes to a growing body of literature aiming to decipher the genetic basis of recently evolved complex behaviour.
Collapse
Affiliation(s)
- Nicolas Dussex
- Department of Anatomy, University of Otago, Dunedin, New Zealand.,Department of Bioinformatics and Genetics, Centre for Palaeogenetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Verena E Kutschera
- Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden.,Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - R Axel W Wiberg
- Centre for Biological Diversity, School of Biology, University of St Andrews, St Andrews, UK.,Department of Environmental Sciences, Evolutionary Biology, University of Basel, Basel, Switzerland
| | - Darren J Parker
- Centre for Biological Diversity, School of Biology, University of St Andrews, St Andrews, UK.,Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Gavin R Hunt
- University of Auckland, Science Centre 302, Auckland, New Zealand
| | - Russell D Gray
- University of Auckland, Science Centre 302, Auckland, New Zealand.,Max Planck Institute for the Science of Human History, Jena, Germany
| | - Kim Rutherford
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Hideaki Abe
- Department of Anatomy, University of Otago, Dunedin, New Zealand.,Wildlife Research Center, Kyoto University, Kyoto, Japan
| | - Robert C Fleischer
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, Washington, DC, USA
| | - Michael G Ritchie
- Centre for Biological Diversity, School of Biology, University of St Andrews, St Andrews, UK
| | - Christian Rutz
- Centre for Biological Diversity, School of Biology, University of St Andrews, St Andrews, UK
| | - Jochen B W Wolf
- Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden.,Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany
| | - Neil J Gemmell
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| |
Collapse
|
19
|
Kutschera VE, Poelstra JW, Botero-Castro F, Dussex N, Gemmell NJ, Hunt GR, Ritchie MG, Rutz C, Wiberg RAW, Wolf JBW. Purifying Selection in Corvids Is Less Efficient on Islands. Mol Biol Evol 2020; 37:469-474. [PMID: 31633794 PMCID: PMC6993847 DOI: 10.1093/molbev/msz233] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Theory predicts that deleterious mutations accumulate more readily in small populations. As a consequence, mutation load is expected to be elevated in species where life-history strategies and geographic or historical contingencies reduce the number of reproducing individuals. Yet, few studies have empirically tested this prediction using genome-wide data in a comparative framework. We collected whole-genome sequencing data for 147 individuals across seven crow species (Corvus spp.). For each species, we estimated the distribution of fitness effects of deleterious mutations and compared it with proxies of the effective population size Ne. Island species with comparatively smaller geographic range sizes had a significantly increased mutation load. These results support the view that small populations have an elevated risk of mutational meltdown, which may contribute to the higher extinction rates observed in island species.
Collapse
Affiliation(s)
- Verena E Kutschera
- Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden.,Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | | | - Fidel Botero-Castro
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany
| | - Nicolas Dussex
- Department of Anatomy, University of Otago, Dunedin, New Zealand.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Neil J Gemmell
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | | | - Michael G Ritchie
- Centre for Biological Diversity, School of Biology, University of St Andrews, St Andrews, United Kingdom
| | - Christian Rutz
- Centre for Biological Diversity, School of Biology, University of St Andrews, St Andrews, United Kingdom
| | - R Axel W Wiberg
- Centre for Biological Diversity, School of Biology, University of St Andrews, St Andrews, United Kingdom.,Department of Environmental Sciences, Evolutionary Biology, University of Basel, Basel, Switzerland
| | - Jochen B W Wolf
- Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden.,Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany
| |
Collapse
|
20
|
Weissensteiner MH, Bunikis I, Catalán A, Francoijs KJ, Knief U, Heim W, Peona V, Pophaly SD, Sedlazeck FJ, Suh A, Warmuth VM, Wolf JBW. Discovery and population genomics of structural variation in a songbird genus. Nat Commun 2020; 11:3403. [PMID: 32636372 PMCID: PMC7341801 DOI: 10.1038/s41467-020-17195-4] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 06/16/2020] [Indexed: 02/07/2023] Open
Abstract
Structural variation (SV) constitutes an important type of genetic mutations providing the raw material for evolution. Here, we uncover the genome-wide spectrum of intra- and interspecific SV segregating in natural populations of seven songbird species in the genus Corvus. Combining short-read (N = 127) and long-read re-sequencing (N = 31), as well as optical mapping (N = 16), we apply both assembly- and read mapping approaches to detect SV and characterize a total of 220,452 insertions, deletions and inversions. We exploit sampling across wide phylogenetic timescales to validate SV genotypes and assess the contribution of SV to evolutionary processes in an avian model of incipient speciation. We reveal an evolutionary young (~530,000 years) cis-acting 2.25-kb LTR retrotransposon insertion reducing expression of the NDP gene with consequences for premating isolation. Our results attest to the wealth and evolutionary significance of SV segregating in natural populations and highlight the need for reliable SV genotyping.
Collapse
Affiliation(s)
- Matthias H Weissensteiner
- Department of Evolutionary Biology and Science for Life Laboratory, Uppsala University, 752 36, Uppsala, Sweden.
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Grosshaderner Str. 2, 82152, Planegg-Martinsried, Germany.
- Department of Biology, Pennsylvania State University, 310 Wartik Lab, University Park, PA, 16802, USA.
| | - Ignas Bunikis
- Uppsala Genome Center, Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, BMC, Box 815, 752 37, Uppsala, Sweden
| | - Ana Catalán
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Grosshaderner Str. 2, 82152, Planegg-Martinsried, Germany
| | | | - Ulrich Knief
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Grosshaderner Str. 2, 82152, Planegg-Martinsried, Germany
| | - Wieland Heim
- Institute of Landscsape Ecology, University of Münster, Heisenbergstrasse 2, 48149, Münster, Germany
| | - Valentina Peona
- Department of Evolutionary Biology and Science for Life Laboratory, Uppsala University, 752 36, Uppsala, Sweden
- Department of Organismal Biology - Systematic Biology, Uppsala University, 752 36, Uppsala, Sweden
| | - Saurabh D Pophaly
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Grosshaderner Str. 2, 82152, Planegg-Martinsried, Germany
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center at Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Alexander Suh
- Department of Evolutionary Biology and Science for Life Laboratory, Uppsala University, 752 36, Uppsala, Sweden
- Department of Organismal Biology - Systematic Biology, Uppsala University, 752 36, Uppsala, Sweden
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TU, UK
| | - Vera M Warmuth
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Grosshaderner Str. 2, 82152, Planegg-Martinsried, Germany
| | - Jochen B W Wolf
- Department of Evolutionary Biology and Science for Life Laboratory, Uppsala University, 752 36, Uppsala, Sweden.
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Grosshaderner Str. 2, 82152, Planegg-Martinsried, Germany.
| |
Collapse
|
21
|
Tao YT, Suo F, Tusso S, Wang YK, Huang S, Wolf JBW, Du LL. Intraspecific Diversity of Fission Yeast Mitochondrial Genomes. Genome Biol Evol 2020; 11:2312-2329. [PMID: 31364709 PMCID: PMC6736045 DOI: 10.1093/gbe/evz165] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/18/2019] [Indexed: 02/07/2023] Open
Abstract
The fission yeast Schizosaccharomyces pombe is an important model organism, but its natural diversity and evolutionary history remain under-studied. In particular, the population genomics of the S. pombe mitochondrial genome (mitogenome) has not been thoroughly investigated. Here, we assembled the complete circular-mapping mitogenomes of 192 S. pombe isolates de novo, and found that these mitogenomes belong to 69 nonidentical sequence types ranging from 17,618 to 26,910 bp in length. Using the assembled mitogenomes, we identified 20 errors in the reference mitogenome and discovered two previously unknown mitochondrial introns. Analyzing sequence diversity of these 69 types of mitogenomes revealed two highly distinct clades, with only three mitogenomes exhibiting signs of inter-clade recombination. This diversity pattern suggests that currently available S. pombe isolates descend from two long-separated ancestral lineages. This conclusion is corroborated by the diversity pattern of the recombination-repressed K-region located between donor mating-type loci mat2 and mat3 in the nuclear genome. We estimated that the two ancestral S. pombe lineages diverged about 31 million generations ago. These findings shed new light on the evolution of S. pombe and the data sets generated in this study will facilitate future research on genome evolution.
Collapse
Affiliation(s)
- Yu-Tian Tao
- National Institute of Biological Sciences, Beijing, China.,Graduate School of Peking Union Medical College, Beijing, China
| | - Fang Suo
- National Institute of Biological Sciences, Beijing, China
| | - Sergio Tusso
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany.,Science for Life Laboratories, Department of Evolutionary Biology, Uppsala University, Sweden
| | - Yan-Kai Wang
- National Institute of Biological Sciences, Beijing, China
| | - Song Huang
- National Institute of Biological Sciences, Beijing, China.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
| | - Jochen B W Wolf
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany.,Science for Life Laboratories, Department of Evolutionary Biology, Uppsala University, Sweden
| | - Li-Lin Du
- National Institute of Biological Sciences, Beijing, China.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
| |
Collapse
|
22
|
Knief U, Bossu CM, Wolf JBW. Extra-pair paternity as a strategy to reduce the costs of heterospecific reproduction? Insights from the crow hybrid zone. J Evol Biol 2020; 33:727-733. [PMID: 32069366 DOI: 10.1111/jeb.13607] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 01/22/2020] [Accepted: 02/17/2020] [Indexed: 12/30/2022]
Abstract
Within hybrid zones of socially monogamous species, the number of mating opportunities with a conspecific can be limited. As a consequence, individuals may mate with a heterospecific (social) partner despite possible fitness costs to their hybrid offspring. Extra-pair copulations with a conspecific may thus arise as a possible post hoc strategy to reduce the costs of hybridization. We here assessed the rate of extra-pair paternity in the hybrid zone between all-black carrion crows (Corvus (corone) corone) and grey hooded crows (C. (c.) cornix) and tested whether extra-pair paternity (EPP) was more likely in broods where parents differed in plumage colour. The proportion of broods with at least one extra-pair offspring and the proportion of extra-pair offspring were low overall (6.98% and 2.90%, respectively) with no evidence of hybrid broods having higher EPP rates than purebred nests.
Collapse
Affiliation(s)
- Ulrich Knief
- Division of Evolutionary Biology, Ludwig Maximilian University of Munich, Planegg-Martinsried, Germany
| | - Christen M Bossu
- Science for Life Laboratories and Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden.,Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, CA, USA
| | - Jochen B W Wolf
- Division of Evolutionary Biology, Ludwig Maximilian University of Munich, Planegg-Martinsried, Germany.,Science for Life Laboratories and Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden
| |
Collapse
|
23
|
Mugal CF, Kutschera VE, Botero-Castro F, Wolf JBW, Kaj I. Polymorphism Data Assist Estimation of the Nonsynonymous over Synonymous Fixation Rate Ratio ω for Closely Related Species. Mol Biol Evol 2020; 37:260-279. [PMID: 31504782 PMCID: PMC6984366 DOI: 10.1093/molbev/msz203] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The ratio of nonsynonymous over synonymous sequence divergence, dN/dS, is a widely used estimate of the nonsynonymous over synonymous fixation rate ratio ω, which measures the extent to which natural selection modulates protein sequence evolution. Its computation is based on a phylogenetic approach and computes sequence divergence of protein-coding DNA between species, traditionally using a single representative DNA sequence per species. This approach ignores the presence of polymorphisms and relies on the indirect assumption that new mutations fix instantaneously, an assumption which is generally violated and reasonable only for distantly related species. The violation of the underlying assumption leads to a time-dependence of sequence divergence, and biased estimates of ω in particular for closely related species, where the contribution of ancestral and lineage-specific polymorphisms to sequence divergence is substantial. We here use a time-dependent Poisson random field model to derive an analytical expression of dN/dS as a function of divergence time and sample size. We then extend our framework to the estimation of the proportion of adaptive protein evolution α. This mathematical treatment enables us to show that the joint usage of polymorphism and divergence data can assist the inference of selection for closely related species. Moreover, our analytical results provide the basis for a protocol for the estimation of ω and α for closely related species. We illustrate the performance of this protocol by studying a population data set of four corvid species, which involves the estimation of ω and α at different time-scales and for several choices of sample sizes.
Collapse
Affiliation(s)
- Carina F Mugal
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Verena E Kutschera
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden.,Science for Life Laboratory, Stockholm University, Stockholm, Sweden.,Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Fidel Botero-Castro
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany
| | - Jochen B W Wolf
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden.,Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany
| | - Ingemar Kaj
- Department of Mathematics, Uppsala University, Uppsala, Sweden
| |
Collapse
|
24
|
Holtmann B, Buskas J, Steele M, Solokovskis K, Wolf JBW. Dominance relationships and coalitionary aggression against conspecifics in female carrion crows. Sci Rep 2019; 9:15922. [PMID: 31685854 PMCID: PMC6828704 DOI: 10.1038/s41598-019-52177-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 10/07/2019] [Indexed: 11/21/2022] Open
Abstract
Cooperation is a prevailing feature of many animal systems. Coalitionary aggression, where a group of individuals engages in coordinated behaviour to the detriment of conspecific targets, is a form of cooperation involving complex social interactions. To date, evidence has been dominated by studies in humans and other primates with a clear bias towards studies of male-male coalitions. We here characterize coalitionary aggression behaviour in a group of female carrion crows consisting of recruitment, coordinated chase, and attack. The individual of highest social rank liaised with the second most dominant individual to engage in coordinated chase and attack of a lower ranked crow on several occasions. Despite active intervention by the third most highly ranked individual opposing the offenders, the attack finally resulted in the death of the victim. All individuals were unrelated, of the same sex, and naïve to the behaviour excluding kinship, reproduction, and social learning as possible drivers. Instead, the coalition may reflect a strategy of the dominant individual to secure long-term social benefits. Overall, the study provides evidence that members of the crow family engage in coordinated alliances directed against conspecifics as a possible means to manipulate their social environment.
Collapse
Affiliation(s)
- Benedikt Holtmann
- Division of Evolutionary Biology, Department of Biology, LMU Munich, Großhaderner Straße 2, 82152, Planegg-Martinsried, Germany. .,Behavioural Ecology Group, Department of Biology, LMU Munich, Großhaderner Straße 2, 82152, Planegg-Martinsried, Germany.
| | - Julia Buskas
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 14-18, 75236, Uppsala, Sweden
| | - Matthew Steele
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 14-18, 75236, Uppsala, Sweden
| | - Kristaps Solokovskis
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 14-18, 75236, Uppsala, Sweden
| | - Jochen B W Wolf
- Division of Evolutionary Biology, Department of Biology, LMU Munich, Großhaderner Straße 2, 82152, Planegg-Martinsried, Germany.,Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 14-18, 75236, Uppsala, Sweden
| |
Collapse
|
25
|
Abstract
Mutation and recombination are key evolutionary processes governing phenotypic variation and reproductive isolation. We here demonstrate that biodiversity within all globally known strains of Schizosaccharomyces pombe arose through admixture between two divergent ancestral lineages. Initial hybridization was inferred to have occurred ∼20-60 sexual outcrossing generations ago consistent with recent, human-induced migration at the onset of intensified transcontinental trade. Species-wide heritable phenotypic variation was explained near-exclusively by strain-specific arrangements of alternating ancestry components with evidence for transgressive segregation. Reproductive compatibility between strains was likewise predicted by the degree of shared ancestry. To assess the genetic determinants of ancestry block distribution across the genome, we characterized the type, frequency, and position of structural genomic variation using nanopore and single-molecule real-time sequencing. Despite being associated with double-strand break initiation points, over 800 segregating structural variants exerted overall little influence on the introgression landscape or on reproductive compatibility between strains. In contrast, we found strong ancestry disequilibrium consistent with negative epistatic selection shaping genomic ancestry combinations during the course of hybridization. This study provides a detailed, experimentally tractable example that genomes of natural populations are mosaics reflecting different evolutionary histories. Exploiting genome-wide heterogeneity in the history of ancestral recombination and lineage-specific mutations sheds new light on the population history of S. pombe and highlights the importance of hybridization as a creative force in generating biodiversity.
Collapse
Affiliation(s)
- Sergio Tusso
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany
- Department of Evolutionary Biology, Science for Life Laboratories, Uppsala University, Uppsala, Sweden
| | - Bart P S Nieuwenhuis
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - John W Davey
- Bioscience Technology Facility, Department of Biology, University of York, York, United Kingdom
| | - Daniel C Jeffares
- Department of Biology, University of York, York, United Kingdom
- York Biomedical Research Institute (YBRI), University of York, York, United Kingdom
| | - Jochen B W Wolf
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany
- Department of Evolutionary Biology, Science for Life Laboratories, Uppsala University, Uppsala, Sweden
| |
Collapse
|
26
|
Ellegren H, Wolf JBW. Parallelism in genomic landscapes of differentiation, conserved genomic features and the role of linked selection. J Evol Biol 2019; 30:1516-1518. [PMID: 28786191 DOI: 10.1111/jeb.13113] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 05/01/2017] [Accepted: 05/03/2017] [Indexed: 01/01/2023]
Affiliation(s)
- H Ellegren
- Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden
| | - J B W Wolf
- Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden.,Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| |
Collapse
|
27
|
Foote AD, Martin MD, Louis M, Pacheco G, Robertson KM, Sinding MHS, Amaral AR, Baird RW, Baker CS, Ballance L, Barlow J, Brownlow A, Collins T, Constantine R, Dabin W, Dalla Rosa L, Davison NJ, Durban JW, Esteban R, Ferguson SH, Gerrodette T, Guinet C, Hanson MB, Hoggard W, Matthews CJD, Samarra FIP, de Stephanis R, Tavares SB, Tixier P, Totterdell JA, Wade P, Excoffier L, Gilbert MTP, Wolf JBW, Morin PA. Killer whale genomes reveal a complex history of recurrent admixture and vicariance. Mol Ecol 2019; 28:3427-3444. [PMID: 31131963 DOI: 10.1111/mec.15099] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 04/06/2019] [Accepted: 04/08/2019] [Indexed: 02/06/2023]
Abstract
Reconstruction of the demographic and evolutionary history of populations assuming a consensus tree-like relationship can mask more complex scenarios, which are prevalent in nature. An emerging genomic toolset, which has been most comprehensively harnessed in the reconstruction of human evolutionary history, enables molecular ecologists to elucidate complex population histories. Killer whales have limited extrinsic barriers to dispersal and have radiated globally, and are therefore a good candidate model for the application of such tools. Here, we analyse a global data set of killer whale genomes in a rare attempt to elucidate global population structure in a nonhuman species. We identify a pattern of genetic homogenisation at lower latitudes and the greatest differentiation at high latitudes, even between currently sympatric lineages. The processes underlying the major axis of structure include high drift at the edge of species' range, likely associated with founder effects and allelic surfing during postglacial range expansion. Divergence between Antarctic and non-Antarctic lineages is further driven by ancestry segments with up to four-fold older coalescence time than the genome-wide average; relicts of a previous vicariance during an earlier glacial cycle. Our study further underpins that episodic gene flow is ubiquitous in natural populations, and can occur across great distances and after substantial periods of isolation between populations. Thus, understanding the evolutionary history of a species requires comprehensive geographic sampling and genome-wide data to sample the variation in ancestry within individuals.
Collapse
Affiliation(s)
- Andrew D Foote
- CMPG, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | | | - Marie Louis
- Department of Biology, Section for Evolutionary Genomics, University of Copenhagen, Copenhagen, Denmark.,Scottish Oceans Institute, East Sands, University of St. Andrews, St. Andrews, UK
| | - George Pacheco
- Department of Biology, Section for Evolutionary Genomics, University of Copenhagen, Copenhagen, Denmark
| | - Kelly M Robertson
- Marine Mammal and Turtle Division, National Marine Fisheries Service, National Oceanographic and Atmospheric Administration, Southwest Fisheries Science Center, La Jolla, California
| | - Mikkel-Holger S Sinding
- Department of Biology, Section for Evolutionary Genomics, University of Copenhagen, Copenhagen, Denmark.,Greenland Institute of Natural Resources, Nuuk, Greenland
| | - Ana R Amaral
- American Museum of Natural History, New York City, New York.,Faculdade de Ciências Universidade de Lisboa, Centre for Ecology, Evolution and Environmental Changes, Lisboa, Portugal
| | | | - Charles Scott Baker
- Department of Fisheries and Wildlife, Marine Mammal Institute, Oregon State University, Newport, Oregon.,School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Lisa Ballance
- Marine Mammal and Turtle Division, National Marine Fisheries Service, National Oceanographic and Atmospheric Administration, Southwest Fisheries Science Center, La Jolla, California
| | - Jay Barlow
- Marine Mammal and Turtle Division, National Marine Fisheries Service, National Oceanographic and Atmospheric Administration, Southwest Fisheries Science Center, La Jolla, California
| | - Andrew Brownlow
- Scottish Marine Animal Stranding Scheme, SRUC Veterinary Services Drummondhill, Inverness, UK
| | - Tim Collins
- Ocean Giants Program, Wildlife Conservation Society, New York City, New York
| | | | - Willy Dabin
- Observatoire Pelagis, Université de La Rochelle-CNRS, La Rochelle, France
| | - Luciano Dalla Rosa
- Laboratório de Ecologia e Conservação da Megafauna Marinha, Instituto de Oceanografia, Universidade Federal do Rio Grande, Rio Grande, Brazil
| | - Nicholas J Davison
- Scottish Marine Animal Stranding Scheme, SRUC Veterinary Services Drummondhill, Inverness, UK
| | - John W Durban
- Marine Mammal and Turtle Division, National Marine Fisheries Service, National Oceanographic and Atmospheric Administration, Southwest Fisheries Science Center, La Jolla, California
| | - Ruth Esteban
- CIRCE, Conservation, Information and Research on Cetaceans, Algeciras, Spain
| | | | - Tim Gerrodette
- Marine Mammal and Turtle Division, National Marine Fisheries Service, National Oceanographic and Atmospheric Administration, Southwest Fisheries Science Center, La Jolla, California
| | - Christophe Guinet
- Centre d'Etudes Biologiques de Chizé (CEBC), CNRS-ULR, UMR, Chizé, France
| | - M Bradley Hanson
- National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Northwest Fisheries Science Center, Seattle, Washington
| | - Wayne Hoggard
- National Marine Fisheries Service, NOAA, Southeast Fisheries Science Center, Pascagoula, Mississippi
| | | | | | - Renaud de Stephanis
- CIRCE, Conservation, Information and Research on Cetaceans, Algeciras, Spain
| | - Sara B Tavares
- Scottish Oceans Institute, East Sands, University of St. Andrews, St. Andrews, UK
| | - Paul Tixier
- Centre d'Etudes Biologiques de Chizé (CEBC), CNRS-ULR, UMR, Chizé, France.,School of Life and Environmental Sciences (Burwood Campus), Deakin University, Geelong, Victoria, Australia
| | - John A Totterdell
- Marine Information and Research Group-Australia (MIRG), Quinns Rocks, Western Australia, Australia
| | - Paul Wade
- National Marine Mammal Laboratory, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Alaska Fisheries Science Center, Seattle, Washington
| | - Laurent Excoffier
- CMPG, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - M Thomas P Gilbert
- NTNU University Museum, Trondheim, Norway.,Department of Biology, Section for Evolutionary Genomics, University of Copenhagen, Copenhagen, Denmark
| | - Jochen B W Wolf
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany.,Department of Evolutionary Biology, Science of Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Phillip A Morin
- Marine Mammal and Turtle Division, National Marine Fisheries Service, National Oceanographic and Atmospheric Administration, Southwest Fisheries Science Center, La Jolla, California
| |
Collapse
|
28
|
Grosser S, Sauer J, Paijmans AJ, Caspers BA, Forcada J, Wolf JBW, Hoffman JI. Fur seal microbiota are shaped by the social and physical environment, show mother–offspring similarities and are associated with host genetic quality. Mol Ecol 2019; 28:2406-2422. [DOI: 10.1111/mec.15070] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 02/26/2019] [Indexed: 12/15/2022]
Affiliation(s)
- Stefanie Grosser
- Department of Animal Behaviour Bielefeld University Bielefeld Germany
- Division of Evolutionary Biology, Faculty of Biology LMU Munich Planegg‐Martinsried Germany
| | - Jan Sauer
- Department of Animal Behaviour Bielefeld University Bielefeld Germany
| | | | | | - Jaume Forcada
- British Antarctic Survey Natural Environment Research Council Cambridge UK
| | - Jochen B. W. Wolf
- Division of Evolutionary Biology, Faculty of Biology LMU Munich Planegg‐Martinsried Germany
- Department of Evolutionary Biology Uppsala University Uppsala Sweden
| | - Joseph I. Hoffman
- Department of Animal Behaviour Bielefeld University Bielefeld Germany
- British Antarctic Survey Natural Environment Research Council Cambridge UK
| |
Collapse
|
29
|
Knief U, Bossu CM, Saino N, Hansson B, Poelstra J, Vijay N, Weissensteiner M, Wolf JBW. Epistatic mutations under divergent selection govern phenotypic variation in the crow hybrid zone. Nat Ecol Evol 2019; 3:570-576. [PMID: 30911146 PMCID: PMC6445362 DOI: 10.1038/s41559-019-0847-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 02/18/2019] [Indexed: 12/22/2022]
Abstract
The evolution of genetic barriers opposing inter-specific gene flow is key to the origin of new species. Drawing from information of over 400 admixed genomes sourced from replicate transects across the European hybrid zone between all-black carrion crows and grey-coated hooded crows, we decipher the interplay between phenotypic divergence and selection at the molecular level. Over 68% of plumage variation was explained by epistasis between the gene NDP and a ~2.8 Mb region on chromosome 18 with suppressed recombination. Both pigmentation loci showed evidence for divergent selection resisting introgression. This study reveals how few, large-effect loci can govern prezygotic isolation and shield phenotypic divergence from gene flow.
Collapse
Affiliation(s)
- Ulrich Knief
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Munich, Germany
| | - Christen M Bossu
- Science for Life Laboratories and Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden.,Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden.,Institute of the Environment and Sustainability, Center for Tropical Research, University of California, Los Angeles, CA, USA
| | - Nicola Saino
- Department of Environmental Science and Policy, University of Milan, Milan, Italy
| | - Bengt Hansson
- Department of Biology, Lund University, Lund, Sweden
| | - Jelmer Poelstra
- Science for Life Laboratories and Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden.,Biology Department, Duke University, Durham, NC, USA
| | - Nagarjun Vijay
- Science for Life Laboratories and Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden.,Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, India
| | - Matthias Weissensteiner
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Munich, Germany.,Science for Life Laboratories and Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden
| | - Jochen B W Wolf
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Munich, Germany. .,Science for Life Laboratories and Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden.
| |
Collapse
|
30
|
Wu CC, Klaesson A, Buskas J, Ranefall P, Mirzazadeh R, Söderberg O, Wolf JBW. In situ quantification of individual mRNA transcripts in melanocytes discloses gene regulation of relevance to speciation. J Exp Biol 2019; 222:jeb194431. [PMID: 30718374 PMCID: PMC6650291 DOI: 10.1242/jeb.194431] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 01/31/2019] [Indexed: 01/12/2023]
Abstract
Functional validation of candidate genes involved in adaptation and speciation remains challenging. Here, we exemplify the utility of a method quantifying individual mRNA transcripts in revealing the molecular basis of divergence in feather pigment synthesis during early-stage speciation in crows. Using a padlock probe assay combined with rolling circle amplification, we quantified cell-type-specific gene expression in the histological context of growing feather follicles. Expression of Tyrosinase Related Protein 1 (TYRP1), Solute Carrier Family 45 member 2 (SLC45A2) and Hematopoietic Prostaglandin D Synthase (HPGDS) was melanocyte-limited and significantly reduced in follicles from hooded crow, explaining the substantially lower eumelanin content in grey versus black feathers. The central upstream Melanocyte Inducing Transcription Factor (MITF) only showed differential expression specific to melanocytes - a feature not captured by bulk RNA-seq. Overall, this study provides insight into the molecular basis of an evolutionary young transition in pigment synthesis, and demonstrates the power of histologically explicit, statistically substantiated single-cell gene expression quantification for functional genetic inference in natural populations.
Collapse
Affiliation(s)
- Chi-Chih Wu
- Science of Life Laboratories and Department of Evolutionary Biology, Uppsala University, SE-752 36 Uppsala, Sweden
| | - Axel Klaesson
- Department of Pharmaceutical Biosciences, Uppsala University, SE-752 36 Uppsala, Sweden
| | - Julia Buskas
- Science of Life Laboratories and Department of Evolutionary Biology, Uppsala University, SE-752 36 Uppsala, Sweden
- Department of Physics, Chemistry and Biology (IFM), Linköping University, SE-581 83 Linköping, Sweden
| | - Petter Ranefall
- Science of Life Laboratories and Department of Information Technology, Uppsala University, SE-752 36 Uppsala, Sweden
| | - Reza Mirzazadeh
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm SE-17165, Sweden
| | - Ola Söderberg
- Department of Pharmaceutical Biosciences, Uppsala University, SE-752 36 Uppsala, Sweden
| | - Jochen B W Wolf
- Science of Life Laboratories and Department of Evolutionary Biology, Uppsala University, SE-752 36 Uppsala, Sweden
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, D-82152 Planegg-Martinsried, Germany
| |
Collapse
|
31
|
Hooper R, Brealey JC, van der Valk T, Alberdi A, Durban JW, Fearnbach H, Robertson KM, Baird RW, Bradley Hanson M, Wade P, Gilbert MTP, Morin PA, Wolf JBW, Foote AD, Guschanski K. Host-derived population genomics data provides insights into bacterial and diatom composition of the killer whale skin. Mol Ecol 2019; 28:484-502. [PMID: 30187987 PMCID: PMC6487819 DOI: 10.1111/mec.14860] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 08/15/2018] [Accepted: 08/27/2018] [Indexed: 12/20/2022]
Abstract
Recent exploration into the interactions and relationship between hosts and their microbiota has revealed a connection between many aspects of the host's biology, health and associated micro-organisms. Whereas amplicon sequencing has traditionally been used to characterize the microbiome, the increasing number of published population genomics data sets offers an underexploited opportunity to study microbial profiles from the host shotgun sequencing data. Here, we use sequence data originally generated from killer whale Orcinus orca skin biopsies for population genomics, to characterize the skin microbiome and investigate how host social and geographical factors influence the microbial community composition. Having identified 845 microbial taxa from 2.4 million reads that did not map to the killer whale reference genome, we found that both ecotypic and geographical factors influence community composition of killer whale skin microbiomes. Furthermore, we uncovered key taxa that drive the microbiome community composition and showed that they are embedded in unique networks, one of which is tentatively linked to diatom presence and poor skin condition. Community composition differed between Antarctic killer whales with and without diatom coverage, suggesting that the previously reported episodic migrations of Antarctic killer whales to warmer waters associated with skin turnover may control the effects of potentially pathogenic bacteria such as Tenacibaculum dicentrarchi. Our work demonstrates the feasibility of microbiome studies from host shotgun sequencing data and highlights the importance of metagenomics in understanding the relationship between host and microbial ecology.
Collapse
Affiliation(s)
- Rebecca Hooper
- Animal EcologyDepartment of Ecology and GeneticsEvolutionary Biology CentreUppsala UniversityUppsalaSweden
| | - Jaelle C. Brealey
- Animal EcologyDepartment of Ecology and GeneticsEvolutionary Biology CentreUppsala UniversityUppsalaSweden
| | - Tom van der Valk
- Animal EcologyDepartment of Ecology and GeneticsEvolutionary Biology CentreUppsala UniversityUppsalaSweden
| | - Antton Alberdi
- Centre for GeoGeneticsNatural History Museum of DenmarkUniversity of CopenhagenCopenhagen KDenmark
| | - John W. Durban
- Marine Mammal and Turtle DivisionSouthwest Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationLa JollaCalifornia
| | - Holly Fearnbach
- SR3, SeaLife Response, Rehabilitation, and ResearchSeattleWashington
| | - Kelly M. Robertson
- Marine Mammal and Turtle DivisionSouthwest Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationLa JollaCalifornia
| | | | - M. Bradley Hanson
- Northwest Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationSeattleWashington
| | - Paul Wade
- National Marine Mammal LaboratoryAlaska Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationSeattleWashington
| | - M. Thomas P. Gilbert
- Centre for GeoGeneticsNatural History Museum of DenmarkUniversity of CopenhagenCopenhagen KDenmark
- NTNU University MuseumTrondheimNorway
| | - Phillip A. Morin
- Marine Mammal and Turtle DivisionSouthwest Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationLa JollaCalifornia
| | - Jochen B. W. Wolf
- Science of Life Laboratories and Department of Evolutionary BiologyEvolutionary Biology CentreUppsala UniversityUppsalaSweden
- Section of Evolutionary BiologyFaculty of BiologyLMU MunichMunichGermany
| | - Andrew D. Foote
- Molecular Ecology and Fisheries Genetics LaboratorySchool of Biological SciencesBangor UniversityBangorGwyneddUK
| | - Katerina Guschanski
- Animal EcologyDepartment of Ecology and GeneticsEvolutionary Biology CentreUppsala UniversityUppsalaSweden
| |
Collapse
|
32
|
Stoffel MA, Humble E, Paijmans AJ, Acevedo-Whitehouse K, Chilvers BL, Dickerson B, Galimberti F, Gemmell NJ, Goldsworthy SD, Nichols HJ, Krüger O, Negro S, Osborne A, Pastor T, Robertson BC, Sanvito S, Schultz JK, Shafer ABA, Wolf JBW, Hoffman JI. Demographic histories and genetic diversity across pinnipeds are shaped by human exploitation, ecology and life-history. Nat Commun 2018; 9:4836. [PMID: 30446730 PMCID: PMC6240053 DOI: 10.1038/s41467-018-06695-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 09/18/2018] [Indexed: 12/22/2022] Open
Abstract
A central paradigm in conservation biology is that population bottlenecks reduce genetic diversity and population viability. In an era of biodiversity loss and climate change, understanding the determinants and consequences of bottlenecks is therefore an important challenge. However, as most studies focus on single species, the multitude of potential drivers and the consequences of bottlenecks remain elusive. Here, we combined genetic data from over 11,000 individuals of 30 pinniped species with demographic, ecological and life history data to evaluate the consequences of commercial exploitation by 18th and 19th century sealers. We show that around one third of these species exhibit strong signatures of recent population declines. Bottleneck strength is associated with breeding habitat and mating system variation, and together with global abundance explains much of the variation in genetic diversity across species. Overall, bottleneck intensity is unrelated to IUCN status, although the three most heavily bottlenecked species are endangered. Our study reveals an unforeseen interplay between human exploitation, animal biology, demographic declines and genetic diversity. Historical hunting has caused documented declines in pinnipeds, but the extent to which hunting caused genetic bottlenecks among species was unknown. Here, the authors show evidence of severe bottlenecks in several pinniped species, particularly those that breed on land.
Collapse
Affiliation(s)
- M A Stoffel
- Department of Animal Behaviour, Bielefeld University, Postfach 100131, 33501, Bielefeld, Germany.,School of Natural Sciences and Psychology, Faculty of Science, Liverpool John Moores University, Liverpool, L3 3AF, UK
| | - E Humble
- Department of Animal Behaviour, Bielefeld University, Postfach 100131, 33501, Bielefeld, Germany.,British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 OET, UK
| | - A J Paijmans
- Department of Animal Behaviour, Bielefeld University, Postfach 100131, 33501, Bielefeld, Germany
| | - K Acevedo-Whitehouse
- Unit for Basic and Applied Microbiology, School of Natural Sciences, Autonomous University of Queretaro, Avenida de las Ciencias S/N, Queretaro, 76230, Mexico
| | - B L Chilvers
- Wildbase, Institute of Veterinary, Animal and Biomedical Science, Massey University, Private Bag 11222, Palmerston North, 4442, New Zealand
| | - B Dickerson
- National Marine Mammal Laboratory, Alaska Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, 98115, WA, USA
| | - F Galimberti
- Elephant Seal Research Group, Sea Lion Island, FIQQ 1ZZ, Falkland Islands
| | - N J Gemmell
- Department of Anatomy, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
| | - S D Goldsworthy
- South Australian Research and Development Institute, West Beach, SA, 5024, Australia
| | - H J Nichols
- School of Natural Sciences and Psychology, Faculty of Science, Liverpool John Moores University, Liverpool, L3 3AF, UK.,Department of Animal Behaviour Bielefeld University, Postfach 100131 33501, Bielefeld, Germany.,Department of Biosciences, Swansea University, Swansea, SA2 8PP, UK
| | - O Krüger
- Department of Animal Behaviour, Bielefeld University, Postfach 100131, 33501, Bielefeld, Germany
| | - S Negro
- UMR de Génétique Quantitative et Évolution - Le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, 91190, France.,GIGA-R, Medical Genomics - BIO3, Université of Liège, Liège, 4000, Belgium
| | - A Osborne
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, New Zealand, 8140
| | - T Pastor
- EUROPARC Federation, Carretera de l'Església, 92, 08017, Barcelona, Spain
| | - B C Robertson
- Department of Zoology, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
| | - S Sanvito
- Elephant Seal Research Group, Sea Lion Island, FIQQ 1ZZ, Falkland Islands
| | - J K Schultz
- National Marine Fisheries Service, National Oceanic and Atmospheric Administration, 1315 East West Highway, Silver Spring, MD, 20910, USA
| | - A B A Shafer
- Forensic Science & Environmental Life Sciences, Trent University, Peterborough, ON, Canada, K9J 7B8
| | - J B W Wolf
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Planegg-Martinstried, Munich, 82152, Germany.,Science of Life Laboratory and Department of Evolutionary Biology, Uppsala University, Uppsala, 752 36, Sweden
| | - J I Hoffman
- Department of Animal Behaviour, Bielefeld University, Postfach 100131, 33501, Bielefeld, Germany. .,British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 OET, UK.
| |
Collapse
|
33
|
Vijay N, Weissensteiner M, Burri R, Kawakami T, Ellegren H, Wolf JBW. Genomewide patterns of variation in genetic diversity are shared among populations, species and higher-order taxa. Mol Ecol 2017; 26:4284-4295. [PMID: 28570015 DOI: 10.1111/mec.14195] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Revised: 05/10/2017] [Accepted: 05/17/2017] [Indexed: 12/15/2022]
Abstract
Genomewide screens of genetic variation within and between populations can reveal signatures of selection implicated in adaptation and speciation. Genomic regions with low genetic diversity and elevated differentiation reflective of locally reduced effective population sizes (Ne ) are candidates for barrier loci contributing to population divergence. Yet, such candidate genomic regions need not arise as a result of selection promoting adaptation or advancing reproductive isolation. Linked selection unrelated to lineage-specific adaptation or population divergence can generate comparable signatures. It is challenging to distinguish between these processes, particularly when diverging populations share ancestral genetic variation. In this study, we took a comparative approach using population assemblages from distant clades assessing genomic parallelism of variation in Ne . Utilizing population-level polymorphism data from 444 resequenced genomes of three avian clades spanning 50 million years of evolution, we tested whether population genetic summary statistics reflecting genomewide variation in Ne would covary among populations within clades, and importantly, also among clades where lineage sorting has been completed. All statistics including population-scaled recombination rate (ρ), nucleotide diversity (π) and measures of genetic differentiation between populations (FST , PBS, dxy ) were significantly correlated across all phylogenetic distances. Moreover, genomic regions with elevated levels of genetic differentiation were associated with inferred pericentromeric and subtelomeric regions. The phylogenetic stability of diversity landscapes and stable association with genomic features support a role of linked selection not necessarily associated with adaptation and speciation in shaping patterns of genomewide heterogeneity in genetic diversity.
Collapse
Affiliation(s)
- Nagarjun Vijay
- Department of Evolutionary Biology and SciLifeLab, Uppsala University, Uppsala, Sweden.,Lab of Molecular and Genomic Evolution, Department of Ecology and Evolutionary Biology, College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, MI, USA
| | - Matthias Weissensteiner
- Department of Evolutionary Biology and SciLifeLab, Uppsala University, Uppsala, Sweden.,Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Reto Burri
- Department of Evolutionary Biology and SciLifeLab, Uppsala University, Uppsala, Sweden.,Department of Population Ecology, Friedrich Schiller University Jena, Jena, Germany
| | - Takeshi Kawakami
- Department of Evolutionary Biology and SciLifeLab, Uppsala University, Uppsala, Sweden.,Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Hans Ellegren
- Department of Evolutionary Biology and SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Jochen B W Wolf
- Department of Evolutionary Biology and SciLifeLab, Uppsala University, Uppsala, Sweden.,Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| |
Collapse
|
34
|
Weissensteiner MH, Pang AWC, Bunikis I, Höijer I, Vinnere-Petterson O, Suh A, Wolf JBW. Combination of short-read, long-read, and optical mapping assemblies reveals large-scale tandem repeat arrays with population genetic implications. Genome Res 2017; 27:697-708. [PMID: 28360231 PMCID: PMC5411765 DOI: 10.1101/gr.215095.116] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 03/10/2017] [Indexed: 12/27/2022]
Abstract
Accurate and contiguous genome assembly is key to a comprehensive understanding of the processes shaping genomic diversity and evolution. Yet, it is frequently constrained by constitutive heterochromatin, usually characterized by highly repetitive DNA. As a key feature of genome architecture associated with centromeric and subtelomeric regions, it locally influences meiotic recombination. In this study, we assess the impact of large tandem repeat arrays on the recombination rate landscape in an avian speciation model, the Eurasian crow. We assembled two high-quality genome references using single-molecule real-time sequencing (long-read assembly [LR]) and single-molecule optical maps (optical map assembly [OM]). A three-way comparison including the published short-read assembly (SR) constructed for the same individual allowed assessing assembly properties and pinpointing misassemblies. By combining information from all three assemblies, we characterized 36 previously unidentified large repetitive regions in the proximity of sequence assembly breakpoints, the majority of which contained complex arrays of a 14-kb satellite repeat or its 1.2-kb subunit. Using whole-genome population resequencing data, we estimated the population-scaled recombination rate (ρ) and found it to be significantly reduced in these regions. These findings are consistent with an effect of low recombination in regions adjacent to centromeric or subtelomeric heterochromatin and add to our understanding of the processes generating widespread heterogeneity in genetic diversity and differentiation along the genome. By combining three different technologies, our results highlight the importance of adding a layer of information on genome structure that is inaccessible to each approach independently.
Collapse
Affiliation(s)
- Matthias H Weissensteiner
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala, Sweden
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilian University of Munich, 82152 Planegg-Martinsried, Germany
| | | | - Ignas Bunikis
- SciLife Lab Uppsala, Uppsala University SE-751 85 Uppsala, Sweden
| | - Ida Höijer
- SciLife Lab Uppsala, Uppsala University SE-751 85 Uppsala, Sweden
| | | | - Alexander Suh
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala, Sweden
| | - Jochen B W Wolf
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala, Sweden
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilian University of Munich, 82152 Planegg-Martinsried, Germany
| |
Collapse
|
35
|
Shafer ABA, Peart CR, Tusso S, Maayan I, Brelsford A, Wheat CW, Wolf JBW. Bioinformatic processing of RAD‐seq data dramatically impacts downstream population genetic inference. Methods Ecol Evol 2016. [DOI: 10.1111/2041-210x.12700] [Citation(s) in RCA: 189] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Aaron B. A. Shafer
- Department of Evolutionary Biology Evolutionary Biology Centre Uppsala University Norbyvägen 18D SE‐752 36 Uppsala Sweden
- Forensic Science and Environmental & Life Sciences Trent University 2014 East Bank Dr K9J 7B8 Peterborough Canada
| | - Claire R. Peart
- Department of Evolutionary Biology Evolutionary Biology Centre Uppsala University Norbyvägen 18D SE‐752 36 Uppsala Sweden
| | - Sergio Tusso
- Department of Evolutionary Biology Evolutionary Biology Centre Uppsala University Norbyvägen 18D SE‐752 36 Uppsala Sweden
| | - Inbar Maayan
- Department of Evolutionary Biology Evolutionary Biology Centre Uppsala University Norbyvägen 18D SE‐752 36 Uppsala Sweden
| | - Alan Brelsford
- Department of Ecology and Evolution University of Lausanne CH‐1015 Lausanne Switzerland
| | | | - Jochen B. W. Wolf
- Department of Evolutionary Biology Evolutionary Biology Centre Uppsala University Norbyvägen 18D SE‐752 36 Uppsala Sweden
- Division of Evolutionary Biology Faculty of Biology Ludwig‐Maximilians University of Munich Grosshaderner Str. 2 82152 Planegg‐Martinsried Germany
| |
Collapse
|
36
|
Vijay N, Bossu CM, Poelstra JW, Weissensteiner MH, Suh A, Kryukov AP, Wolf JBW. Evolution of heterogeneous genome differentiation across multiple contact zones in a crow species complex. Nat Commun 2016; 7:13195. [PMID: 27796282 PMCID: PMC5095515 DOI: 10.1038/ncomms13195] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 09/09/2016] [Indexed: 12/31/2022] Open
Abstract
Uncovering the genetic basis of species diversification is a central goal in evolutionary biology. Yet, the link between the accumulation of genomic changes during population divergence and the evolutionary forces promoting reproductive isolation is poorly understood. Here, we analysed 124 genomes of crow populations with various degrees of genome-wide differentiation, with parallelism of a sexually selected plumage phenotype, and ongoing hybridization. Overall, heterogeneity in genetic differentiation along the genome was best explained by linked selection exposed on a shared genome architecture. Superimposed on this common background, we identified genomic regions with signatures of selection specific to independent phenotypic contact zones. Candidate pigmentation genes with evidence for divergent selection were only partly shared, suggesting context-dependent selection on a multigenic trait architecture and parallelism by pathway rather than by repeated single-gene effects. This study provides insight into how various forms of selection shape genome-wide patterns of genomic differentiation as populations diverge.
Collapse
Affiliation(s)
- Nagarjun Vijay
- Department of Evolutionary Biology and Science for Life Laboratories, Uppsala University, Norbyvägen 18D, Uppsala 75236, Sweden
| | - Christen M Bossu
- Department of Evolutionary Biology and Science for Life Laboratories, Uppsala University, Norbyvägen 18D, Uppsala 75236, Sweden.,Department of Zoology, Population Genetics, Stockholm University, Stockholm SE-106 91, Sweden
| | - Jelmer W Poelstra
- Department of Evolutionary Biology and Science for Life Laboratories, Uppsala University, Norbyvägen 18D, Uppsala 75236, Sweden
| | - Matthias H Weissensteiner
- Department of Evolutionary Biology and Science for Life Laboratories, Uppsala University, Norbyvägen 18D, Uppsala 75236, Sweden
| | - Alexander Suh
- Department of Evolutionary Biology and Science for Life Laboratories, Uppsala University, Norbyvägen 18D, Uppsala 75236, Sweden
| | - Alexey P Kryukov
- Laboratory of Evolutionary Zoology and Genetics, Institute of Biology and Soil Science, Far East Branch Russian Academy of Sciences, Vladivostok 690022, Russia
| | - Jochen B W Wolf
- Department of Evolutionary Biology and Science for Life Laboratories, Uppsala University, Norbyvägen 18D, Uppsala 75236, Sweden.,Division of Evolutionary Biology, Ludwig Maximilian University of Munich, Grosshaderner Street 2, Planegg-Martinsried 82152, Germany
| |
Collapse
|
37
|
Trillmich F, Meise K, Kalberer S, Mueller B, Piedrahita P, Pörschmann U, Wolf JBW, Krüger O. On the Challenge of Interpreting Census Data: Insights from a Study of an Endangered Pinniped. PLoS One 2016; 11:e0154588. [PMID: 27148735 PMCID: PMC4858284 DOI: 10.1371/journal.pone.0154588] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 04/16/2016] [Indexed: 11/18/2022] Open
Abstract
Population monitoring is vital for conservation and management. However, simple counts of animals can be misleading and this problem is exacerbated in seals (pinnipeds) where individuals spend much time foraging away from colonies. We analyzed a 13-year-series of census data of Galapagos sea lions (Zalophus wollebaeki) from the colony of Caamaño, an islet in the center of the Galapagos archipelago where a large proportion of animals was individually marked. Based on regular resighting efforts during the cold, reproductive (cold-R; August to January) and the warm, non-reproductive (warm-nR; February to May) season, we document changes in numbers for different sex and age classes. During the cold-R season the number of adults increased as the number of newborn pups increased. Numbers were larger in the morning and evening than around mid-day and not significantly influenced by tide levels. More adults frequented the colony during the warm-nR season than the cold-R season. Raw counts suggested a decline in numbers over the 13 years, but Lincoln-Petersen (LP-) estimates (assuming a closed population) did not support that conclusion. Raw counts and LP estimates were not significantly correlated, demonstrating the overwhelming importance of variability in attendance patterns of individuals. The probability of observing a given adult in the colony varied between 16% (mean for cold-R season) and 23% (warm-nR season) and may be much less for independent 2 to 4 year olds. Dependent juveniles (up to the age of about 2 years) are observed much more frequently ashore (35% during the cold-R and 50% during the warm-nR seasons). Simple counts underestimate real population size by a factor of 4-6 and may lead to erroneous conclusions about trends in population size.
Collapse
Affiliation(s)
- Fritz Trillmich
- Animal Behaviour, University of Bielefeld, Bielefeld, Germany
| | - Kristine Meise
- Animal Behaviour, University of Bielefeld, Bielefeld, Germany
- Department of Evolution, Ecology and Behaviour, Institute of Integrative Biology, University of Liverpool, Biosciences Building, Liverpool, United Kingdom
| | | | - Birte Mueller
- Center for Biology Education, University of Münster, Münster, Germany
| | - Paolo Piedrahita
- Animal Behaviour, University of Bielefeld, Bielefeld, Germany
- Facultad de Ciencias de la Vida, Escuela Superior Politécnica del Litoral, ESPOL, Guayaquil, Ecuador
| | | | | | - Oliver Krüger
- Animal Behaviour, University of Bielefeld, Bielefeld, Germany
| |
Collapse
|
38
|
Abstract
Recent advancements in animal tracking technology and high-throughput sequencing are rapidly changing the questions and scope of research in the biological sciences. The integration of genomic data with high-tech animal instrumentation comes as a natural progression of traditional work in ecological genetics, and we provide a framework for linking the separate data streams from these technologies. Such a merger will elucidate the genetic basis of adaptive behaviors like migration and hibernation and advance our understanding of fundamental ecological and evolutionary processes such as pathogen transmission, population responses to environmental change, and communication in natural populations.
Collapse
Affiliation(s)
| | - Joseph M. Northrup
- Colorado State University, Department of Fish, Wildlife, and Conservation Biology, Fort Collins, Colorado, United States of America
| | - Martin Wikelski
- Max Planck Institute for Ornithology, Radolfzell, Germany
- University of Konstanz, Biology, Konstanz, Germany
| | - George Wittemyer
- Colorado State University, Department of Fish, Wildlife, and Conservation Biology, Fort Collins, Colorado, United States of America
| | - Jochen B. W. Wolf
- Uppsala University, Department of Ecology and Genetics, Uppsala, Sweden
| |
Collapse
|
39
|
Camus MF, Wolf JBW, Morrow EH, Dowling DK. Single Nucleotides in the mtDNA Sequence Modify Mitochondrial Molecular Function and Are Associated with Sex-Specific Effects on Fertility and Aging. Curr Biol 2015; 25:2717-22. [PMID: 26455309 DOI: 10.1016/j.cub.2015.09.012] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 09/04/2015] [Accepted: 09/08/2015] [Indexed: 02/05/2023]
Abstract
Mitochondria underpin energy conversion in eukaryotes. Their small genomes have been the subject of increasing attention, and there is evidence that mitochondrial genetic variation can affect evolutionary trajectories and shape the expression of life-history traits considered to be key human health indicators [1, 2]. However, it is not understood how genetic variation across a diminutive genome, which in most species harbors only about a dozen protein-coding genes, can exert broad-scale effects on the organismal phenotype [2, 3]. Such effects are particularly puzzling given that the mitochondrial genes involved are under strong evolutionary constraint and that mitochondrial gene expression is highly conserved across diverse taxa [4]. We used replicated genetic lines in the fruit fly, Drosophila melanogaster, each characterized by a distinct and naturally occurring mitochondrial haplotype placed alongside an isogenic nuclear background. We demonstrate that sequence variation within the mitochondrial DNA (mtDNA) affects both the copy number of mitochondrial genomes and patterns of gene expression across key mitochondrial protein-coding genes. In several cases, haplotype-mediated patterns of gene expression were gene-specific, even for genes from within the same transcriptional units. This invokes post-transcriptional processing of RNA in the regulation of mitochondrial genetic effects on organismal phenotypes. Notably, the haplotype-mediated effects on gene expression could be traced backward to the level of individual nucleotides and forward to sex-specific effects on fertility and longevity. Our study thus elucidates how small-scale sequence changes in the mitochondrial genome can achieve broad-scale regulation of health-related phenotypes and even contribute to sex-related differences in longevity.
Collapse
Affiliation(s)
- M Florencia Camus
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia.
| | - Jochen B W Wolf
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala SE-75236, Sweden
| | - Edward H Morrow
- School of Life Sciences, University of Sussex, Brighton BN1 9QG, United Kingdom
| | - Damian K Dowling
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia.
| |
Collapse
|
40
|
Foote AD, Liu Y, Thomas GWC, Vinař T, Alföldi J, Deng J, Dugan S, van Elk CE, Hunter ME, Joshi V, Khan Z, Kovar C, Lee SL, Lindblad-Toh K, Mancia A, Nielsen R, Qin X, Qu J, Raney BJ, Vijay N, Wolf JBW, Hahn MW, Muzny DM, Worley KC, Gilbert MTP, Gibbs RA. Convergent evolution of the genomes of marine mammals. Nat Genet 2015; 47:272-5. [PMID: 25621460 DOI: 10.1038/ng.3198] [Citation(s) in RCA: 262] [Impact Index Per Article: 29.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Accepted: 12/29/2014] [Indexed: 12/13/2022]
Abstract
Marine mammals from different mammalian orders share several phenotypic traits adapted to the aquatic environment and therefore represent a classic example of convergent evolution. To investigate convergent evolution at the genomic level, we sequenced and performed de novo assembly of the genomes of three species of marine mammals (the killer whale, walrus and manatee) from three mammalian orders that share independently evolved phenotypic adaptations to a marine existence. Our comparative genomic analyses found that convergent amino acid substitutions were widespread throughout the genome and that a subset of these substitutions were in genes evolving under positive selection and putatively associated with a marine phenotype. However, we found higher levels of convergent amino acid substitutions in a control set of terrestrial sister taxa to the marine mammals. Our results suggest that, whereas convergent molecular evolution is relatively common, adaptive molecular convergence linked to phenotypic convergence is comparatively rare.
Collapse
Affiliation(s)
- Andrew D Foote
- 1] Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark. [2] Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Yue Liu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Gregg W C Thomas
- School of Informatics and Computing, Indiana University, Bloomington, Indiana, USA
| | - Tomáš Vinař
- Faculty of Mathematics, Physics and Informatics, Comenius University, Bratislava, Slovakia
| | - Jessica Alföldi
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Jixin Deng
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Shannon Dugan
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | | | - Margaret E Hunter
- Sirenia Project, Southeast Ecological Science Center, US Geological Survey, Gainesville, Florida, USA
| | - Vandita Joshi
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Ziad Khan
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Christie Kovar
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Sandra L Lee
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Kerstin Lindblad-Toh
- 1] Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA. [2] Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Annalaura Mancia
- 1] Marine Biomedicine and Environmental Science Center, Medical University of South Carolina, Charleston, South Carolina, USA. [2] Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Rasmus Nielsen
- Center for Theoretical Evolutionary Genomics, University of California, Berkeley, Berkeley, California, USA
| | - Xiang Qin
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Jiaxin Qu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Brian J Raney
- Center for Biomolecular Science and Engineering, University of California, Santa Cruz, Santa Cruz, California, USA
| | - Nagarjun Vijay
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Jochen B W Wolf
- 1] Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden. [2] Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Matthew W Hahn
- 1] School of Informatics and Computing, Indiana University, Bloomington, Indiana, USA. [2] Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Kim C Worley
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - M Thomas P Gilbert
- 1] Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark. [2] Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, Perth, Western Australia, Australia
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| |
Collapse
|
41
|
Shafer ABA, Gattepaille LM, Stewart REA, Wolf JBW. Demographic inferences using short-read genomic data in an approximate Bayesian computation framework: in silico evaluation of power, biases and proof of concept in Atlantic walrus. Mol Ecol 2015; 24:328-45. [DOI: 10.1111/mec.13034] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 11/29/2014] [Accepted: 12/03/2014] [Indexed: 01/01/2023]
Affiliation(s)
- Aaron B. A. Shafer
- Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala SE-75236 Sweden
| | - Lucie M. Gattepaille
- Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala SE-75236 Sweden
| | - Robert E. A. Stewart
- Fisheries and Oceans Canada; Freshwater Institute; 501 University Crescent Winnipeg Manitoba R3T 2N6 Canada
| | - Jochen B. W. Wolf
- Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala SE-75236 Sweden
| |
Collapse
|
42
|
Abstract
Genome sequencing projects were long confined to biomedical model organisms and required the concerted effort of large consortia. Rapid progress in high-throughput sequencing technology and the simultaneous development of bioinformatic tools have democratized the field. It is now within reach for individual research groups in the eco-evolutionary and conservation community to generate de novo draft genome sequences for any organism of choice. Because of the cost and considerable effort involved in such an endeavour, the important first step is to thoroughly consider whether a genome sequence is necessary for addressing the biological question at hand. Once this decision is taken, a genome project requires careful planning with respect to the organism involved and the intended quality of the genome draft. Here, we briefly review the state of the art within this field and provide a step-by-step introduction to the workflow involved in genome sequencing, assembly and annotation with particular reference to large and complex genomes. This tutorial is targeted at scientists with a background in conservation genetics, but more generally, provides useful practical guidance for researchers engaging in whole-genome sequencing projects.
Collapse
Affiliation(s)
- Robert Ekblom
- Department of Evolutionary Biology, Uppsala University Uppsala, Sweden
| | - Jochen B W Wolf
- Department of Evolutionary Biology, Uppsala University Uppsala, Sweden
| |
Collapse
|
43
|
Krüger O, Wolf JBW, Jonker RM, Hoffman JI, Trillmich F. DISENTANGLING THE CONTRIBUTION OF SEXUAL SELECTION AND ECOLOGY TO THE EVOLUTION OF SIZE DIMORPHISM IN PINNIPEDS. Evolution 2014; 68:1485-96. [DOI: 10.1111/evo.12370] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Accepted: 01/17/2014] [Indexed: 11/29/2022]
Affiliation(s)
- Oliver Krüger
- Department of Animal Behaviour; Bielefeld University; PO Box 10 01 31 33501 Bielefeld Germany
| | - Jochen B. W. Wolf
- Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala University; Norbyvägen 18D 75236 Uppsala Sweden
| | - Rudy M. Jonker
- Department of Animal Behaviour; Bielefeld University; PO Box 10 01 31 33501 Bielefeld Germany
| | - Joseph I. Hoffman
- Department of Animal Behaviour; Bielefeld University; PO Box 10 01 31 33501 Bielefeld Germany
| | - Fritz Trillmich
- Department of Animal Behaviour; Bielefeld University; PO Box 10 01 31 33501 Bielefeld Germany
| |
Collapse
|
44
|
Abstract
The ratio of divergence at nonsynonymous and synonymous sites, dN/dS, is a widely used measure in evolutionary genetic studies to investigate the extent to which selection modulates gene sequence evolution. Originally tailored to codon sequences of distantly related lineages, dN/dS represents the ratio of fixed nonsynonymous to synonymous differences. The impact of ancestral and lineage-specific polymorphisms on dN/dS, which we here show to be substantial for closely related lineages, is generally neglected in estimation techniques of dN/dS. To address this issue, we formulate a codon model that is firmly anchored in population genetic theory, derive analytical expressions for the dN/dS measure by Poisson random field approximation in a Markovian framework and validate the derivations by simulations. In good agreement, simulations and analytical derivations demonstrate that dN/dS is biased by polymorphisms at short time scales and that it can take substantial time for the expected value to settle at its time limit where only fixed differences are considered. We further show that in any attempt to estimate the dN/dS ratio from empirical data the effect of the intrinsic fluctuations of a ratio of stochastic variables, can even under neutrality yield extreme values of dN/dS at short time scales or in regions of low mutation rate. Taken together, our results have significant implications for the interpretation of dN/dS estimates, the McDonald-Kreitman test and other related statistics, in particular for closely related lineages.
Collapse
Affiliation(s)
- Carina F Mugal
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | | | | |
Collapse
|
45
|
Poelstra JW, Ellegren H, Wolf JBW. An extensive candidate gene approach to speciation: diversity, divergence and linkage disequilibrium in candidate pigmentation genes across the European crow hybrid zone. Heredity (Edinb) 2013; 111:467-73. [PMID: 23881172 DOI: 10.1038/hdy.2013.68] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Revised: 05/24/2013] [Accepted: 06/12/2013] [Indexed: 11/09/2022] Open
Abstract
Colouration patterns have an important role in adaptation and speciation. The European crow system, in which all-black carrion crows and grey-coated hooded crows meet in a narrow hybrid zone, is a prominent example. The marked phenotypic difference is maintained by assortative mating in the absence of neutral genetic divergence, suggesting the presence of few pigmentation genes of major effect. We made use of the rich phenotypic and genetic resources in mammals and identified a comprehensive panel of 95 candidate pigmentation genes for birds. Based on functional annotation, we chose a subset of the most promising 37 candidates, for which we developed a marker system that demonstrably works across the avian phylogeny. In total, we sequenced 107 amplicons (∼3 loci per gene, totalling 60 kb) in population samples of crows (n=23 for each taxon). Tajima's D, Fu's FS, DHEW and HKA (Hudson-Kreitman-Aguade) statistics revealed several amplicons that deviated from neutrality; however, none of these showed significantly elevated differentiation between the two taxa. Hence, colour divergence in this system may be mediated by uncharacterized pigmentation genes or regulatory regions outside genes. Alternatively, the observed high population recombination rate (4Ner∼0.03), with overall linkage disequilibrium dropping rapidly within the order of few 100 bp, may compromise the power to detect causal loci with nearby markers. Our results add to the debate as to the utility of candidate gene approaches in relation to genomic features and the genetic architecture of the phenotypic trait in question.
Collapse
Affiliation(s)
- J W Poelstra
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala, Sweden
| | | | | |
Collapse
|
46
|
Lenz TL, Mueller B, Trillmich F, Wolf JBW. Divergent allele advantage at MHC-DRB through direct and maternal genotypic effects and its consequences for allele pool composition and mating. Proc Biol Sci 2013; 280:20130714. [PMID: 23677346 DOI: 10.1098/rspb.2013.0714] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
It is still debated whether main individual fitness differences in natural populations can be attributed to genome-wide effects or to particular loci of outstanding functional importance such as the major histocompatibility complex (MHC). In a long-term monitoring project on Galápagos sea lions (Zalophus wollebaeki), we collected comprehensive fitness and mating data for a total of 506 individuals. Controlling for genome-wide inbreeding, we find strong associations between the MHC locus and nearly all fitness traits. The effect was mainly attributable to MHC sequence divergence and could be decomposed into contributions of own and maternal genotypes. In consequence, the population seems to have evolved a pool of highly divergent alleles conveying near-optimal MHC divergence even by random mating. Our results demonstrate that a single locus can significantly contribute to fitness in the wild and provide conclusive evidence for the 'divergent allele advantage' hypothesis, a special form of balancing selection with interesting evolutionary implications.
Collapse
Affiliation(s)
- Tobias L Lenz
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany
| | | | | | | |
Collapse
|
47
|
Shafer ABA, Wolf JBW. Widespread evidence for incipient ecological speciation: a meta-analysis of isolation-by-ecology. Ecol Lett 2013; 16:940-50. [PMID: 23627762 DOI: 10.1111/ele.12120] [Citation(s) in RCA: 187] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Revised: 02/12/2013] [Accepted: 04/03/2013] [Indexed: 12/14/2022]
Abstract
Ecologically mediated selection has increasingly become recognised as an important driver of speciation. The correlation between neutral genetic differentiation and environmental or phenotypic divergence among populations, to which we collectively refer to as isolation-by-ecology (IBE), is an indicator of ecological speciation. In a meta-analysis framework, we determined the strength and commonality of IBE in nature. On the basis of 106 studies, we calculated a mean effect size of IBE with and without controlling for spatial autocorrelation among populations. Effect sizes were 0.34 (95% CI 0.24-0.42) and 0.26 (95% CI 0.13-0.37), respectively, indicating that an average of 5% of the neutral genetic differentiation among populations was explained purely by ecological contrast. Importantly, spatial autocorrelation reduced IBE correlations for environmental variables, but not for phenotypes. Through simulation, we showed how the influence of isolation-by-distance and spatial autocorrelation of ecological variables can result in false positives or underestimated correlations if not accounted for in the IBE model. Collectively, this meta-analysis showed that ecologically induced genetic divergence is pervasive across time-scales and taxa, and largely independent of the choice of molecular marker. We discuss the importance of these results in the context of adaptation and ecological speciation and suggest future research avenues.
Collapse
Affiliation(s)
- Aaron B A Shafer
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.
| | | |
Collapse
|
48
|
Wolf JBW. Principles of transcriptome analysis and gene expression quantification: an
RNA
‐seq tutorial. Mol Ecol Resour 2013; 13:559-72. [DOI: 10.1111/1755-0998.12109] [Citation(s) in RCA: 139] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Revised: 03/18/2013] [Accepted: 03/21/2013] [Indexed: 01/03/2023]
Affiliation(s)
- Jochen B. W. Wolf
- Department of Evolutionary Biology Uppsala University Uppsala Sweden
- Science of Life Laboratory Uppsala Sweden
| |
Collapse
|
49
|
Ellegren H, Smeds L, Burri R, Olason PI, Backström N, Kawakami T, Künstner A, Mäkinen H, Nadachowska-Brzyska K, Qvarnström A, Uebbing S, Wolf JBW. The genomic landscape of species divergence in Ficedula flycatchers. Nature 2012; 491:756-60. [PMID: 23103876 DOI: 10.1038/nature11584] [Citation(s) in RCA: 427] [Impact Index Per Article: 35.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Accepted: 09/12/2012] [Indexed: 12/29/2022]
Abstract
Unravelling the genomic landscape of divergence between lineages is key to understanding speciation. The naturally hybridizing collared flycatcher and pied flycatcher are important avian speciation models that show pre- as well as postzygotic isolation. We sequenced and assembled the 1.1-Gb flycatcher genome, physically mapped the assembly to chromosomes using a low-density linkage map and re-sequenced population samples of each species. Here we show that the genomic landscape of species differentiation is highly heterogeneous with approximately 50 'divergence islands' showing up to 50-fold higher sequence divergence than the genomic background. These non-randomly distributed islands, with between one and three regions of elevated divergence per chromosome irrespective of chromosome size, are characterized by reduced levels of nucleotide diversity, skewed allele-frequency spectra, elevated levels of linkage disequilibrium and reduced proportions of shared polymorphisms in both species, indicative of parallel episodes of selection. Proximity of divergence peaks to genomic regions resistant to sequence assembly, potentially including centromeres and telomeres, indicate that complex repeat structures may drive species divergence. A much higher background level of species divergence of the Z chromosome, and a lower proportion of shared polymorphisms, indicate that sex chromosomes and autosomes are at different stages of speciation. This study provides a roadmap to the emerging field of speciation genomics.
Collapse
Affiliation(s)
- Hans Ellegren
- Dept of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
50
|
Vijay N, Poelstra JW, Künstner A, Wolf JBW. Challenges and strategies in transcriptome assembly and differential gene expression quantification. A comprehensivein silicoassessment of RNA-seq experiments. Mol Ecol 2012; 22:620-34. [DOI: 10.1111/mec.12014] [Citation(s) in RCA: 187] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Revised: 06/13/2012] [Accepted: 07/11/2012] [Indexed: 01/13/2023]
Affiliation(s)
- Nagarjun Vijay
- Department of Evolutionary Biology and Science for Life Laboratory; Uppsala University; Norbyvägen 18D; Uppsala; SE-752 36; Sweden
| | - Jelmer W. Poelstra
- Department of Evolutionary Biology and Science for Life Laboratory; Uppsala University; Norbyvägen 18D; Uppsala; SE-752 36; Sweden
| | - Axel Künstner
- Department of Molecular Biology; Max Planck Institute for Developmental Biology; Spemannstrasse 37-39; 72076; Tübingen; Germany
| | - Jochen B. W. Wolf
- Department of Evolutionary Biology and Science for Life Laboratory; Uppsala University; Norbyvägen 18D; Uppsala; SE-752 36; Sweden
| |
Collapse
|